Method for identifying the presence and / or concentration and / or amount of protein or proteome

Abstract

The present disclosure relates to methods for identifying the presence and / or concentration and / or amount of one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest in a sample based on the measured labels, amino acid concentrations, or numbers of two or more labeled amino acid types in the sample.

Description

[Technical Field]

[0001] Reference: I36031WO Description of the Invention The present invention relates to a method for identifying the presence and / or concentration and / or amount of one or more target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes in a sample. [Background technology]

[0002] Proteins are biological polymers composed of sequences of amino acids. Proteomics is the large-scale study of proteins. This allows for the identification and quantification of proteins. In the field of proteomics, there are several established methods for determining the presence or absence of proteins in a sample. Determining the presence or absence of a subproteome or proteome in a sample is difficult because it involves the sequential identification of all proteins. Some proteomics methods allow for the quantification of the concentration or amount of a single protein in a sample.

[0003] The most common method for identifying the presence of proteins in a sample is mass spectrometry. Mass spectrometry measures the mass-to-charge ratio of ions present in a sample. The mass spectrum of a sample is a plot of ion signals as a function of the mass-to-charge ratio. Using this spectrum, the isotopic signature and particle mass of the sample are determined, and these are used to provide the chemical attributes or structure of chemical compounds. However, mass spectrometry is labor-intensive and inherently inequal, as various peptides are ionized and detected with varying efficiencies. To counteract this, approaches such as isotope-encoded affinity tags (ICAT) are used, but these can only quantify a subset of the proteins being identified. Most quantitative mass spectrometry approaches can only determine relative changes in protein concentration or quantity between samples, rather than providing absolute quantification of the sample. Mass spectrometry proteomics also has limited coverage, especially for higher organisms. Top-down mass spectrometry proteomics, which analyzes the entire protein, allows for the identification of only 10% of the protein studied, while bottom-up mass spectrometry proteomics, which analyzes the protein after it has been digested into fragments, allows for the identification of 8-25% of the protein studied. Due to the complexity of the resulting mass spectra, mixtures and complex samples must be separated into their components, for example, by two-dimensional gel electrophoresis or high-performance liquid chromatography (HPLC), before they can be analyzed sequentially by mass spectrometry.

[0004] An alternative approach to identifying the presence of proteins is to use protein microarrays. Protein microarrays immobilize an array of proteins or probes onto a support surface and are particularly suitable for multiple detection. Tagged probes or tagged proteins are added to the array, and the binding interaction between the protein and probe is detected. However, protein microarrays are labor-intensive and suffer from problems with reproducibility and accuracy. Since detection requires a binding event near the surface, the binding event (i.e., the accuracy of detection) can be affected by the surface. Furthermore, this method can only identify proteins for which a corresponding probe (e.g., a specific antibody) is already available.

[0005] For example, several methods, such as Zhang et al., “Top-down proteomics on a microfluidic platform” (2019), eprint 1910.11861 arXiv physics.bio-ph, aim to identify proteins through physical parameters characteristic of proteins. In this microfluidic method, the hydrodynamic radius (R) of the protein is the size of the protein in solution. H ) is used along with the ratio of fluorescent signals from Trp / Lys and Tyr / Lys residues within the protein for protein identification. Lysine (Lys) residues are fluorescently labeled, while tryptophan (Trp) and tyrosine (Tyr) residues are not labeled. Seven known proteins are measured four times, and a protein is identified when the value obtained from the fourth protein measurement matches the values ​​obtained from the other three protein measurements of that protein. The measured values ​​have been shown to be characteristic of known proteins under a certain set of experimental conditions in that the measured proteins are distinguishable from one another based on these values, but none of the values ​​can predict the protein of interest. For amino acid sequences that are unknown and often partially intrinsically disordered, R HIt is not possible to predict this. Those skilled in the art will understand that the innate fluorescence from tryptophan and tyrosine residues depends in a complex way on the local physical environment surrounding the tryptophan and tyrosine residues within the protein structure, which cannot currently be predicted from the amino acid sequence. Therefore, R H The Trp and Tyr signals all change with solution conditions; for example, different readings will be obtained for the same protein if the protein is placed in different buffers or interacts with other biomolecules. This method cannot quantify proteins because none of the values ​​used for protein identification provide information about the amount or concentration of the protein. Due to the unpredictable nature of the results obtained, this method cannot be used to analyze proteins or mixtures of proteomes.

[0006] Alternatively, cutting-edge techniques include newly developed protein sequencing methods such as those described by Swaminathan, J et al. Nat Biotechnology 36, 1076-1082 (2018). Sparse fluorosequencing involves performing classical Edman decomposition sequencing on a single peptide fragment molecule that is fluorescently labeled on specific amino acids before immobilization on a surface, and observing the pattern of fluorescence disappearance from the surface as the fluorescently labeled amino acids are sequentially cleaved from the N-terminus of the peptide. The fluorescence decrease pattern reveals the position of the labeled amino acids within the peptide being read, providing a sparse peptide sequence. These sparse peptide sequences can be used to predict the target protein based on information-rich constraints regarding protease cleavage specificity, surface connectivity chemistry, labeling chemistry, and the position of the labeled amino acids within the predicted peptide fragment for the target protein. In practice, this labor-intensive and data-intensive method is prone to errors due to various causes, and correct readings are observed approximately 40% of the time for a single purified peptide. Quantification of this method has not been evaluated. This method relies on coupling with chromatographic and / or mass spectrometry separation methods such as HPLC to first verify that all amino acids (e.g., all lysine and all cysteine ​​amino acids) are quantitatively fluorescently labeled within each peptide fragment, and then performs sequencing. Peptide fragments within a two-component mixture are identified, which requires that the peptide fragments are spatially separated from each other via surface connections at different locations on the surface, resulting in the observation of separate fluorescence disappearance trajectories for each peptide. Similar to conventional Edman sequencing, this method is slow, requiring one hour per Edman cycle, and is unsuitable for analyzing N-terminally modified peptides or reading peptide fragments longer than 30 amino acids. Due to its reliance on Edman sequencing, this method is considered better suited to identifying shorter peptides than longer protein molecules. The average length of a protein molecule in the human proteome is 558 amino acids.This method cannot be used to analyze a mixture of proteins or proteomes.

[0007] There is a recognized need for the development of simple and general alternative methods for protein identification based on mass spectrometry, enabling the identification of the entire protein as the target protein. There is also a recognized need for efficient methods to characterize complex mixtures of proteins, such as mixtures of disease-related proteins. A rapid and general method for diagnosing any infection is greatly needed. Preferably, these methods would allow for the quantification of proteins. Therefore, there is a need for more efficient, cost-effective, and general methods to identify the presence and / or concentration and / or amount of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome in a sample. [Overview of the Initiative] [Problems that the invention aims to solve]

[0008] This invention is based on the discovery that by labeling and measuring two or more amino acid types in a sample, the presence and / or concentration and / or amount of one or more target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes in the sample can be identified. This is based on the measured label, amino acid concentration, or number of each labeled amino acid type in the sample. [Means for solving the problem]

[0009] It has been discovered that each protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome has a unique signature based on two or more amino acid type label values, amino acid concentrations, or the number of amino acids for each protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome at each concentration.

[0010] The signatures of the label values ​​or amino acid concentrations for two or more amino acid types of a protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome are unique to each protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome at each concentration. The signatures of the number of amino acids for two or more amino acid types of a protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome are also unique to each protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome.

[0011] Therefore, by comparing the signature of a sample with the signature of one or more target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes, the presence and / or concentration and / or amount of one or more target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes in the sample can be identified.

[0012] The signatures of known label values ​​or amino acid concentrations of two or more amino acid types in a target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome are a function of the concentration of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome, and are unique to each target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome at each concentration. Therefore, by comparing the measured label values ​​or amino acid concentrations of two or more amino acid types in a sample with the known label values ​​or amino acid concentrations of the same two or more amino acid types labeled in the sample for the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome, it is possible to provide a positive identification of the presence and / or concentration and / or amount of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome in the sample. The signature of the number of amino acids of two or more amino acid types in a target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome is unique to each target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome. Therefore, the number of each of the two or more amino acid types in a sample can be compared to the number of amino acids of the same two or more amino acid types labeled in the sample for the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome to provide a positive identification of its presence in the sample.

[0013] In some embodiments, this comparison can be visualized using n-dimensional space, where the number of dimensions is equal to the number of n different amino acid types labeled and measured by the method of the present invention. For example, two labeled amino acid types are visualized in two-dimensional space, and three labeled amino acid types are visualized in three-dimensional space. This dimensional space increases as each additional amino acid type is labeled and measured in the sample. The amino acid concentrations or label values ​​of two or more amino acid types form a straight line in n-dimensional space. The number of each amino acid in two or more amino acid types forms a point in n-dimensional space. For n labeled amino acid types in the sample, n dimensions exist.

[0014] We have discovered that in order to identify the presence and / or concentration and / or amount of a target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome in a sample, it is necessary to label two or more amino acid types, measure amino acid concentrations, or measure only the number of amino acids. Labeling and measuring two or more amino acid types is essential to the method of the present invention because when two or more amino acid types are labeled and measured, they provide a unique signature for each target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome. If only one amino acid type is labeled and measured, all target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes will have the same baseline; therefore, it is necessary to label and measure two amino acid types. By comparing a sample point with p lines representing p types of target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes, the function of each concentration, the presence and / or concentration and / or amount of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome in the sample are simultaneously determined. In this solution-phase method, the amount of protein contained in the sample is determined simply by multiplying the concentration of the identified protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome in the sample by the volume of solution in the sample. It is not necessary or efficient to measure labeling, amino acid concentration, or number of amino acids for every amino acid type in the sample.

[0015] All target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, and proteomes have a unique signature of two or more known amino acid types, their label values, amino acid concentrations, or number of amino acids. To determine the presence and / or concentration and / or amount of members of a target category (i.e., protein, peptide, oligopeptide, polypeptide, protein complex, mixture, subproteome, or proteome) in a sample, it is not necessary to know, or suspect, which category of molecules the sample contains. For example, two or more labeled amino acid types in a sample are tryptophan (W) and lysine (K). The measured label of tryptophan (W) is used to determine the concentration of tryptophan (W) in the sample, and the measured label of lysine (K) is used to determine the concentration of lysine (K) in the sample. The sample contains 10.9 μM of W and 27.9 μM of K. The sample is identified for the target protein, chicken egg white lysozyme, and the target proteome, HIV. Chicken egg white lysozyme has 6W and 6K amino acids per protein sequence, while HIV has 10.9W and 27.9K amino acids per protein sequence. The absence of chicken egg white lysozyme in the sample is identified by the absence of the chicken egg white lysozyme protein concentration obtained when measuring the sample's signature. However, the signature of the sample (10.9 μM W and 27.9 μM K) is the same as the signature of HIV (10.9 W and 27.9 K) at a protein concentration of 1 μM, thus identifying the presence of 1 μM of HIV in the sample.

[0016] The key is to compare the label, amino acid concentration, or number of each labeled amino acid type in the sample with known target values, amino acid concentrations, or amino acid numbers of the same amino acid type in the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome, rather than comparing the amino acid sequence in the sample with the amino acid sequence in the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome. Other state-of-the-art methods for peptide or protein identification require determining the amino acid sequence within the peptide or protein sequence of the sample.

[0017] Two or more amino acid types in a sample are labeled. An amino acid type is defined by an R group (i.e., a side chain). The R group is specific to each amino acid type. The R group of one amino acid type is distinguishable from the R group of any other amino acid type. For example, the R group for tryptophan (W) is an indole group. Every W amino acid has an indole group. Therefore, the W amino acid type is defined by an indole R group. In another example, the R group for lysine (K) is an ε-primary amino group. Every K amino acid has this ε-primary amino group. Therefore, the K amino acid type is defined by an ε-primary amino R group. In yet another example, the R group for tyrosine (Y) is a phenol group. Every Y amino acid has a phenol group. Therefore, the Y amino acid type is defined by a phenol R group. The R group of amino acid type W is distinguishable from the R group of amino acid type K and amino acid type Y. Therefore, amino acid type W is distinguishable from amino acid type K and amino acid type Y because the R group differs between these amino acid types. All amino acid types are distinguishable from one another by their specific R groups. In some embodiments, one amino acid type is labeled independently of other amino acid types. In some embodiments, this is the R group of each amino acid in the labeled amino acid type. In some embodiments, each R group (i.e., each amino acid type) has a unique label, so each R group (i.e., each amino acid type) is labeled independently of other R groups (i.e., other amino acid types). In some embodiments, two or more R groups (i.e., two or more amino acid types) are labeled with the same label, but each labeled R group (i.e., each labeled amino acid type) is detected in a different way than another labeled R group (i.e., another labeled amino acid type). In some embodiments, each label targets a particular amino acid type. In some embodiments, each label is specific to a particular amino acid type.

[0018] In some embodiments, two or more amino acid types are selected from alanine (A), arginine (R), asparagine (N), aspartic acid (D), cysteine ​​(C), glutamic acid (E), glutamine (Q), glycine (G), histidine (H), isoleucine (I), leucine (L), lysine (K), methionine (M), phenylalanine (F), proline (P), pyrrolidine (S), selenocysteine ​​(O), threonine (T), tryptophan (W), tyrosine (Y), and valine (V), or synthetic amino acids. In some embodiments, the amino acid type includes modified amino acids and / or unmodified amino acids. In some embodiments, the amino acid type includes modified amino acids. In some embodiments, the amino acid type includes unmodified amino acids. In some embodiments, the amino acid type includes both modified and unmodified amino acids. In some embodiments, when both modified and unmodified amino acids of a given amino acid type are labeled, the modified amino acid is first converted to the unmodified amino acid.

[0019] In some embodiments, proteins in a sample are fluorescently labeled with molecules that "turn on" to fluorescence only after reaction with the desired amino acid type. Therefore, separation of the labeled amino acids from the unreacted dye is not necessary, as the unreacted dye is not fluorescent and does not provide a signal. Other state-of-the-art methods for peptide or protein identification require the separation of labeled amino acids from the unreacted dye before peptide or protein identification can be performed.

[0020] The label of each labeled amino acid type in the sample is measured. For example, if there are two or more labeled amino acid types in the sample, such as tryptophan (W) and lysine (K), the label of tryptophan (W) is measured, and the label of lysine (K) is measured.

[0021] In some embodiments, the measured label of each amino acid type is used to calculate the concentration of that labeled amino acid type and / or the number of amino acids of that labeled amino acid type in the sample. The measured label of each amino acid type may be linearly related to the concentration of the amino acid type, the number of amino acids of that amino acid type, and the concentration of the sample. For example, if there are two or more labeled amino acid types in the sample, such as tryptophan (W) and lysine (K), the label of tryptophan (W) is measured, and the label of lysine (K) is measured. The measured label of tryptophan (W) is used to calculate the amino acid concentration of tryptophan (W) and / or the number of tryptophan (W) amino acids and / or the concentration of the sample. The measured label of tryptophan is linearly related to the concentration of tryptophan amino acids, the number of tryptophan amino acids, and the concentration of the sample. The measured label of lysine (K) is used to calculate the amino acid concentration of lysine (K) and / or the number of lysine (K) amino acids and / or the concentration of the sample. The measured label of lysine is linearly related to the concentration of lysine, the number of lysine amino acids, and the protein concentration of the sample.

[0022] In some embodiments, a calibration curve or standard is used to convert the measured label (e.g., signal) value to the amino acid concentration for each of two or more labeled amino acid types in the sample. The calibration curve or standard shows how the instrument's response changes using known concentrations of the analyte. The standard or calibration curve provides label values ​​for one or more known amino acid concentrations for each amino acid type. This conversion can be applied to a sample or to a target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome. For example, the calibration curve for amino acid type tryptophan (W) is used to determine the known label value for a target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome at an amino acid concentration of 10 μM W by multiplying this amino acid concentration by 100.

number

number

[0023] In some embodiments, the number of amino acids of each labeled amino acid type in a sample is calculated by dividing the concentration of each labeled amino acid type by the molar protein concentration of the sample. Therefore, in order to use the value of the number of amino acids in the sample, it is necessary to know the molar protein concentration of the sample. In this embodiment, the positive identification of the presence of a target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome in the sample can be based on the number of amino acids of each labeled amino acid type in the sample.

[0024] When the amino acid concentrations or known label values ​​of n amino acids for a target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome are plotted as a function of their concentrations, a line is provided in n-dimensional space, from which the concentration of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome in the sample can be determined using the equation of the line. In some embodiments, the line starts at the origin. In alternative embodiments, the line includes amino acid concentrations or known label values ​​corresponding to concentrations within a known concentration range. The amino acid concentrations or measured labels for labeled amino acid types in the sample become points in n-dimensional space. By comparing the points of the sample with the line in n-dimensional space, the presence and / or concentration and / or amount of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome in the sample can be determined.

[0025] For example, if there are four target proteins (protein-A, protein-B, protein-C, and protein-D) represented in two-dimensional space, dimensions 1 and 2 are the label values ​​for cysteine ​​(C) and tryptophan (W), respectively. The cysteine ​​(C) and tryptophan (W) amino acid forms are labeled in the sample and measured. Figure 1 plots the measured target values ​​of the cysteine ​​(C) and tryptophan (W) amino acid forms labeled in the sample, which are represented as points in two-dimensional space, against the known label values ​​of cysteine ​​(C) and tryptophan (W), which are represented as lines in two-dimensional space, for each of the four target proteins. The known label values ​​of the cysteine ​​(C) and tryptophan (W) amino acid forms are plotted as a function of the protein concentration for the target proteins, protein-A, protein-B, protein-C, and protein-D. The known label values ​​represent separate lines in two-dimensional space for each of the four target proteins.

[0026] In some embodiments, this line is a baseline. In Figure 1, each point on the baseline for each of the four target proteins corresponds to the concentration of the respective target protein. As the protein concentration of the target protein increases, the known label values ​​for each amino acid type provided by the baseline move further away from its origin. The point corresponding to a 1 μM concentration of each target protein is shown as a shaded circle. The label values ​​for each cysteine ​​(C) and tryptophan (W) amino acid type in the sample are measured and these points are shown as white squares. In some embodiments, the shortest distance between the sample point and each baseline is calculated.

[0027] In some embodiments, the sample point is located on a baseline for the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome. The presence of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome in the sample is identified, and the concentration of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome is such that the measured label value or amino acid concentration of each of the two or more labeled amino acid types in the sample is equivalent to the known label value or amino acid concentration of each of the same two or more amino acid types that have been previously labeled in the sample.

[0028] In other embodiments, the sample point is not on the baseline, and the distance between the sample point and the reference line is calculated. In some embodiments, this distance is the length of a vector or line segment relative to the baseline connecting the sample point and the baseline. The sample point is closest to a single point on the baseline for the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome, and corresponds to the amino acid concentrations or known label values ​​of n different amino acid types for a single concentration of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome.

[0029] In some embodiments, the presence of a target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome is identified in the sample if the distance between the sample point and the nearest point on a baseline for the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome is less than or equal to a tolerance. In some embodiments, the tolerance is a distance threshold. If the presence of a target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome is identified in the sample, it is present at the protein concentration of the nearest point on the baseline to the sample point.

[0030] In Figure 1, the shortest distance between the sample point and the four baselines corresponding to the four target proteins was the distance between the sample point and the baseline for protein-B. The presence of protein-B, the target protein, in the sample is identified. Each point on the baseline for protein-B, the target protein, indicates the cysteine ​​(C) and tryptophan (W) amino acid type labels for distinct protein concentrations of protein-B, the target protein. The sample is identified as the protein concentration at the point on the protein-B baseline that provided the smallest distance. Here, the protein concentration of the sample is 0.5 μM. Thus, the positive identification of protein-B, the target protein, in the sample can be made, and the concentration of protein-B, the target protein, at 0.5 μM in the sample is simultaneously determined.

[0031] In some embodiments, if the molar protein concentration of a sample is known and therefore the number of amino acids of two or more amino acid types in the sample is available, the number of amino acids of the same two corresponding amino acid types is plotted in n-dimensional space to provide a point for each of the target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes. For each of the target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes, there is only one point. Thus, the points in the sample can be compared to the points for each of the target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes, and if the points in the sample are the same as the points for the target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes, the presence of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome is identified in the sample. In some embodiments, the distance between a sample point and a point for each of the target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes can be calculated, and the presence of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome is identified in the sample if the distance between the sample point and the point for the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome is less than or equal to the tolerance.

[0032] In some embodiments, if the measured label and / or amino acid concentration and / or number of each labeled amino acid type in the sample is equivalent to, or within an acceptable margin of error, known label values ​​and / or amino acid concentrations and / or numbers of the same amino acid type previously labeled in the sample within the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome, the presence and / or concentration and / or amount of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome in the sample can be positively identified. For example, if the amino acid concentrations of tryptophan (W) amino acid and lysine (K) amino acid in a sample are equivalent to, or within an acceptable margin of error for, the amino acid concentrations of tryptophan (W) amino acid and lysine (K) amino acid in the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome, then the presence and / or concentration and / or amount of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome in the sample can be positively identified.

[0033] In some embodiments, the minimum distance is calculated between the measured label values, amino acid concentrations, or number of amino acids of two or more labeled amino acid types in a sample and the known label values, amino acid concentrations, or number of amino acids of two or more amino acid types provided for the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome, and this distance is compared to a tolerance.

[0034] In some embodiments, the reference is a set of known label values, amino acid concentrations, and / or amino acid numbers for two or more amino acid types provided for each of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome. In some embodiments, the reference is obtained from a database. Alternatively, the reference can be calculated.

[0035] Each unit of each labeled amino acid type in the sample (i.e., the measured label, amino acid concentration, and / or number of amino acids) must be compared to the same unit of the same amino acid type (i.e., known label value, amino acid concentration, and / or number of amino acids) in the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome (e.g., reference). For example, if the number of amino acids W and Y is determined in the sample, the unit (number of amino acids) in the sample must be compared to the number of amino acids W and Y in the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome (e.g., reference), so as to the same unit (number of amino acids) in the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome (e.g., reference). If the amino acid concentrations of W and Y are determined in a sample, the unit (amino acid concentration) of the sample must be compared to the same unit (amino acid concentration) of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome (e.g., reference). If the measured labels of W and Y in the sample are not used to determine the amino acid concentrations or number of amino acids of W and Y in the sample, the measured labels of W and Y in the sample must be compared to the same unit (known label value) of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome (e.g., reference). For example, the measured fluorescence intensities of W and Y in a sample are compared to the known fluorescence intensities of W and Y in the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome (e.g., reference).

[0036] In some embodiments, if the units measured for a sample (i.e., measured label, amino acid concentration, and / or number of amino acids) differ from the units of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome (i.e., known label value, amino acid concentration, and / or number of amino acids), the units of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome are converted to the same units measured for the sample. In some embodiments, the number of amino acids of a specific amino acid type in one or more target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes is multiplied by the concentration of the protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome to provide the amino acid concentration of each amino acid type in the target one or more target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes. For example, if the amino acid concentrations of W and Y are measured in a sample, the number of W and Y amino acids in one or more target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes is converted to the corresponding amino acid concentrations of W and Y in each target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome. This makes it possible to compare the units of the sample with the same units of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome. In other words, it becomes possible to compare the measured amino acid concentrations of W and Y in the sample with the amino acid concentrations of W and Y in the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome.

[0037] In some embodiments, the known label values, amino acid concentrations, and / or number of amino acids of the corresponding amino acid types in one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest are calculated from any experimental information relating to one or more amino acid sequences and / or post-translational modifications of each of the proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest. In some embodiments, the number of amino acids of each amino acid type previously labeled in a sample of one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest is calculated using any experimental information relating to the amino acid sequences and / or post-translational modifications of each of the proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest. For example, if two or more labeled amino acid types in a sample are tryptophan (W) and lysine (K), the number of tryptophan (W) amino acids and lysine (K) amino acids in the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome is calculated from one or more protein sequences of that target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome. For example, if two or more labeled amino acid types in a sample are tryptophan (W) and lysine (K), and the target protein in the sample is bovine serum albumin, the number of tryptophan (W) and lysine (K) amino acids in the amino acid sequence of bovine serum albumin is calculated as 2W and 59K from the amino acid sequence of bovine serum albumin. As another example, if the target protein has three post-translational modifications on the lysine (K) amino acids that prevent these lysine amino acids from reacting to the label by the method disclosed herein, -3 is added to the number of lysine amino acids in this target protein.

[0038] In some embodiments, the amino acid sequences of one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest are known (e.g., obtained from a database). In some embodiments, the amino acid sequences of one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest are determined using standard techniques of the art (e.g., Edman degradation or mass spectrometry).

[0039] In some embodiments, the number of amino acids of two or more labeled amino acid types in one or more target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes is determined using a method disclosed herein. That is, two or more amino acid types are labeled, the labels are measured, and the measured labels are used to determine the number of amino acids of each amino acid type in one or more target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes, or the amino acid concentration of each amino acid type in a sample containing each of the target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes. In this way, the presence and / or concentration and / or amount of target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes whose amino acid sequences are unknown or not completely unknown can be determined.

[0040] In some embodiments, it is the number of each of two or more amino acid types in the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome, and not the order of each of the two or more amino acid types in the protein sequence, or the relative composition of each of the two or more amino acid types in the protein sequence, used to calculate the corresponding amino acid concentrations and / or known label values ​​of these amino acid types in one or more concentrations of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome.

[0041] It has been found that known label values ​​or unique amino acid concentration signatures for each target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome can provide a set of vector functions or parametric equations depending on a common parameter of the concentration of each target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome. In some embodiments, this set of vector functions or parametric equations can be described and used to calculate a baseline disclosed herein, and the baseline can be quantitatively compared with a sample point to identify the presence and / or concentration and / or amount of one or more target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes in the sample. The set of parametric equations describes a group of amounts as a function of a common independent variable called a parameter. Alternatively, the set of parametric equations can be expressed as an equivalent vector function, which can simplify subsequent calculations. By comparing the values ​​of labels or amino acid concentrations of two or more labeled amino acid types measured in a sample with the values ​​of known labels or amino acid concentrations of the same two or more amino acid types provided as a function of the (unknown) concentration of each of the target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes, it is possible to identify one or more target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes in a sample and simultaneously determine the concentration and / or amount of that target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome in the sample. Optionally, this can be achieved by constructing a set of vector functions or parametric equations that describe any target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome.

[0042] In some embodiments, a set of parametric equations provides signatures for the amino acid concentrations that can be measured for two or more amino acid types in a protein, peptide, oligopeptide, polypeptide, or protein complex of interest. The number of parametric equations describing a protein, peptide, oligopeptide, polypeptide, or protein complex of interest is the number of two or more amino acid types labeled and measured in the sample. The parametric equations describe the amino acid concentration of each of the two or more amino acid types labeled and measured in a sample of the protein, peptide, oligopeptide, polypeptide, or protein complex of interest as a function of concentration t. Set of parametric equations 1 is:

number

number

number

[0043] The set of parametric equations 1 can alternatively be described collectively as vector functions describing the same baseline or baseline curve. The representations are interchangeable. In this representation, vector function 1 is:

number

number

number

number

number

[0044] For example, there are two target proteins and one target protein complex. The first target protein is BSA. The K(a1), C(a2), and W(a3) amino acid types are labeled and measured in the sample. Since there are 59, 35, and 2 amino acid types for K, C, and W within the BSA protein sequence, respectively, a1=59, a2=35, and a3=2. The vector function that provides the amino acid concentration as a function of the BSA protein concentration is as follows:

number

number

[0045] Transthyretin is the target protein complex. Since all protein sequences containing the target protein complex contain 32, 4, and 8 amino acid types of K, C, and W amino acids, a1=32, a2=4, and a3=8 (sum of the number of amino acids in each of the four subunits of the protein complex). The vector function that provides the amino acid concentration as a function of transthyretin (TTR) concentration is as follows:

number

[0046] The vector equation for BSA provides a baseline for BSA in n-dimensional space (3-dimensional space, since three amino acid types are labeled and measured in the experiment), the vector equation for LYZ provides a baseline for LYZ in n-dimensional space, and the vector equation for TTR provides a baseline for TTR in n-dimensional space. These vector equations and their corresponding baselines are plotted in Figure 2 along with the sample point. To determine the presence and / or concentration and / or amount of one of these target proteins or protein complexes in the sample, the distance between the sample point and each of the baselines provided for BSA, LYZ, and TTR is calculated and compared.

[0047] Previously, no method was available for identifying the entire proteome or subproteome within a sample. Identifying the proteome or subproteome within a sample required the separation of proteins, peptides, oligopeptides, polypeptides, and protein complexes containing the proteome or subproteome, followed by the sequential identification of each protein, peptide, oligopeptide, polypeptide, and protein complex within the proteome or subproteome.

[0048] It has been found that it is not necessary to separate the proteome, subproteome, or other mixtures of proteins in a sample in order to identify the proteome, subproteome, or other mixtures and to determine the concentration or amount of the proteome, subproteome, or other mixtures. It has also been found that it is not necessary to identify every protein in the proteome, subproteome, or other mixtures in order to identify and determine the concentration or amount of the proteome, subproteome, or other mixtures. Instead, it is only necessary to perform a single measurement of the amino acid concentration, label value, or number of amino acids of two or more amino acid types in the proteome, subproteome, or other mixtures contained in the sample.

[0049] The proteome or subproteome within a sample may be substituted for an average protein sequence, which is the weighted average of the number of amino acids in each protein, peptide, oligopeptide, polypeptide, or protein complex sequence within the proteome or subproteome. It has been found that its concentration in the sample represents the total molar protein concentration of all proteins, peptides, oligopeptides, polypeptides, or protein complexes, including the proteome or subproteome. Since these signatures have been found to be unique to each proteome or subproteome, unseparated proteomes or subproteomes within a sample can be identified and quantified using this method. The order of amino acids within this average protein sequence is not calculated, and the number of amino acids of two or more amino acid types within any such average protein sequence is unique to all proteomes and subproteomes. For example, the number of amino acids of two or more amino acid types within any average protein sequence is unique to all known bacterial proteomes and all known viral proteomes (Figure 3). This is shown for 7,581 known bacterial reference proteomes and 9,377 known viral reference proteomes. The reference proteome is a complete proteome. Therefore, all known bacterial proteomes and all known viral proteomes have distinct signatures that can be readily detected in a sample using the method of the present invention without separating the proteins, peptides, oligopeptides, polypeptides, or protein complexes containing the proteome from one another. This is a counterintuitive result, because while the number of amino acids of two or more amino acid types in proteins, oligopeptides, polypeptides, and protein complexes within a proteome is expected to vary depending on the distribution, the average distribution for each proteome is expected to cluster around a single value determined by its biological function.Furthermore, the average number of amino acids of two or more amino acid types across the proteome does not follow the x=y=z trend, suggesting that this variability cannot be explained by differences in the average lengths of protein, oligopeptide, polypeptide, and protein complex sequences across the proteome.

[0050] Current methods for diagnosing infections such as SARS-CoV-2 infection rely on reverse transcription polymerase chain reaction (RT-PCR) for the (generally quantitative) determination of SARS-CoV-2 RNA in patient samples. However, these tests have a 30% false-negative rate, which has significant implications for patient care, infection control, and modeling.

[0051] In addition to providing a novel approach for the rapid diagnosis of any infection, the method of the present invention can be applied to the identification of the presence and / or concentration and / or amount of subproteomes associated with the target disease in a patient sample. For example, the subproteome signature of type 1 diabetes can be identified and quantified in saliva. In some embodiments, the subproteome signature of human ovarian cancer, human pancreatic cancer, human prostate cancer, or human colorectal cancer can be identified and quantified in blood plasma samples. In some embodiments, the subproteome signature of human bladder cancer, human prostate cancer, or human kidney cancer can be identified and quantified in urine samples.

[0052] In some embodiments, when one or more sub-proteomes or proteomes are of interest, the number of amino acids of a particular amino acid type is the weighted average of the amino acids of that particular amino acid type across all proteins in the sub-proteome or proteome of interest. For example, if two or more labeled amino acid types in a sample are tryptophan (W) and lysine (K), and the proteome of interest in the sample is the SARS-CoV-2 proteome, the weighted average of tryptophan (W) and the weighted average of lysine (K) amino acids in the average amino acid sequence of all proteins of the SARS-CoV-2 proteome are calculated to be 11.3W and 60.6K from the amino acid sequence of the SARS-CoV-2 proteome.

[0053] It has been discovered that any proteome or sub-proteome of interest can be described by a set of parametric equations. In some embodiments, the parametric equations provide a signature of amino acid concentrations that can be measured for two or more amino acid types in the proteome or sub-proteome. A set of parametric equations according to a common parameter of concentration is set 2 of the parametric equations,

Number

[0054] The unique signature of the amino acid concentrations provided for the target proteome or subproteome is obtained using the vector function 2.

number

number

[0055] In some embodiments, the average number of each amino acid of the same two or more amino acid types previously labeled and measured in the sample within the target proteome or subproteome is the weighted average number of each amino acid of the same two or more amino acid types previously labeled and measured in the sample. In some embodiments, the weights of the weighted average are provided by the proportion of that protein sequence within the total number of protein sequences in the target proteome or subproteome. For example, the weighted average number of tryptophan (W) amino acids per proteome is equal to the product of a linear combination of the number of tryptophan amino acids per protein sequence multiplied by the proportion of that protein sequence within all protein sequences, including the target proteome or subproteome, and the weighted average number of lysine (K) amino acids per proteome is equal to the product of a linear combination of the number of tryptophan amino acids per protein sequence multiplied by the proportion of that protein sequence within all protein sequences, including the target proteome or subproteome.

[0056] The amino acid concentrations measured for two or more labeled amino acid types in the sample are compared with the amino acid concentrations of the same two or more amino acid types provided for one or more target proteomes or subproteomes. This makes it possible to identify the sample as one of the target proteomes or subproteomes, and to determine the concentration or amount of the target proteome or subproteome present in the sample.

[0057] In some embodiments, the concentration of each of two or more amino acid types is the concentration of its labeled amino acid type in each of the target proteins, peptides, oligopeptides, polypeptides, or protein complexes. In some embodiments, the concentration of each of two or more amino acid types in each of the target proteomes or subproteomes is the total concentration of its labeled amino acid type across the proteins in the target proteome or subproteome. This is because the concentration of an amino acid type is equal to the average number of amino acids per sequence in the proteome multiplied by the total protein concentration of the proteome.

[0058] In many cases, the molar protein concentration of an unknown sample is unknown. This is because the standard method in the art is to measure the absorbance (A) of the sample. 280 ) Or, when used to determine the mass protein concentration, if the molecular weight of the sample is unknown, it cannot be converted to the molar protein concentration of the sample, and since the attributes of the sample are unknown, the molecular weight of the sample is unknown.

[0059] In some embodiments, the molar protein concentration of the sample is known. The known molar protein concentration of the sample is denoted as a constant SC. Therefore, the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome p is obtained. i However, if present in the sample, it is present at the molar protein concentration of the sample, so t=SC. The results for this special case are considered using an example from Set 1 of parametric equations.

number

number

[0060] In some embodiments, the amino acid concentrations of each of the two or more amino acid types of one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest are used to determine the corresponding label values ​​for each of the same two or more amino acid types of the one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest using a set of parametric equations.

[0061] This is achieved by incorporating a calibration function or calibration coefficient that converts between the measured label for each amino acid type and the amino acid concentration for each amino acid type into a parametric equation that describes the amino acid concentration of any protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome of interest.

[0062] In some embodiments, the parametric equation provides a unique signature of the label value (e.g., label signal) for a target protein, peptide, oligopeptide, polypeptide, or protein complex as a function of its concentration t, using parametric equation 3.

number

number

number

[0063] The equations that make up the set of parametric equations 3 can be similarly described together as vector functions 3.

number

number

number

number

[0064] In other embodiments, the parametric equations describing the unique signature of the label value (e.g., the label signal) for a target proteome or subproteome at any concentration t are a set of four parametric equations:

number

number

[0065] The set of parametric equations in this embodiment can, alternatively, be described collectively using the vector function 4.

number

[0066] Therefore, a set of parametric equations, or vector functions, can be constructed for any protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome of interest based on one or more amino acid sequences of the protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome alone, describing the label values ​​(e.g., signals) or unique signatures of amino acid concentrations of two or more amino acid types of the protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome of interest as a function of the concentration of the protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome of interest. For example, if only the labels of W and Y are measured in a sample and this has not been converted to the amino acid concentrations or numbers of the W and Y amino acid types in the sample, the number of W and Y amino acids in the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome is converted to the corresponding known label values ​​of W and Y as a function of the unknown concentrations of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome. This allows for comparison of the measured labels of W and Y in the sample with the known label values ​​of W and Y in the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome, and enables the determination of the presence and / or concentration and / or amount of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome in the sample. In some embodiments, no calculations are required for the signals measured for the sample.

[0067] It has been discovered that, from the vector form of a baseline or baseline curve for each target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome, it is possible to directly calculate the concentration of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome, providing known labeled values ​​or amino acid concentrations for two or more amino acid types that are closest to the corresponding two or more amino acid types labeled and measured in the sample (i.e., the distance between the sample point and the baseline is minimized).

[0068] This is achieved by finding the dot product of the direction of the reference line and the vector between the sample point and any point on the reference line, setting that dot product to a value equal to 0, and determining the density of the reference line that provides a perpendicular line between the sample point and the reference line. The dot product is a scalar number that represents the angular relationship between two vectors A and B, i.e.,

number

number

number

[0069] In some embodiments, if a sample point is below an acceptable error or distance threshold from more than one of the target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes, a mixture of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome is identified in the sample. If a component in the mixture constitutes a larger proportion of the mixture, its signature has a greater effect on the sample signature than the signature of a component that constitutes a smaller proportion of the mixture. The proportion of components in the mixture can also be utilized using the method of the present invention. The proportion of each protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome in the mixture is calculated by comparing the distance between the sample and each protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome identified as being present in the sample, where a smaller distance indicates a larger proportion of the component in the mixture. In some embodiments, the calculated distance from the sample point to a baseline for each identified component of the mixture is compared. It is found that the proportion of each component in the mixture is determined by the reciprocal of the normalized distance for each identified component of the mixture. The maximum distance for all identified components is calculated and divided by the distance for each identified component. In some embodiments, the proportion of a identified component in the mixture is calculated by dividing its inversely normalized distance by the sum of the inversely normalized distances for all components in the mixture.

[0070] The method of the present invention does not require the order (i.e., position) of amino acids in the determined amino acid sequence to identify the presence and / or concentration and / or amount of one or more target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes in a sample. The method of the present invention does not require the sequence of amino acids in the proteins in the determined sample to identify the presence and / or concentration and / or amount of one or more target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes in a sample.

[0071] The methods of the present invention can provide criteria for a target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome, described algebraically using the formulas disclosed herein. A variable (which is protein concentration) is present in the criteria. The criteria provide measurable amino acid concentrations or fluorescence intensities for any concentration of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome. This feature makes it possible to quantify the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome when identified. Therefore, the methods disclosed herein provide a quantitative technique.

[0072] term Typical features are shown in the following sections, and these may be used individually or in any combination, in conjunction with one or more features disclosed in the documents and / or drawings of this specification.

[0073] 1a. A method for identifying the presence and / or concentration and / or amount of one or more target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes in a sample, wherein the method is a) Labeling two or more amino acid types in a sample, wherein the amino acid type is defined by the R group of the amino acid. b) Measure the labeling of each labeled amino acid type in the sample, c) Selectively calculate the amino acid concentration of each labeled amino acid type from the measured labels, d) Selectively calculate the number of amino acids for each labeled amino acid type, e) A method for identifying the presence and / or concentration and / or amount of one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes in a sample by comparing the measured label and / or amino acid concentration of each labeled amino acid type in the sample with known label values ​​and / or amino acid concentrations of the same two or more amino acid types labeled in each sample of one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest at one or more concentrations; or by comparing the number of amino acids of each labeled amino acid type in the sample with the number of known amino acids of the same two or more amino acid types labeled in the sample of one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest.

[0074] 1b. A method for diagnosing bacterial and / or viral and / or parasitic diseases in a sample, wherein this method is a) Labeling two or more amino acid types in a sample, wherein the amino acid type is defined by the R group of the amino acid. b) Measure the labeling of each labeled amino acid type in the sample, c) Selectively calculate the amino acid concentration of each labeled amino acid type from the measured labels, d) Selectively calculate the number of amino acids for each labeled amino acid type, e) A method for identifying a bacterial and / or viral and / or parasitic disease in a sample by comparing the measured label and / or amino acid concentration of each labeled amino acid type in the sample with the known label values ​​and / or amino acid concentrations of the same two or more amino acid types labeled in each sample of one or more bacterial, viral and / or parasitic proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest at one or more concentrations; or by comparing the number of amino acids of each labeled amino acid type in the sample with the number of known amino acids of the same two or more amino acid types labeled in the sample of one or more viral, bacterial and / or parasitic proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest; or by identifying the presence and / or concentration and / or amount of one or more bacterial, viral and / or parasitic proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest in the sample.

[0075] 1c. A method for identifying one or more bacterial proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes in a sample, wherein this method is a) Labeling two or more amino acid types in a sample, wherein the amino acid type is defined by the R group of the amino acid. b) Measure the labeling of each labeled amino acid type in the sample, c) Selectively calculate the amino acid concentration of each labeled amino acid type from the measured labels, d) Selectively calculate the number of amino acids for each labeled amino acid type, e) A method comprising identifying the presence and / or concentration and / or amount of one or more bacterial proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes in a sample by comparing the measured label, amino acid concentration, or number of each labeled amino acid type in the sample with known label values ​​or amino acid concentrations of the same two or more amino acid types in one or more bacterial proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest at one or more concentrations, or the number of amino acids of the same two or more amino acid types in one or more bacterial proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest.

[0076] 1d. A method for identifying one or more viral proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes in a sample, wherein this method is a) Labeling two or more amino acid types in a sample, wherein the amino acid type is defined by the R group of the amino acid. b) Measure the labeling of each labeled amino acid type in the sample, c) Selectively calculate the amino acid concentration of each labeled amino acid type from the measured labels, d) Selectively calculate the number of amino acids for each labeled amino acid type, e) A method for identifying the presence and / or concentration and / or amount of one or more viral proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest in a sample by comparing the measured label and / or amino acid concentration of each labeled amino acid type in the sample with known label values ​​and / or amino acid concentrations of the same two or more amino acid types labeled in each sample of one or more viral proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest at one or more concentrations; or by comparing the number of amino acids of each labeled amino acid type in the sample with the number of known amino acids of the same two or more amino acid types labeled in the sample of one or more viral proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest.

[0077] 1e. A method for identifying one or more parasitic proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes in a sample, wherein this method is a) Labeling two or more amino acid types in a sample, wherein the amino acid type is defined by the R group of the amino acid. b) Measure the labeling of each labeled amino acid type in the sample, c) Selectively calculate the amino acid concentration of each labeled amino acid type from the measured labels, d) Selectively calculate the number of amino acids for each labeled amino acid type, e) A method for identifying the presence and / or concentration and / or amount of one or more parasitic proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes in a sample by comparing the measured label and / or amino acid concentration of each labeled amino acid type in the sample with known label values ​​and / or amino acid concentrations of the same two or more amino acid types labeled in each sample of one or more parasitic proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest at one or more concentrations; or by comparing the number of amino acids of each labeled amino acid type in the sample with the number of known amino acids of the same two or more amino acid types labeled in the sample of one or more parasitic proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest.

[0078] 1f. A method for identifying one or more human proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes in a sample, wherein this method is a) Labeling two or more amino acid types in a sample, wherein the amino acid type is defined by the R group of the amino acid. b) Measure the labeling of each labeled amino acid type in the sample, c) Selectively calculate the amino acid concentration of each labeled amino acid type from the measured labels, d) Selectively calculate the number of amino acids for each labeled amino acid type, e) A method for identifying the presence and / or concentration and / or amount of one or more human proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest in a sample by comparing the measured label and / or amino acid concentration of each labeled amino acid type in the sample with known label values ​​and / or amino acid concentrations of the same two or more amino acid types labeled in each sample of one or more human proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest at one or more concentrations; or by comparing the number of amino acids of each labeled amino acid type in the sample with the number of known amino acids of the same two or more amino acid types labeled in the sample of one or more human proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest.

[0079] 1g. A method for detecting infection or identifying a host response to infection, wherein the method is a) Labeling two or more amino acid types in a sample, wherein the amino acid type is defined by the R group of the amino acid. b) Measure the labeling of each labeled amino acid type in the sample, c) Selectively calculate the amino acid concentration of each labeled amino acid type from the measured labels, d) Selectively calculate the number of amino acids for each labeled amino acid type, e) A method for identifying the presence and / or concentration and / or amount of one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes related to infection or a host response to infection in a sample by comparing the measured label and / or amino acid concentration of each labeled amino acid type in the sample with known label values ​​and / or amino acid concentrations of the same two or more amino acid types labeled in each sample of one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes related to infection or a host response to infection in one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes related to infection or a host response to infection in a sample.

[0080] 1h. A method for detecting cancer, wherein this method a) Labeling two or more amino acid types in a sample, wherein the amino acid type is defined by the R group of the amino acid. b) Measure the labeling of each labeled amino acid type in the sample, c) Selectively calculate the amino acid concentration of each labeled amino acid type from the measured labels, d) Selectively calculate the number of amino acids for each labeled amino acid type, e) A method for identifying the presence and / or concentration and / or amount of one or more cancer-related proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes in a sample by comparing the measured label and / or amino acid concentration of each labeled amino acid type in the sample with known label values ​​and / or amino acid concentrations of the same two or more amino acid types labeled in each sample of one or more target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest related to cancer at one or more concentrations; or by comparing the number of amino acids of each labeled amino acid type in the sample with the number of known amino acids of the same two or more amino acid types labeled in the sample of one or more target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest related to cancer.

[0081] 2. One of the methods described in items 1a to 1h, wherein the sample is a body fluid sample.

[0082] 3. The method of item 2, wherein the bodily fluid sample is a whole blood sample, blood serum sample, blood plasma sample, saliva sample, sputum sample, fecal sample, urine sample, semen sample, nasal swab sample, nasopharyngeal aspirate sample, throat swab, lower respiratory tract sample, cerebrospinal fluid (CSF) sample, breast milk sample, sexual health sample, or tissue sample or fluid produced by a disease.

[0083] 4. The method of item 3, wherein the sexual health sample is a urethral swab, cervical swab, vaginal swab, or rectal swab.

[0084] 4a. The method of item 2, wherein the sample is a blood sample or a urine sample.

[0085] 5. The method of item 3, wherein the lower respiratory tract sample is a lower respiratory tract mucus aspirate sample.

[0086] 6. The method described in item 3, where the tissue sample is a tissue biopsy.

[0087] 7. The method of item 6, where the tissue is a solid tumor.

[0088] 8. The method of item 6, wherein the tissue is a sarcoma, lymphoma, carcinoma, and melanoma.

[0089] 9. The sample is a veterinary sample, using one of the methods described in items 1a to 1h.

[0090] 10. The method of item 9, wherein the veterinary specimen is a cat specimen, dog specimen, cattle specimen, pig specimen, horse specimen, donkey specimen, sheep specimen, goat specimen, fish specimen, crab specimen, coral specimen, fomarin specimen, ostracine specimen, reptile specimen, bird specimen, garin specimen, meleagrin specimen, duck specimen, anserine specimen, deer specimen, rabbit (leporine) specimen, rabbit (lapine) specimen, noctilionine specimen, mouse specimen, flea specimen, ancarine specimen, mosquito specimen, macaque specimen, or folidota specimen.

[0091] 11. One of the methods described in items 1a to 1h, wherein the sample is a soil sample, environmental sample, crop sample, food sample, beverage sample, or laboratory sample.

[0092] 12. The method of item 11, wherein the environmental sample is a water sample such as a drinking water sample or a wastewater sample, or a sample suspected of being used in biological warfare, or an astrobiological sample.

[0093] 13. The method of item 11, wherein the food sample is a functional food sample.

[0094] 14. The method of item 13, wherein the functional food sample is an infant formula sample or a sports nutrition sample.

[0095] 15. The method of item 11, wherein the food sample is a nutritional supplement sample.

[0096] 16. The method of item 11, wherein the food sample is a fermented food sample.

[0097] 17. The method of item 11, wherein the food sample is a dairy product sample, egg sample, gelatin sample, soybean sample, wheat sample, vegetable sample, bean sample, nut sample, or extracted soybean product sample.

[0098] 18. Any method of item 11 in which a food sample is suspected to contain an allergen, bacteria, virus, or parasite.

[0099] 19. The method of item 18, wherein the food sample is a meat sample and the meat sample is suspected to contain Escherichia Coli, Salmonella, Staphylococcus Aureus, Listeria Monocytogenes, Yersinia Enterocolitica, Salmonella Enteritidis, Campylobacter Jejuni, Clostridium perfringens, Clostridium perfringens, norovirus, Toxoplasma gondii, tapeworm, roundworm, or Anisakis.

[0100] 20. The method of item 18, wherein the allergen is peanuts, gluten, lactose, shellfish, fish, sesame, pollen, casein, lipocalin, type C lysozyme, protease inhibitors, tropomyosin, parvalbumin, cat dander, or dog dander.

[0101] 21. The method of item 11, wherein the beverage sample is a milk sample, a water sample, a fruit juice sample, a kefir sample, or a kombucha sample.

[0102] 22. The method described in sections 1a-1h, where the sample is a vaccine.

[0103] 23. The method of item 22, wherein the sample is an influenza vaccine, SARS-CoV-2 vaccine, 6-in-1 vaccine, Pneumococcal vaccine, MenB vaccine, Hib / MenC vaccine, MMR vaccine, 4-in-1 preschool booster vaccine, HPV vaccine, 3-in-1 teen booster vaccine, tetanus vaccine, herpes zoster vaccine, BCG (TB) vaccine, hepatitis B vaccine, or varicella vaccine.

[0104] 24. Any one of items 1 to 23, wherein one or more proteins or peptides of interest are selected from the group consisting of α-synuclein, lysozyme, bovine serum albumin, ovalbumin, β-lactoglobulin, insulin, glucagon, amyloid-β, angiotensin-converting enzyme 2, angiotensin-converting enzyme, bradykinin, chordin-like protein 1, tumor necrosis factor β, osteomodulin precursor, matrix metalloproteinase, pleiotrophin, secretogranin-3, human growth hormone, insulin-like growth factor 1, leptin, telomerase, thyroid-stimulating hormone, and any combination thereof.

[0105] 25. One of the methods described in items 1 to 23, wherein one or more target proteomes are one or more human proteomes.

[0106] 26.1 or more types of human proteomes, including human plasma proteome, human ocular proteome, retina, heart, skeletal muscle, smooth muscle, adrenal gland, parathyroid gland, thyroid gland, pituitary gland, lung, bone marrow, lymphoid tissue, liver, gallbladder, testis, epididymis, prostate, seminal vesicles, vas deferens, adipose tissue, brain, salivary gland, esophagus, tongue, stomach, intestine, pancreas, kidney, urinary tract, bladder, breast, vagina, cervix, endometrium, fallopian tube, ovary, placenta, skin or blood proteome, human metabolic proteome, human secretory proteome, stem cell proteome, erythrocyte proteome, neutrophil proteome, eosinophil proteome, basophil proteome, monocyte proteome, lymphocyte proteome, neuron proteome, nerve The method of item 25, selected from the group consisting of transgliculopreme, skeletal muscle proteome, cardiac muscle proteome, smooth muscle proteome, chondrocyte proteome, osteoblast proteome, osteoclast proteome, osteocyte proteome, bone-lining cell proteome, keratinocyte proteome, melanocyte proteome, Merkel cell proteone, Langerhans cell proteome, endothelial cell proteome, epithelial cell proteome, white adipocyte proteome, brown adipocyte proteome, upper respiratory tract cell proteome, sperm proteome, or oocyte proteome, and any combination thereof.

[0107] 27. Any one of items 1 to 23, wherein one or more target proteomes are one or more human cancer subproteomes and / or proteomes.

[0108] 28.1 or more types of human cancer proteomes and / or subproteomes include human pancreatic cancer proteome, human glioma proteome, human head and neck proteome, human thyroid proteome, human lung proteome, human liver proteome, human testicular proteome, human prostate proteome, human gastric proteome, human colon / rectal proteome, human breast proteome, human endometrial proteome, human ovarian proteome, human cervical proteome, human pancreatic proteome, human kidney proteome, human urinary tract and bladder proteome, human melanoma proteome, human type 1 diabetes subproteome, human type 2 diabetes subproteome, Alzheimer's disease subproteome The method of item 27, selected from the group consisting of a proteome, a human Parkinson's disease subproteome, a human Lewy body dementia subproteome, a human dementia subproteome, a human metabolic syndrome subproteome, a human obesity subproteome, a human cardiovascular disease subproteome, a human Down syndrome subproteome, a human aging subproteome, a human cytokine subproteome, a human immune subproteome, a human subproteome responsive to bacterial infection, a human subproteome responsive to viral infection, a human subproteome responsive to coronavirus infection, a human subproteome responsive to SARS-CoV-2 infection, a human subproteome responsive to SARS-CoV-2 infection including IFN, IL-6, IL1RA, CCL2, CCL8, CXCL2, CXCL8, CXCL9, and CXCL16, and any combination thereof.

[0109] 28a. The method of item 28, wherein one or more cancer proteomes are selected from the group consisting of human ovarian cancer proteome, human pancreatic cancer proteome, human colorectal cancer proteome, human bladder cancer proteome, human prostate cancer proteome, and human kidney cancer proteome.

[0110] 28b. The method of item 27, wherein 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, and 25 types of human cancer proteomes are detected in the sample and selected from the group consisting of pancreatic cancer, colorectal cancer, human glioma, head and neck cancer, thyroid cancer, lung cancer, liver cancer, testicular cancer, prostate cancer, gastric cancer, colorectal cancer, breast cancer, endometrial cancer, ovarian cancer, cervical cancer, kidney cancer, renal cancer, lymphoma, bladder cancer, human melanoma, brain cancer, endometrial cancer, leukemia, ureteral cancer, and any combination thereof.

[0111] 28c. The method of section 27, 28a, or 28b, wherein the method determines the amount of one or more cancer proteomes in a sample, and the amount of cancer refers to the stage or grade of cancer in the sample.

[0112] 28d. The method of item 28c, wherein the stage is stage I, stage II, stage III, or stage IV, or the TNM staging system, for example, T1, T2, T3, T4, N0, N1, N2, N3, M0, or M1.

[0113] 28e. The method of paragraph 28c, wherein the grade is grade I, II, or III.

[0114] 28f. The method of paragraph 27, 28a, or 28b, wherein the presence of cancer refers to the location of cancer in the patient.

[0115] 29. One of the methods described in items 1 to 23, wherein the target proteome is one or more viral proteomes.

[0116] 30.1 or more types of viral proteomes, including human papillomavirus (HPV) proteome, human immunodeficiency virus (HIV) proteome, orthomyxoviridae proteome, Epstein-Barr proteome, Ebola virus proteome, rabies lyssavirus proteome, coronavirus proteome, novovirus proteome, hepatitis A proteome, hepatitis B proteome, hepatitis C proteome, hepatitis E proteome, hepatitis delta proteome, herpesvirus proteome, papillomavirus proteome, rhinovirus proteome, and measles virus proteome. The method of item 29, selected from the group consisting of mumps virus proteome, poliovirus proteome, rabies proteome, rotavirus proteome, West Nile virus proteome, yellow fever virus proteome, Zika virus proteome, Caudovirales proteome, Nimaviridae proteome, Riboviria proteome, Inoviridae proteome, Fuselloviridae proteome, Herpesvirales proteome, Asfarviridae proteome, Bicaudaviridae proteome, tuberculosis proteome, bovine tuberculosis proteome, and any combination thereof.

[0117] 31. The method of item 30, wherein the Orthomyxoviridae proteome is the influenza proteome.

[0118] 32. The method of paragraph 30, wherein the influenza proteome is the influenza A proteome, the influenza A subtype H1N1 proteome, the influenza B proteome, the influenza C proteome, and / or the influenza D proteome, or any combination thereof.

[0119] 33. The method of paragraph 30, wherein the coronavirus proteome is the SARS-CoV-2 proteome, the SARS-CoV proteome, and / or the MERS-CoV proteome.

[0120] 34. The method of paragraph 33, wherein the coronavirus proteome is the SARS-CoV-2 proteome and any variant thereof.

[0121] 35. One of the methods described in items 1 to 34, wherein the target proteome is one or more bacterial proteomes.

[0122] 36. The method of item 35, wherein one or more bacterial proteomes are selected from the group consisting of Escherichia coli (E. coli) proteome, Pseudomonas aeruginosa (P. aeruginosa) proteome, Salmonella proteome, Staphylococcus aureus proteome, Acinetobacter baumannii proteome, Bacteroides fragilis proteome, Burkholderia cepacia proteome, Clostridium difficile proteome, Clostridium sordellii proteome, Enterobacteriaceae proteome, Enterococcus faecalis proteome, Klebsiella pneumoniae proteome, methicillin-resistant Staphylococcus aureus proteome, Morganella morganii proteome, Mycobacterium proteome, and any combination thereof.

[0123] 37. The method of section 36, wherein the Mycobacterium proteome is the Mycobacterium tuberculosis proteome.

[0124] 38. One of the methods described in items 1 to 23, wherein the target proteome is one or more parasitic proteomes.

[0125] 39. The method of item 38, wherein one or more parasitic proteomes are selected from the group consisting of Plasmodium proteome, Toxoplasma gondii proteome, Trichomonas vaginalis proteome, Giardia duodenalis proteome, Cryptosporidiu proteome, or any combination thereof.

[0126] 40. The method of item 39, wherein the Plasmodium proteome is the Plasmodium falciparum proteome, the Plasmodium knowlesi proteome, the Plasmodium malariae proteome, the Plasmodium ovale proteome and / or the Plasmodium vivax proteome.

[0127] 41. The methods of items 1a, 1b, 1e-1h, wherein one or more target subproteomes are host responses to parasitic proteomes.

[0128] 42. The method of item 1a, 1g, or 1h, wherein one or more of the target proteomes are archaeal proteomes.

[0129] 43. Any one of the methods from items 1 to 41, wherein the target proteome is a mixture of one or more bacterial proteomes, one or more viral proteomes, and / or one or more parasitic proteomes, and any combination thereof.

[0130] 44. One of the methods described in items 1 to 23, wherein one or more of the target proteomes are pathogenic proteomes.

[0131] 45. The method of item 44, wherein the pathogenic proteome is a bacterial proteome and / or a viral proteome.

[0132] 46. ​​One of the methods described in items 1 to 23, wherein one or more target proteins are prions.

[0133] 47. Prions cause Creutzfeldt-Jakob disease (CJD) by the method described in paragraph 46.

[0134] 48. One of the methods described in items 1 to 23, wherein one or more of the target proteomes are proteomes within any family of bacteria of interest.

[0135] 49. One of the methods described in items 1 to 23, wherein one or more subproteomes of interest are host responses to a bacterial proteome.

[0136] 50. One of the methods described in items 1 to 23, by which the presence of the bacterial proteome and host response subproteome is detected in the sample.

[0137] 51. The method of item 29, wherein one or more target viral proteomes are veterinary viral proteomes.

[0138] 52. The method of paragraph 51, wherein the veterinary viral proteome is the rhabdovirus proteome, foot-and-mouth disease virus proteome, pestivirus proteome, arterivirus proteome, coronavirus proteome, torovirus proteome, influenza proteome, blue tongue virus, or circovirus proteome, and any combination thereof.

[0139] 53. The method of paragraph 52, wherein the influenza proteome is an avian influenza proteome or a swine influenza proteome.

[0140] 54. The method of paragraph 52, wherein the circovirus proteome is a herpesvirus proteome, an African swine fever virus proteome, a retrovirus proteome, a flavivirus proteome, a paramyxovirus proteome, or a parlovirus proteome.

[0141] 55. One of the methods from items 1 to 54, wherein the amino acid type is selected from the group consisting of alanine (A), arginine (R), asparagine (N), aspartic acid (D), cysteine ​​(C), glutamic acid (E), glutamine (Q), glycine (G), histidine (H), isoleucine (I), leucine (L), lysine (K), methionine (M), phenylalanine (F), proline (P), pyrrolidine (O), selenocysteine ​​(U), serine (S), threonine (T), tryptophan (W), tyrosine (Y), and valine (V), or synthetic amino acids, their N-terminus and C-terminus, and any combination thereof.

[0142] 56. The method of item 55, wherein two or more amino acid types are selected from the group consisting of alanine (A), arginine (R), asparagine (N), aspartic acid (D), cysteine ​​(C), glutamic acid (E), glutamine (Q), glycine (G), histidine (H), isoleucine (I), leucine (L), lysine (K), methionine (M), phenylalanine (F), proline (P), pyrrolidine (O), selenocysteine ​​(U), serine (S), threonine (T), tryptophan (W), tyrosine (Y), and valine (V), and any combination thereof.

[0143] 57. The method of item 55, wherein 2 or more amino acid types are selected from the group consisting of arginine (R), asparagine (N), aspartic acid (D), cysteine ​​(C), glutamic acid (E), glutamine (Q), glycine (G), histidine (H), lysine (K), methionine (M), phenylalanine (F), proline (P), pyrrolidine (O), selenocysteine ​​(U), serine (S), threonine (T), tryptophan (W), tyrosine (Y), and any combination thereof.

[0144] 58. The method of item 55, wherein two or more amino acid types are selected from the group consisting of alanine (A), arginine (R), asparagine (N), aspartic acid (D), cysteine ​​(C), glutamic acid (E), glutamine (Q), histidine (H), isoleucine (I), leucine (L), lysine (K), methionine (M), phenylalanine (F), proline (P), pyrrolidine (O), selenocysteine ​​(U), serine (S), threonine (T), tryptophan (W), tyrosine (Y), and valine (V), and any combination thereof.

[0145] 59. The method of item 55, wherein two or more amino acid types labeled in the sample are selected from the group consisting of tryptophan (W), cysteine ​​(C), tyrosine (Y), lysine (K), arginine (R), histidine (H), proline (P), aspartic acid (D), glutamic acid (E), asparagine (B), glutamine (Q), serine (S), or threonine (T), and any combination thereof.

[0146] 60. Two or more amino acid types labeled in the sample are lysine and tryptophan, cysteine ​​(C) and tryptophan (W), lysine (K) and cysteine ​​(C), lysine (K) and tyrosine (Y), cysteine ​​(C) and tyrosine (Y), tryptophan (W) and tyrosine (Y), leucine (L) and serine (S), leucine (L) and lysine (K), glutamic acid (E) and leucine (L), glycine (G) and leucine (L), alanine (A), and The method of claim 55, selected from the group consisting of bileucine(L), aspartic acid(D) and leucine(L), leucine(L) and serine(S), leucine(L) and proline(P), leucine(L) and valine(V), lysine(K) and serine(S), glutamic acid(E) and leucine(L), alanine(A) and arginine(R), alanine(A) and glutamic acid(E), alanine(A) and glycine(G), or alanine(A) and isoleucine(I).

[0147] 61. The method of item 55, wherein two or more types of amino acid types labeled in the sample are selected from the group consisting of tryptophan (W), cysteine (C), tyrosine (Y), lysine (K), arginine (R), histidine (H), proline (P), aspartic acid (D), glutamic acid (E), asparagine (B), and / or glutamine (Q), and any combination thereof.

[0148] 62. The method of item 55, wherein two or more types of amino acid types labeled in the sample are selected from the group consisting of tryptophan (W), cysteine (C), tyrosine (Y), and / or lysine (K), and any combination thereof.

[0149] 63. The method of item 55, wherein two or more amino acids are selected from cysteine (C), arginine (R), histidine (H), and / or aspartic acid (D), and any combination thereof.

[0150] 64. The method of item 55, wherein two or more types of amino acid types are selected from cysteine (C), arginine (R), histidine (H), and / or glutamic acid (E), and any combination thereof.

[0151] 65. The method of item 55, wherein two or more types of amino acid types are selected from cysteine (C), arginine (R), histidine (H), and / or glutamine (Q), and any combination thereof.

[0152] 66. The method of item 55, wherein two or more types of amino acid types are selected from cysteine (C), arginine (R), tryptophan (W), and / or aspartic acid (D), and any combination thereof.

[0153] 67. The method of item 55, wherein two or more types of amino acid types are selected from lysine (K), arginine (R), histidine (H), and / or aspartic acid (D), and any combination thereof.

[0154] 68. The method of claim 55, wherein two or more types of amino acid types are selected from lysine (K), tryptophan (W), arginine (R), and / or glutamic acid (E), and any combination thereof.

[0155] 69. The method of claim 55, wherein two or more types of amino acid types are selected from tyrosine (Y), lysine (K), cysteine (C), and / or aspartic acid (D), and any combination thereof.

[0156] 70. The method of claim 55, wherein two or more types of amino acid types are selected from tyrosine (Y), lysine (K), cysteine (C), and / or glutamic acid (E), and any combination thereof.

[0157] 71. The method of claim 55, wherein two or more types of amino acid types are selected from proline (P), cysteine (C), arginine (R), and / or glutamic acid (E), and any combination thereof.

[0158] 72. The method of claim 55, wherein two or more types of amino acid types are selected from proline (P), cysteine (C), arginine (R), and / or aspartic acid (D), and any combination thereof.

[0159] 73. The method of claim 55, wherein two or more types of amino acid types are selected from cysteine (C), asparagine (B), arginine (R), and / or aspartic acid (D), and any combination thereof.

[0160] 74. The method of claim 55, wherein two or more types of amino acid types are selected from cysteine (C), asparagine (B), arginine (R), and / or glutamic acid (E), and any combination thereof.

[0161] 75. The method of claim 55, wherein two or more types of amino acid types are selected from lysine (K), asparagine (B), tryptophan (W), and / or cysteine (C), and any combination thereof.

[0162] 76. The method of claim 55, wherein one or more amino acid types are selected from arginine (R), histidine (H), proline (P), and / or aspartic acid (D), and any combination thereof.

[0163] 77. The method of item 55, wherein one or more amino acid types are selected from arginine (R), lysine (K), cysteine ​​(C), and / or aspartic acid (D), and any combination thereof.

[0164] 78. The method of item 55, wherein one or more amino acid types are selected from arginine (R), lysine (K), cysteine ​​(C), and / or glutamic acid (E), and any combination thereof.

[0165] 79. The method of item 55, wherein one or more amino acid types are selected from arginine (R), lysine (K), cysteine ​​(C), and / or tryptophan (W), and any combination thereof.

[0166] The method of claim 55, wherein 80.2 or more amino acid types are selected from arginine (R), lysine (K), cysteine ​​(C), and / or tyrosine (Y), and any combination thereof.

[0167] 81. The method of item 55, wherein one or more amino acid types are selected from arginine (R), lysine (K), histidine (H), and / or tryptophan (W), and any combination thereof.

[0168] The method of item 55, wherein 82.2 or more amino acid types are selected from arginine (R), lysine (K), histidine (H), and / or cysteine ​​(C), and any combination thereof.

[0169] 83. The method of item 55, wherein one or more amino acid types are selected from arginine (R), lysine (K), histidine (H), and / or tyrosine (Y), and any combination thereof.

[0170] The method of item 55, wherein two or more types of amino acid types are selected from arginine (R), cysteine (C), tryptophan (W), and / or tyrosine (Y), and any combination thereof.

[0171] The method of item 55, wherein two or more types of amino acid types are selected from arginine (R), cysteine (C), tryptophan (W), and / or proline (P), and any combination thereof.

[0172] The method of item 55, wherein two or more types of amino acid types are selected from tryptophan (W), cysteine (C), and / or lysine (K), and any combination thereof.

[0173] The method of item 55, wherein two or more types of amino acid types are selected from lysine (K), tryptophan (W), and / or tyrosine (Y), and any combination thereof.

[0174] The method of item 55, wherein two or more types of amino acid types are selected from tryptophan (W), tyrosine (Y), and / or cysteine (C), and any combination thereof.

[0175] The method of item 55, wherein two or more types of amino acid types are selected from tryptophan (W), tyrosine (Y), and / or lysine (K), and any combination thereof.

[0176] The method of item 55, wherein two or more types of amino acid types are selected from cysteine (C), tryptophan (W), and / or tyrosine (Y), and any combination thereof.

[0177] The method of items 1a - 1h, wherein two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, sixteen, seventeen, eighteen, nineteen, or twenty, twenty - one, twenty - two, twenty - three, twenty - four, twenty - five, twenty - six, twenty - seven, twenty - eight, twenty - nine, thirty, thirty - one, thirty - two, thirty - three, thirty - four, thirty - five, thirty - six, thirty - seven, thirty - eight, thirty - nine, or forty types of amino acid types are labeled in the sample.

[0178] 92. The method of item 91, wherein two types of amino acid forms are labeled.

[0179] 93. The method of item 92, wherein the two labeled amino acid types are selected from the group consisting of alanine (A), arginine (R), asparagine (N), aspartic acid (D), cysteine ​​(C), glutamic acid (E), glutamine (Q), glycine (G), histidine (H), isoleucine (I), leucine (L), lysine (K), methionine (M), phenylalanine (F), proline (P), pyrrolidine (O), selenocysteine ​​(U), serine (S), threonine (T), tryptophan (W), tyrosine (Y), and valine (V), and any combination thereof.

[0180] The method of item 92, wherein the amino acid forms are leucine (L) and serine (S).

[0181] The method of item 92, wherein the amino acid types are leucine (L) and lysine (K).

[0182] The method of item 92, wherein the amino acid types are leucine (L) and glutamic acid (E).

[0183] The method of item 92, wherein the acid forms are glycine (G) and leucine (L).

[0184] The method of item 92, wherein the amino acid types are alanine (A) and leucine (L).

[0185] The method of item 92, wherein the amino acid forms are aspartic acid (D) and leucine (L).

[0186] 100. The method of item 92, wherein the amino acid types are leucine (L) and proline (P).

[0187] 101. The method of item 92, wherein the amino acid types are leucine (L) and valine (V).

[0188] 102. The method of item 92, wherein the amino acid forms are lysine (K) and serine (S).

[0189] 103. The method of item 92, wherein the amino acid forms are glutamic acid (E) and leucine (L).

[0190] 104. The method of item 92, wherein the amino acid types are alanine (A) and arginine (R).

[0191] 105. The method of item 92, wherein the two amino acids are alanine (A) and glutamic acid (E).

[0192] 106. The method of item 92, wherein the two amino acids are alanine (A) and glycine (G).

[0193] 107. The method of item 91, in which three types of amino acid forms are labeled.

[0194] 108. The method of item 107, wherein the three labeled amino acid types are selected from the group consisting of alanine (A), arginine (R), asparagine (N), aspartic acid (D), cysteine ​​(C), glutamic acid (E), glutamine (Q), glycine (G), histidine (H), isoleucine (I), leucine (L), lysine (K), methionine (M), phenylalanine (F), proline (P), pyrrolidine (O), selenocysteine ​​(U), serine (S), threonine (T), tryptophan (W), tyrosine (Y), and valine (V), and any combination thereof.

[0195] 109. The method of item 107, wherein the three labeled amino acid forms are tryptophan (W), cysteine ​​(C), and tyrosine (Y).

[0196] 110. The method of item 107, wherein the three labeled amino acid types are cysteine ​​(C), tyrosine (Y), and lysine (K).

[0197] 111. The method of item 107, wherein the amino acid forms are tryptophan (W), cysteine ​​(C), and lysine (K).

[0198] 112. The method of item 107, wherein the amino acid forms are lysine (K), tryptophan (W), and tyrosine (Y).

[0199] 113. The method of item 107, wherein the amino acid forms are tryptophan (W), tyrosine (Y), and cysteine ​​(C).

[0200] 114. The method of item 107, wherein the amino acid forms are tryptophan (W), tyrosine (Y), and lysine (K).

[0201] 115. The method of item 107, wherein the three labeled amino acid types are cysteine ​​(C), tryptophan (W), and tyrosine (Y).

[0202] 116. The method of item 107, wherein the three labeled amino acid forms are asparagine (R), glutamic acid (E), and glycine (G).

[0203] 117. The method of item 107, wherein the three labeled amino acid forms are alanine (A), leucine (L), and serine (S).

[0204] 118. The method of item 107, wherein the three labeled amino acid forms are asparagine (A), glutamic acid (E), and leucine (L).

[0205] 119. The method of item 107, wherein the three labeled amino acid forms are alanine (A), aspartic acid (D), and leucine (L).

[0206] 120. The method of item 107, wherein the three labeled amino acid forms are alanine (A), leucine (L), and proline (P).

[0207] 121. The method of item 107, wherein the three labeled amino acid forms are alanine (A), glutamic acid (E), and leucine (L).

[0208] 122. The method of item 107, wherein the three labeled amino acid forms are leucine (L), serine (S), and valine (S).

[0209] 123. The method of item 107, wherein the three labeled amino acid types are glutamic acid (E), isoleucine (I), and proline (P).

[0210] 124. The method of item 107, wherein the three labeled amino acid types are glutamic acid (E), glycine (G), and valine (V).

[0211] 125. The method of item 107, wherein the three labeled amino acid forms are arginine (R), serine (S), and valine (V).

[0212] 126. The method of item 107, wherein the three labeled amino acid forms are alanine (A), leucine (L), and lysine (K).

[0213] 127. The method of item 107, wherein the three labeled amino acid types are alanine (A), arginine (R), and leucine (L).

[0214] 128. The method of item 107, wherein the three labeled amino acid types are alanine (A), leucine (L), and valine (V).

[0215] 129. The method of item 91, in which four types of amino acid forms are labeled.

[0216] 130. The method of item 129, wherein the four labeled amino acid types are selected from the group consisting of alanine (A), arginine (R), asparagine (N), aspartic acid (D), cysteine ​​(C), glutamic acid (E), glutamine (Q), glycine (G), histidine (H), isoleucine (I), leucine (L), lysine (K), methionine (M), phenylalanine (F), proline (P), pyrrolidine (O), selenocysteine ​​(U), serine (S), threonine (T), tryptophan (W), tyrosine (Y), and valine (V), and any combination thereof.

[0217] 131. The method of item 129, wherein the four labeled amino acid types are tryptophan (W), tyrosine (Y), lysine (K), and cysteine ​​(C).

[0218] 132. The method of item 129, wherein the four labeled amino acid types are cysteine ​​(C), arginine (R), histidine (H), and aspartic acid (D).

[0219] 133. The method of item 129, wherein the four labeled amino acid types are cysteine ​​(C), arginine (R), histidine (H), and glutamic acid (E).

[0220] 134. The method of item 129, wherein the four labeled amino acid types are cysteine ​​(C), arginine (R), histidine (H), and glutamine (Q).

[0221] 135. The method of item 129, wherein the four labeled amino acid types are cysteine ​​(C), arginine (R), tryptophan (W), and aspartic acid (D).

[0222] 136. The method of item 129, wherein the four labeled amino acid types are lysine (K), arginine (R), histidine (H), and aspartic acid (D).

[0223] 137. The method of item 129, wherein the four labeled amino acid forms are lysine (K), tryptophan (W), arginine (R), and glutamic acid (E).

[0224] 138. The method of item 129, wherein the four labeled amino acid types are tyrosine (Y), lysine (K), cysteine ​​(C), and aspartic acid (D).

[0225] 139. The method of item 129, wherein the four labeled amino acid types are tyrosine (Y), lysine (K), cysteine ​​(C), and glutamic acid (E).

[0226] 140. The method of item 129, wherein the four labeled amino acid types are proline (P), cysteine ​​(C), arginine (R), and glutamic acid (E).

[0227] 141. The method of item 129, wherein the four labeled amino acid types are proline (P), cysteine ​​(C), arginine (R), and aspartic acid (D).

[0228] 142. The method of item 129, wherein the four labeled amino acid types are cysteine ​​(C), asparagine (B), arginine (R), and aspartic acid (D).

[0229] 143. The method of item 129, wherein the four labeled amino acid types are cysteine ​​(C), asparagine (B), arginine (R), and glutamic acid (E).

[0230] 144. The method of item 129, wherein the four labeled amino acid types are lysine (K), asparagine (B), tryptophan (W), and cysteine ​​(C).

[0231] 145. The method of item 129, wherein the four labeled amino acid types are arginine (R), histidine (H), proline (P), and aspartic acid (D).

[0232] 146. The method of item 129, wherein the four labeled amino acid types are arginine (R), lysine (K), cysteine ​​(C), and aspartic acid (D).

[0233] 147. The method of item 129, wherein the four labeled amino acid types are arginine (R), lysine (K), cysteine ​​(C), and glutamic acid (E).

[0234] 148. The method of item 129, wherein the four labeled amino acid types are arginine (R), lysine (K), cysteine ​​(C), and tryptophan (W).

[0235] 149. The method of item 129, wherein the four labeled amino acid types are arginine (R), lysine (K), cysteine ​​(C), and tyrosine (Y).

[0236] 150. The method of item 129, wherein the four labeled amino acid types are arginine (R), lysine (K), histidine (H), and tryptophan (W).

[0237] 151. The method of item 129, wherein the four labeled amino acid types are arginine (R), lysine (K), histidine (H), and cysteine ​​(C).

[0238] 152. The method of item 129, wherein the four labeled amino acid types are arginine (R), lysine (K), histidine (H), and tyrosine (Y).

[0239] 153. The method of item 129, wherein the four labeled amino acid types are arginine (R), cysteine ​​(C), tryptophan (W), and tyrosine (Y).

[0240] 154. The method of item 129, wherein the four labeled amino acid types are arginine (R), cysteine ​​(C), tryptophan (W), and proline (P).

[0241] 155. The method of item 129, wherein the four labeled amino acid types are glutamine (Q), leucine (L), lysine (K), and valine (V).

[0242] 156. The method of item 129, wherein the four labeled amino acid forms are arginine (R), isoleucine (I), leucine (L), and serine (S).

[0243] 157. The method of item 129, wherein the four labeled amino acid types are alanine (A), asparagine (N), glutamic acid (E), and serine (S).

[0244] The method of item 91, in which 158.5 different amino acid types are labeled.

[0245] 159. The method of item 158, wherein five labeled amino acid types are selected from the group consisting of alanine (A), arginine (R), asparagine (N), aspartic acid (D), cysteine ​​(C), glutamic acid (E), glutamine (Q), glycine (G), histidine (H), isoleucine (I), leucine (L), lysine (K), methionine (M), phenylalanine (F), proline (P), pyrrolidine (O), selenocysteine ​​(U), serine (S), threonine (T), tryptophan (W), tyrosine (Y), and valine (V), and any combination thereof.

[0246] 160. The method of item 158, wherein the five labeled amino acid types are arginine (R), glutamic acid (E), lysine (K), serine, and glutamine (Q).

[0247] 161. The method of item 158, wherein the five labeled amino acid types are arginine (R), aspartic acid (D), lysine (K), serine, and glutamine (Q).

[0248] 162. The method of item 158, wherein the five labeled amino acid types are arginine (R), glycine (G), lysine (K), serine, and glutamine (Q).

[0249] 163. The method of item 158, wherein the five labeled amino acid types are alanine (A), aspartic acid (D), glycine (G), serine, and arginine (R).

[0250] 164. The method of item 158, wherein the five labeled amino acid types are pyrrolidine (O), aspartic acid (D), glycine (G), serine, and arginine (R).

[0251] 165. The method of item 158, wherein the five labeled amino acid types are pyrrolidine (O), aspartic acid (D), selenocysteine ​​(U), serine, and arginine (R).

[0252] 166. The method of item 158, wherein the five labeled amino acid types are pyrrolidine (O), aspartic acid (D), selenocysteine ​​(U), lysine, and arginine (R).

[0253] 167. Any one of the preceding methods, wherein each of two or more labeled amino acid types includes a modified amino acid and / or an unmodified amino acid of the amino acid type.

[0254] 168. The method of item 167, wherein an amino acid-type modified amino acid is an amino acid-type post-translational modified amino acid.

[0255] 169. The method of item 167 or 168, wherein four amino acid types are labeled, the four amino acid types being cysteine ​​(C), tyrosine (Y), lysine (K), and tryptophan (W), and both unmodified cysteine ​​(CR) amino acids and modified and unmodified cysteine ​​amino acids are labeled.

[0256] 170. The modified amino acid of cysteine ​​is disulfide-bonded cysteine ​​(C D ) The method of item 167 or 168, wherein the amino acid is...

[0257] 171. The method of item 167 or 168, wherein the modified amino acid of arginine is an N-glycosylated arginine (Rg) amino acid.

[0258] 172. The method of item 167 or 168, wherein the modified amino acid of asparagine is an N-glycosylated asparagine (Ng) amino acid.

[0259] 173. The method of item 167 or 168, wherein the modified amino acid of lysine is the N6-(pyridoxal phosphate)lysine (Kp) amino acid.

[0260] 174. The method of item 167 or 168, wherein the modified amino acid of proline is the 4-hydroxyproline (Ph) amino acid.

[0261] 175. The method of item 167 or 168, wherein the modified amino acid of serine is a phosphoserine (Sp) amino acid.

[0262] 176. The method of item 167 or 168, wherein the modified amino acid of threonine is a phosphothreonine (Tp) amino acid.

[0263] 177. The method of item 167 or 168, wherein the modified amino acid of alanine is an N-acetylated alanine (An) amino acid.

[0264] 178. The method of item 167 or 168, wherein the modified amino acid of arginine is a methylated arginine (Rm) amino acid.

[0265] 179. The method of item 167 or 168, wherein the modified amino acid of arginine is a deiminated arginine (Ri) amino acid.

[0266] 180. The method of item 167 or 168, wherein the modified amino acid of asparagine is a deamidated asparagine (Qa) amino acid.

[0267] 181. Amino acid-type modified amino acids undergo phosphorylation, methylation, acetylation, amidation, deamidation, deamidation, formation of pyrrolidone carboxylic acid, isomerization, hydroxylation, sulfation, flavin bonding, cysteine ​​oxidation, cyclization, nitrosylation, acylation, formylation, alkylation, arginylation, amide bond formation, butyrylation, gamma-carboxylation, glycosylation, O-bond glycosylation, malonylation, hydroxylation, iodation, isopeptide bond formation, nucleotide addition, The method of item 167 or 168, wherein the amino acid has been post-translationally modified via N-acetylation, N-myristoylation, phosphorylation, adenylylation, uridilylation, propionylation, pyroglutamate formation, S-glutathionylation, oxidation, sulfenylation, sulfonylation, succinylation, sulfation, SUMOylation, myristoylation, palmitoylation, isoprenylation, prenylation, ubiquitination, and glipyation, and any combination thereof.

[0268] 182. The method of item 167 or 168, wherein both modified and unmodified amino acids of the amino acid type are labeled.

[0269] 183. The method of item 182, wherein both modified and unmodified amino acids of amino acid-type cysteine ​​(C) are labeled.

[0270] 184. The method of item 182, wherein both modified and unmodified amino acids of amino acid-type tryptophan (W) are labeled.

[0271] 185. The method of item 182, wherein both modified and unmodified amino acids of amino acid-type tyrosine (Y) are labeled.

[0272] 186. The method of item 182, wherein both modified and unmodified amino acids of amino acid-type glycine (G) are labeled.

[0273] 187. The method of item 182, wherein both modified and unmodified amino acids of amino acid-type histidine (H) are labeled.

[0274] 188. The method of item 182, wherein both modified and unmodified amino acids of amino acid-type methionine (M) are labeled.

[0275] 189. The method of items 1a to 1h, wherein at least one amino acid type is a synthetic amino acid type selected from amino acid types containing functional groups azide, alkyne, alkene, cyclooctin, diene, acyl, iodine, boronic acid, diazirine, cyclooctene, epoxide, cyclopropane, sulfonic acid, sulfinic acid, biotin, oxime, nitrone, norbornene, tetrazene, tetrazole, quadricyclan, electron-deficient π-system, electron-rich π-system, halogen, NHS ester, maleimide, hydrazine, hydrazone, and / or diazo, and any combination thereof.

[0276] 190. Any one of the preceding items, wherein all or a certain proportion of amino acids of each amino acid type are labeled.

[0277] 191. The method of item 190, wherein all amino acids of each amino acid type are labeled.

[0278] 192. The method of item 190, wherein at least all of the first amino acid type are labeled and at least a certain proportion of the second amino acid type are labeled.

[0279] 193. The method of item 190, wherein three types of amino acids in the sample are labeled, all of the amino acids of the first amino acid type are labeled, and a certain proportion of the amino acids of the second and third amino acid types are labeled.

[0280] 194. The method of item 190, wherein three types of amino acids in the sample are labeled, all of the amino acids of the first and second amino acid types are labeled, and a certain proportion of the amino acids of the third amino acid type are labeled.

[0281] 195. The method of item 190, wherein four types of amino acids in the sample are labeled, all of the amino acids of the first amino acid type are labeled, and a certain proportion of the amino acids of the second, third, and fourth amino acid types are labeled.

[0282] 196. The method of item 190, wherein four types of amino acids in the sample are labeled, all of the amino acids of the first and second amino acid types are labeled, and a certain proportion of the amino acids of the third and fourth amino acid types are labeled.

[0283] 197. The method of item 190, wherein four types of amino acids in the sample are labeled, all of the first, second, and third amino acid types are labeled, and a certain proportion of the amino acids of the fourth amino acid type are labeled.

[0284] 198. The method of item 190, wherein five amino acid types in the sample are labeled, all of the amino acids of the first amino acid type are labeled, and a certain proportion of the amino acids of the second, third, fourth, and fifth amino acid types are labeled.

[0285] 199. The method of item 190, wherein five types of amino acids in the sample are labeled, all of the first, second, third, and fourth amino acid types are labeled, and a certain proportion of the fifth amino acid type is labeled.

[0286] 200. The method of item 190, wherein five types of amino acids in the sample are labeled, all of the amino acids of the first and second amino acid types are labeled, and a certain proportion of the amino acids of the third, fourth, and fifth amino acid types are labeled.

[0287] 201. The method of item 190, in which, depending on item 167 or 168, five amino acid types in the sample are labeled, all amino acids of the first, second and third amino acid types are labeled, a certain proportion of amino acids of the fourth and fifth amino acid types, unmodified amino acids of the first, second and third amino acid types are labeled, and modified amino acids of the fourth and fifth amino acid types are labeled.

[0288] 202. The method of item 190, wherein, as per item 167 or 168, at least all of the first amino acid type are labeled, at least a certain proportion of the second amino acid type are labeled, the unmodified amino acids of the first amino acid type are labeled, and the modified amino acids of the second amino acid type are labeled.

[0289] 203. The method of item 190, in which, depending on item 167 or 168, three amino acid types in the sample are labeled, all of the amino acids of the first amino acid type are labeled, a certain proportion of the amino acids of the second and third amino acid types are labeled, the unmodified amino acids of the first amino acid type are labeled, and the modified amino acids of the second and third amino acid types are labeled.

[0290] 204. The method of item 190, in which, depending on item 167 or 168, three types of amino acids in the sample are labeled, all of the amino acids of the first and second amino acid types are labeled, a certain proportion of the amino acids of the third amino acid type are labeled, the unmodified amino acids of the first and second amino acid types are labeled, and the modified amino acids of the third amino acid type are labeled.

[0291] 205. The method of item 190, in which, depending on item 167 or 168, four amino acid types in the sample are labeled, all amino acids of the first amino acid type are labeled, a certain proportion of amino acids of the second, third and fourth amino acid types are labeled, unmodified amino acids of the first amino acid type are labeled, and modified amino acids of the second, third and fourth amino acid types are labeled.

[0292] 206. The method of item 190, in which, depending on item 167 or 168, four amino acid types in the sample are labeled, all amino acids of the first and second amino acid types are labeled, a certain proportion of amino acids of the third and fourth amino acid types are labeled, unmodified amino acids of the first and second amino acid types are labeled, and modified amino acids of the third and fourth amino acid types are labeled.

[0293] The method of item 190, as per item 167 or 168, wherein four amino acid types in the sample are labeled, all amino acids of the first, second, and third amino acid types are labeled, a certain proportion of amino acids of the fourth amino acid type are labeled, unmodified amino acids of the first, second, and third amino acid types are labeled, and modified amino acids of the fourth amino acid type are labeled.

[0294] 208. The method of item 190, in which, depending on item 167 or 168, five amino acid types in the sample are labeled, all amino acids of the first amino acid type are labeled, a certain proportion of amino acids of the second, third, fourth, and fifth amino acid types are labeled, unmodified amino acids of the first amino acid type are labeled, and modified amino acids of the second, third, fourth, and fifth amino acid types are labeled.

[0295] 209. The method of item 190, in which, according to item 167 or 168, five amino acid types in the sample are labeled, all amino acids of the first, second, third, and fourth amino acid types are labeled, a certain proportion of amino acids of the fifth amino acid type are labeled, unmodified amino acids of the first, second, third, and fourth amino acid types are labeled, and modified amino acids of the fifth amino acid type are labeled.

[0296] 210. The method of item 190, in which, depending on item 167 or 168, five amino acid types in the sample are labeled, all amino acids of the first and second amino acid types are labeled, a certain proportion of amino acids of the third, fourth and fifth amino acid types are labeled, unmodified amino acids of the first and second amino acid types are labeled, and modified amino acids of the third, fourth and fifth amino acid types are labeled.

[0297] 211. The method of item 190, in which, depending on item 167 or 168, five amino acid types in the sample are labeled, all amino acids of the first, second, and third amino acid types are labeled, a certain proportion of amino acids of the fourth and fifth amino acid types are labeled, unmodified amino acids of the first, second, and third amino acid types are labeled, and modified amino acids of the fourth and fifth amino acid types are labeled.

[0298] 212. The method of item 190, in which, depending on item 167 or 168, five amino acid types in the sample are labeled, all amino acids of the first, second, and third amino acid types are labeled, a certain proportion of amino acids of the fourth and fifth amino acid types are labeled, unmodified amino acids of the first, second, and third amino acid types are labeled, and modified amino acids of the fourth and fifth amino acid types are labeled.

[0299] 213. The method of item 190, in which, depending on item 167 or 168, five amino acid types in the sample are labeled, a certain proportion of amino acids of the first, second, and third amino acid types are labeled, all amino acids of the fourth and fifth amino acid types are labeled, modified amino acids of the first, second, and third amino acid types are labeled, and unmodified amino acids of the fourth and fifth amino acid types are labeled.

[0300] 214. The method of item 190, in which, depending on item 167 or 168, three amino acid types in the sample are labeled, all of the amino acids of the first amino acid type are labeled, a certain proportion of the amino acids of the second and third amino acid types are labeled, the modified amino acids of the first amino acid type are labeled, and the unmodified amino acids of the second and third amino acid types are labeled.

[0301] 215. The method of item 190, in which, depending on item 167 or 168, three types of amino acids in the sample are labeled, all of the amino acids of the first and second amino acid types are labeled, a certain proportion of the amino acids of the third amino acid type are labeled, modified amino acids of the first and second amino acid types are labeled, and unmodified amino acids of the third amino acid type are labeled.

[0302] 216. The method of item 190, in which, depending on item 167 or 168, four amino acid types in the sample are labeled, all of the amino acids of the first amino acid type are labeled, a certain proportion of the amino acids of the second, third and fourth amino acid types are labeled, modified amino acids of the first and second amino acid types are labeled, and unmodified amino acids of the third and fourth amino acid types are labeled.

[0303] 217. The method of item 190, in which, depending on item 167 or 168, four amino acid types in the sample are labeled, all amino acids of the first and second amino acid types are labeled, a certain proportion of amino acids of the third and fourth amino acid types are labeled, modified amino acids of the first and second amino acid types are labeled, and unmodified amino acids of the third and fourth amino acid types are labeled.

[0304] 218. The method of item 190, in which, according to item 167 or 168, four types of amino acids in the sample are labeled, all of the amino acids of the first, second, and third amino acid types are labeled, a certain proportion of the amino acids of the fourth amino acid type are labeled, modified amino acids of the first, second, and third amino acid types are labeled, and unmodified amino acids of the fourth amino acid type are labeled.

[0305] 219. The method of item 190, in which, depending on item 167 or 168, five amino acid types in the sample are labeled, all amino acids of the first amino acid type are labeled, a certain proportion of amino acids of the second, third, fourth and fifth amino acid types are labeled, modified amino acids of the first amino acid type are labeled, and unmodified amino acids of the second, third, fourth and fifth amino acid types are labeled.

[0306] 220. The method of item 190, in which, depending on item 167 or 168, five amino acid types in the sample are labeled, all amino acids of the first, second, third, and fourth amino acid types are labeled, a certain proportion of amino acids of the fifth amino acid type are labeled, modified amino acids of the first, second, third, and fourth amino acid types are labeled, and unmodified amino acids of the fifth amino acid type are labeled.

[0307] 221. The method of item 190, in which, depending on item 167 or 168, five amino acid types in the sample are labeled, all amino acids of the first and second amino acid types are labeled, a certain proportion of amino acids of the third, fourth and fifth amino acid types are labeled, modified amino acids of the first and second amino acid types are labeled, and unmodified amino acids of the third, fourth and fifth amino acid types are labeled.

[0308] 222. The method of item 190, in which, depending on item 167 or 168, five amino acid types in the sample are labeled, all amino acids of the first, second, and third amino acid types are labeled, a certain proportion of amino acids of the fourth and fifth amino acid types are labeled, modified amino acids of the first, second, and third amino acid types are labeled, and unmodified amino acids of the fourth and fifth amino acid types are labeled.

[0309] 223. The method of item 190, wherein, as per item 167 or 168, all of the modified amino acids of at least a first amino acid type are labeled and a certain proportion of the unmodified amino acids of at least a second amino acid type are labeled.

[0310] 224. The method of items 1a-1h, wherein step e) includes identifying the presence and / or concentration and / or amount of one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest in a sample by comparing the measured label and / or amino acid concentration of each labeled amino acid type in the sample with known label values ​​and / or amino acid concentrations of the same two or more amino acid types labeled in each sample of one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest at one or more protein concentrations, or by comparing the number of amino acids of each labeled amino acid type in the sample with the number of known amino acids of the same two or more amino acid types labeled in the sample of one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest.

[0311] 225. The method of items 1a-1h or 224, wherein information indicating the known label values ​​and / or amino acid concentrations and / or number of amino acids of two or more amino acid types that are the same as the amino acid type labeled in the sample is used as a criterion for identifying the presence and / or concentration of each target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome.

[0312] 226. The method of item 225, wherein the reference provides known labeled values ​​or amino acid concentrations of two or more amino acid types that are the same as the amino acid types labeled in each sample of the protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome of interest at one or more protein concentrations, or the reference provides the number of amino acids of two or more amino acid types that are the same as the amino acid types labeled in each sample of the protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome of interest.

[0313] 227. The method of item 226, wherein the reference provides known label values ​​or amino acid concentrations as a function of protein concentration for two or more amino acid types that are the same as the amino acid types labeled in each sample of the protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome of interest, or the reference provides the number of amino acids of two or more amino acid types that are the same as the amino acid types labeled in each sample of the protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome of interest.

[0314] 228. Any one of the methods in paragraphs 225-227, wherein the reference provides a reference line or reference curve for each protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome of interest.

[0315] 229. The method of item 228, wherein the baseline or baseline curve for each of the target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes consists of a series of points that provide known label values ​​or amino acid concentrations for each of the target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes at each concentration.

[0316] 230. The method of item 229, wherein the baseline or baseline curve for each of the target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes consists of a series of points that provide known label values ​​or amino acid concentrations for each of the target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes at each protein concentration.

[0317] 231. The method of paragraph 229 or 230, wherein the baseline or baseline curve is parametrically described using a common parameter of concentration or protein concentration.

[0318] 232. The method of paragraph 229 or 230, wherein the baseline or baseline curve is described in vector form using a common independent variable of concentration or protein concentration.

[0319] 233. The method of item 232, wherein the baseline or baseline curve is a vector.

[0320] 234. The method of items 228-233, wherein the measured label values, amino acid concentrations, or number of amino acids of two or more amino acid types labeled in a sample provide points on a baseline or baseline curve.

[0321] 235. The method of item 234, which calculates the shortest distance between a sample point and a reference or reference vector.

[0322] 236. The method of item 235, wherein the shortest distance between the sample point and the reference vector is the perpendicular distance between the sample point and the reference vector.

[0323] 237. The method of section 223, 234, or 235, which determines the vector from the sample point to the reference line.

[0324] 238. The method of paragraphs 233, 234, 235, or 237, wherein the dot product (·) between the vector from the sample point to the reference line and the direction of the reference line is determined, and the perpendicular distance between the sample point and the reference vector is the distance between the sample point and a specific point on the reference vector whose dot product (·) is equal to 0.

[0325] 239. The method of paragraph 237, wherein the equation is solved to provide a concentration or protein concentration that identifies a specific point on a reference line where the vector between the sample point and the reference line is perpendicular.

[0326] 240. The method of item 239, wherein a specific point on a baseline that provides a vertical distance is calculated by inputting a specified value of concentration or protein concentration into a vector function of the baseline.

[0327] 241. The method of paragraphs 236 and 240, wherein the distance between the sample point and this point on a reference line that provides a perpendicular distance is calculated.

[0328] 242. The method of items 1a-1h and 241 for comparing this vertical distance with the tolerance.

[0329] 243. The method of item 242, wherein the presence and / or concentration and / or amount of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome is identified if the vertical distance between the sample point and the reference line is less than or equal to the tolerance, and the concentration of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome or protein concentration is the concentration or protein concentration that provided this vertical distance.

[0330] 244. A certain percentage of amino acids in amino acid form is labeled, and that percentage is approximately 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, and 73% of amino acids in amino acid form. Approximately 74%, 75%, 76%, 77%, 78%, or 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% are labeled by any one of the methods in items 190 or 192-223.

[0331] 245. The method of item 167 or 168, wherein an amino acid-type modified amino acid is labeled independently of an amino acid-type unmodified amino acid.

[0332] 246. The method of item 182, wherein unmodified amino acids of the amino acid type are labeled differently from the total of modified and unmodified amino acids.

[0333] 247. The method of item 245 or 246, wherein modified amino acids of an amino acid type are labeled by first converting them to unmodified amino acids of that amino acid type.

[0334] 248. The method of item 245 or 246, wherein modified amino acids of the amino acid type are first labeled by chemical conversion to unmodified amino acids of the amino acid type.

[0335] 249. The method of item 245 or 246, wherein modified amino acids of the amino acid type are first labeled by converting them to unmodified amino acids of the amino acid type through a chemical reaction.

[0336] 250. The method of item 245 or 246, wherein modified amino acids of the amino acid type are first labeled by a reduction step, which converts them to unmodified amino acids of the amino acid type.

[0337] 251. The method of section 245 or 246, wherein modified amino acids of amino acid form are labeled by first converting them to unmodified amino acids of amino acid form by a PTM cleavage step.

[0338] 252. The method of item 245 or 246, wherein modified amino acids of the amino acid type are first labeled by converting them to unmodified amino acids of the amino acid type by a hydrolysis step.

[0339] 253. The method of section 245 or 246, wherein modified amino acids of the amino acid type are first labeled by converting them to unmodified amino acids of the amino acid type using an enzyme.

[0340] 254. The method of section 253, wherein the enzyme is removed from the sample before the labeling step.

[0341] 255. Cysteine ​​(C R The method of item 246, wherein the unmodified amino acid of the amino acid is labeled differently when both the modified and unmodified amino acids of cysteine ​​are labeled.

[0342] 256. Any one of the preceding methods, wherein labeling each amino acid type is specific to that amino acid type.

[0343] 257. One of the methods described in the preceding section, wherein the R group of an amino acid of the amino acid type is labeled.

[0344] 258. The method of item 257, wherein the R group of an amino acid-type modified amino acid and / or unmodified amino acid is labeled.

[0345] 259. The method of item 258, wherein the R group labeled with an unmodified A amino acid is methyl.

[0346] 260. The method of item 258, wherein the R group labeled with the unmodified R amino acid is an aliphatic guanidino group.

[0347] 261. The method of paragraph 260, wherein the aliphatic guanidino group is a partial primary amine letter and / or an equivalent primary amine letter.

[0348] 262. The method of item 258, wherein the R group labeled with the modified R amino acid (Rg) is a carbohydrate glycoside bonded to a guanidinoamine.

[0349] 263. The method of item 258, wherein the R group labeled with the modified R amino acid (Rm) is a methylated guanidinoamine.

[0350] 264. The method of item 258, wherein the R group labeled with the modified R amino acid (Rc) is citrulline.

[0351] 265. The method of item 258, wherein the R group labeled with modified A amino acid (Aa) is N-acetylated alanine at the N-terminus.

[0352] 266. The method of item 258, wherein the R group labeled with an unmodified N amino acid is a β-carboxamide.

[0353] 267. The method of item 258, wherein the R group labeled with the modified N amino acid (Ng) is a carbohydrate glycoside bonded to a β-carboxamide amine.

[0354] 268. The method of item 258, wherein the R group labeled with a modified N amino acid (Nd) is a carboxylic acid (aspartic acid, D, or isoaspartic acid, iso-D).

[0355] 269. The method of item 258, wherein the R group labeled with a modified D amino acid (Di) is a carboxylic acid (isoaspartic acid).

[0356] 270. The method of item 258, wherein the R group labeled with modified and unmodified C amino acids is a reduced thiol.

[0357] 271. Unmodified C amino acids (C RThe method of item 258, wherein the R group labeled with respect to is a reduced thiol.

[0358] 272. Modified C amino acids (C D The method of item 258, wherein the R group labeled with respect to is an oxidized thiol.

[0359] 273. The method of item 258, wherein the R group labeled with a modified C amino acid (Cfe) is a sulfenic acid.

[0360] 274. The method of item 258, wherein the R group labeled with a modified C amino acid (Cfu) is a sulfonic acid.

[0361] 275. The method of item 258, wherein the R group labeled with a modified C amino acid (Cp) is a palmitoylated thiol.

[0362] 276. The method of item 258, wherein the R group labeled with a modified C amino acid (Cn) is N-acetylated cysteine ​​at the N-terminus.

[0363] 277. The method of item 258, wherein the R group labeled with a modified C amino acid (Cno) is an S-nitrosothiol.

[0364] 278. The method of item 258, wherein the R group labeled with the modified E amino acid (Ep) is a pyroglutamate.

[0365] 279. The method of item 258, wherein the R group labeled with the modified E amino acid (Ep) is a pyroglutamate at the N terminus.

[0366] 280. The method of item 258, wherein the R group labeled with the modified E amino acid (Ec) is a γ-dicarboxylic acid.

[0367] 281. The method of item 258, wherein the R group labeled with the modified E amino acid (Ec) is a γ-dicarboxylic acid.

[0368] 282. The method of item 258, wherein the R group labeled with the modified Q amino acid (Qp) is a pyroglutamate at the N terminus.

[0369] 283. The method of item 258, wherein the R group labeled with the modified Q amino acid (Qe) is a γ-carboxylic acid.

[0370] 284. The method of item 258, wherein the R group labeled with the modified Q amino acid (Qip) is an isopeptide bond with the K amino acid.

[0371] 285. The method of item 258, wherein the R group labeled with the modified G amino acid (Gm) is N-myristoyl at the N terminus.

[0372] 286. The method of item 258, wherein the labeled R group of the modified G amino acid is N-acetyl at the N terminus.

[0373] 287. The method of item 258, wherein the R group labeled with a modified H amino acid (Hp) is a phosphoimidazole.

[0374] 288. The method of item 258, wherein the R group labeled with the modified K amino acid (Ka) is an ε-secondary amino group having an acetyl substituent.

[0375] 289. The method of item 258, wherein the R group labeled with the modified K amino acid (Ku) is an ε-secondary amino group having a ubiquitin substituent.

[0376] 290. The method of item 258, wherein the R group labeled with a modified K amino acid (Ks) is an ε-secondary amino group SUMOyl substituent.

[0377] 291. The method of item 258, wherein the R group labeled with the modified K amino acid (Km) is an ε-secondary amino group having a methyl substituent.

[0378] 292. The method of item 258, wherein the R group labeled with the modified K amino acid (Ki) is an ε-secondary amino group having an isopeptide bond to glutamine.

[0379] 293. The method of item 258, wherein the R group labeled with the modified K amino acid (Kh) is an ε-secondary amino group having a hydroxyl substituent.

[0380] 294. The method of item 258, wherein the R group labeled with the modified M amino acid (Ma) is N-acetyl at the N terminus.

[0381] 295. The method of item 258, wherein the R group labeled with the modified M amino acid (Mu) is a thioester-linked ubiquitin.

[0382] 296. The method of item 258, wherein the R group labeled with a modified M amino acid (Msx) is a sulfoxide.

[0383] 297. The method of item 258, wherein the R group labeled with a modified M amino acid (Mso) is a sulfone.

[0384] 298. The method of item 258, wherein the R group labeled with the modified P amino acid (Ph) is hydroxypyrrolidine.

[0385] 299. The method of item 258, wherein the R group labeled with a modified S amino acid (Sp) is a hydroxymethyl phosphate.

[0386] 300. The method of item 258, wherein the R group labeled with the modified S amino acid (Sg) is a hydroxymethyl glycoside.

[0387] 301. The method of item 258, wherein the labeled R group of the modified S amino acid (Sn) is N-acetyl at the N terminus.

[0388] 302. The method of item 258, wherein the R group labeled with the modified T amino acid (Tp) is a hydroxyphosphate.

[0389] 303. The method of item 258, wherein the R group labeled with the modified T amino acid (Tg) is a hydroxyglycoside.

[0390] 304. The method of item 258, wherein the R group labeled with the modified T amino acid (Tn) is N-acetyl at the N terminus.

[0391] 305. The method of item 258, wherein the R group labeled with the modified W amino acid (Wmo) is indoleol (monohydroxylindole).

[0392] 306. The method of item 258, wherein the R group labeled with the modified W amino acid (Wdo) is indolediol (dihydroxylyindole).

[0393] 307. The method of item 258, wherein the R group labeled with the modified W amino acid (Wk) is kynurenine.

[0394] 308. The method of item 258, wherein the R group labeled with a modified Y amino acid (Ys) is a phenyl sulfate.

[0395] 309. The method of item 258, wherein the R group labeled with a modified Y amino acid (Yp) is phenyl phosphate.

[0396] 310. The method of item 258, wherein the labeled R group of the modified V amino acid (Vn) is N-acetyl at the N terminus.

[0397] 311. The method of item 258, wherein the R group labeled with an unmodified E amino acid is a γ-carboxylic acid.

[0398] 312. The method of item 258, wherein the R group labeled with the unmodified Q amino acid is γ-carboxamide.

[0399] 313. For unmodified G amino acids, the R group is labeled, and the alpha carbon is substituted with a hydrogen atom, as in the method of item 258.

[0400] 314. The method of item 258, wherein the R group labeled with an unmodified H amino acid is an imidazole.

[0401] 315. The method of item 258, wherein the R group labeled with an unmodified I amino acid is a secondary butyl group.

[0402] 316. The method of item 258, wherein the R group labeled with an unmodified L amino acid is isobutyl.

[0403] 317. The method of item 258, wherein the R group labeled with an unmodified K amino acid is an ε-primary amino group.

[0404] 318. The method of item 258, wherein the R group labeled with the modified K amino acid is pyridoxal phosphate aldimine.

[0405] 319. The method of item 258, wherein the R group labeled with an unmodified M amino acid is an S-methyl thioether.

[0406] 320. The method of item 258, wherein the R group labeled with an unmodified F amino acid is benzyl.

[0407] 321. The method of item 258, wherein the R group labeled with an unmodified P amino acid is pyrrolidine.

[0408] 322. The method of item 258, wherein the R group labeled with the modified P amino acid (Ph4) is 4-hydroxypyrrolidine.

[0409] 323. The method of item 258, wherein the R group labeled with an unmodified amino acid is hydroxymethyl.

[0410] 324. The method of item 258, wherein the R group labeled with a modified S amino acid (Sp) is a phosphomethyl ester.

[0411] 325. The method of item 258, wherein the R group labeled with an unmodified T amino acid is hydroxyl.

[0412] 326. The method of item 258, wherein the R group labeled with the modified T amino acid (Tp) is a phosphoester.

[0413] 327. The method of item 258, wherein the R group labeled with an unmodified W amino acid is indole.

[0414] 328. The method of item 258, wherein the R group labeled with an unmodified Y amino acid is phenol.

[0415] 329. The method of item 258, wherein the R group labeled with a modified Y amino acid (Yp) is a phosphophenol.

[0416] 330. The method of item 258, wherein the R group labeled with the unmodified V amino acid is isopropyl.

[0417] 331. The method of item 258, wherein the R group of pyrrolidine (O) is pyrrole (N,2,3-trimethyl-3,4-dihydro-2H-pyrrole-2-carboxamide).

[0418] 332. The method of item 258, wherein the R group of selenocysteine ​​(U) is ethyl selenol.

[0419] 333. The method of item 258, wherein the R group of the modified and unmodified W amino acids is an indole group, the R group of the monooxidized (modified) W amino acid is a hydroxyindole group, and the R group of the dioxidized (modified) W amino acid is a dihydroxyindole group.

[0420] 334. The method of item 258, wherein the R group of the unmodified K amino acid is an ε-primary amino group, the R group of the acetylated (modified) K is an acetylated ε-secondary amino group, the R group of the ubiquitinated (modified) K is a ubiquitinated ε-secondary amino group, the R group of the SUMOylated (modified) K is a SUMOylated ε-secondary amino group, and the R group of the methylated (modified) K is a methylated (alkylated) ε-secondary amino group.

[0421] 335. The method of item 258, wherein the R group of the modified and unmodified Y amino acids is a phenol group, the R group of the sulfated (modified) Y amino acid is a phenol sulfate group, and the R group of the phosphorylated (modified) Y amino acid is a phosphophenol group.

[0422] 336. One of the methods from items 257 to 335, wherein labeling the R group of each amino acid type is specific to that amino acid type.

[0423] 337. Any one of the methods from items 257 to 335, wherein labeling the R group of each unmodified amino acid type is specific to that unmodified amino acid type.

[0424] 338. Any one of the methods from items 257 to 335, wherein labeling the R group of each modified amino acid type is specific to that amino acid type.

[0425] 339. One of the methods from items 257 to 335, wherein labeling the R group of a modified amino acid type having the same substituent is specific to the substituent of the R group.

[0426] 340. The method of item 336, wherein labeling the phosphate-containing R group is specific to the phosphate-containing R group and enables the detection of all phosphorylated amino acid types.

[0427] 341. The method of item 336, wherein labeling of the glycoside-containing R group is specific to the glycoside-containing R group, and includes selective conversion to an azide using TT / n-Bu4NN3 or Ph3P:2,3-dichloro-5,6-dicyanobenzoquinone (DDQ):n-Bu4NN3, followed by a reaction with Fl-DIBO.

[0428] 342. The method of item 336, comprising labeling the fatty acid-containing R group with a bipolar 3-methoxychromone that is specific to the fatty acid-containing R group, thereby enabling the detection of all lipid-containing amino acid types.

[0429] 343. The method of item 336, comprising labeling a phosphate-containing R group, providing a leaving group by activation with carbonyldiimidazole, and subsequently reacting with a cysteine ​​BODIPY dye, which is specific to phosphate-containing R groups and allows detection of all amino acid types modified with phosphate.

[0430] 344. Any one of the preceding items, wherein any peptide, oligopeptide, polypeptide, protein, protein complex, or peptide, oligopeptide, polypeptide, protein, or protein complex within a subproteome or proteome is denatured during or before a labeling reaction to determine the amino acid type in a sample.

[0431] 345. The method of item 344, wherein peptides, oligopeptides, polypeptides, proteins, protein complexes, or peptides, oligopeptides, polypeptides, proteins, or protein complexes within a subproteome or proteome are denatured using an organic solvent during or before a labeling reaction to determine the amino acid type in a sample.

[0432] 346. The method of item 344, wherein peptides, oligopeptides, polypeptides, proteins, protein complexes, or peptides, oligopeptides, polypeptides, proteins, or protein complexes within a subproteome or proteome are denatured using a surfactant during or before a labeling reaction to determine the amino acid type in a sample.

[0433] 347. The method of item 344, wherein peptides, oligopeptides, polypeptides, proteins, protein complexes, or peptides, oligopeptides, polypeptides, proteins, or protein complexes within a subproteome or proteome are denatured using a reducing agent during or before a labeling reaction to determine the amino acid type in a sample.

[0434] 348. The method of item 344, wherein peptides, oligopeptides, polypeptides, proteins, protein complexes, or peptides, oligopeptides, polypeptides, proteins, or protein complexes within a subproteome or proteome are denatured during or before a labeling reaction to determine the amino acid type in a sample, using high pH or low pH conditions.

[0435] 349. The method of item 344, wherein peptides, oligopeptides, polypeptides, proteins, protein complexes, or peptides, oligopeptides, polypeptides, proteins, or protein complexes within a subproteome or proteome are denatured during or before a labeling reaction using an organic solvent, surfactant, reducing agent, or any combination of high pH or low pH conditions.

[0436] 350. One of the methods from items 1a-1h or 2-256, wherein two or more amino acid types are labeled with the same label, and the label is independently identified for each amino acid type.

[0437] 351. The method of item 350, wherein the parameters for detecting the label are separate.

[0438] 352. The method of item 350, wherein the labeling reaction is separate.

[0439] 353. The method of item 350, wherein one amino acid form is converted to a reactive form under different conditions than that of another amino acid form before reacting with a label.

[0440] 354. The method of item 353, wherein different catalysts are used during the labeling reaction.

[0441] 355. The method of item 353, wherein light of different wavelengths is used to catalyze a labeling reaction.

[0442] 356. The method of item 353, which involves performing a different chemical reaction on the amino acid form and incorporating the reactive group before the reaction with the label.

[0443] 357. The method of item 349, wherein different reaction times are used. In some embodiments, one type of amino acid reacts more rapidly with the label than another type of amino acid.

[0444] 358. The method of section 350 or 351, wherein a measured label for one amino acid type is deconvolved from a label for a second amino acid type.

[0445] The method of paragraph 358, wherein a measured label for one amino acid type is deconvolved from a label for a second amino acid type using a deconvolution standard containing only one amino acid from the labeled amino acid type.

[0446] 360. The method of section 358 or 359, wherein amino acid-type tryptophan (W) and tyrosine (Y) are labeled with the same label, and the measured label for amino acid W is deconvolved from the label for amino acid Y.

[0447] 361. The method of paragraph 358 or 359, wherein amino acid-type tryptophan (W) and tyrosine (Y) are labeled with the same label, and the measured label for the W amino acid is detected separately from the measured labels for the W and Y amino acids using different excitation wavelengths.

[0448] 362. The method of paragraph 358 or 359, wherein amino acid-type tryptophan (W) and tyrosine (Y) are labeled with the same label, and the measured label for the W amino acid at an excitation wavelength that labels both the W and Y amino acids is calculated using a deconvolution standard containing only the W amino acid, and this is subtracted from the sum of the labels for both the W and Y amino acids to reveal the label value for the Y amino acid only.

[0449] 363. One of the methods described in the preceding section, in which more than 2 types of amino acids are labeled throughout the entire sample.

[0450] 364. One of the methods from items 1 to 363, wherein the sample is separated into multiple fractions, and a different labeling reaction is performed in each fraction to specifically label two or more of the amino acid types.

[0451] 365. The method of item 364, wherein the fractions have equal volumes.

[0452] 366. The method of item 364 or 365, wherein four amino acid types are labeled, the sample is separated into two fractions before labeling, two amino acid types are labeled in one fraction, and two other amino acid types are labeled in the second fraction.

[0453] 367. The method of item 366, wherein four types of amino acid forms W, K, Y, and C are labeled, and the sample is separated into two fractions before labeling, with the W and K amino acids being labeled in one fraction and the Y and C being labeled in the second fraction.

[0454] 368. The method of item 366, wherein four types of amino acid forms W, K, Y, and C are labeled, and the sample is separated into three fractions before labeling, with W and Y amino acids being labeled in one fraction and C and K amino acids being labeled in separate fractions.

[0455] 369. The method of item 364 or 365, wherein four amino acid types are labeled, the sample is separated into four fractions before labeling, and one amino acid type is labeled in each fraction.

[0456] 370. The method of item 369, wherein amino acid types W, K, Y, and C are labeled, and the sample is separated into four fractions before labeling, with W being labeled in the first fraction, K in the second fraction, C in the third fraction, and Y in the fourth fraction.

[0457] 371. The method of item 364 or 365, wherein the number of fractions is equal to the number of amino acid types labeled in the sample.

[0458] 372. The method of item 364 or 365, wherein each fraction contains all amino acid forms, so that the amino acid forms are contained on intact protein or peptide chains that have not been digested or hydrolyzed.

[0459] 373. The method of item 364 or 365, wherein the number of fractions is not equal to the number of amino acid types labeled in the sample, and more than one amino acid type is labeled per fraction.

[0460] 374. The method of item 364 or 365, wherein two or more amino acid types have the same label, and these are labeled in different fractions.

[0461] 375. One of the preceding methods, in which the labeling reaction is carried out in bulk rather than within a microfluidic device.

[0462] 376. A method, one of the preceding items, by which a sample is labeled, and / or a known label value of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome provides a signal.

[0463] 377. Any one of the preceding methods, wherein the label of the sample is a fluorophore.

[0464] 378. Any one of the preceding methods, wherein the label of the sample is a reactive derivative of a fluorophore.

[0465] 379. The method of item 377 or 378, wherein the label of the sample is a fluorescent label.

[0466] 380. The method of item 379, wherein the fluorescent label is a fluorescent probe.

[0467] 381. The method of item 380, wherein the fluorescent label is a fluorescent tag.

[0468] 382. The method of item 380, wherein the fluorescent label is a fluorescent protein.

[0469] 383. The method of item 380, wherein the fluorescent label is a fluorescent dye.

[0470] 384. The method of item 380, wherein the fluorescent label comprises a reactive group specific to the amino acid type.

[0471] 385. The method of item 380, wherein the fluorescent label comprises a reactive group that targets an amino acid type.

[0472] 386. The method of item 380, wherein the fluorescent label comprises a reactive group that is specific to the R group of an amino acid.

[0473] 387. The method of item 380, wherein the fluorescent label comprises a reactive group that targets the R group of an amino acid.

[0474] 388. The method of item 380, wherein the fluorescent label comprises a reactive group that is specific to the N-terminus or C-terminus of a protein.

[0475] 389. The method of item 380, wherein the fluorescent labeling comprises a reactive group that targets the N-terminus or C-terminus of a protein.

[0476] 390. The method of item 380, wherein the fluorescent label is a quantum dot.

[0477] 391. A method of labeling a sample that includes nanoparticles, one of the methods described in the preceding paragraphs.

[0478] 392. Methods of sections 379-390, wherein the fluorescent labeling includes a fluorophore.

[0479] 393. Fluorophores include hydroxycoumarin, aminocoumarin, methoxycoumarin, Cascade Blue, Pacific Blue, Pacific Orange, Lucifer Yellow, NBD, R-phycoerythrin (PE), PE-Cy5 conjugate, PE-Cy7 conjugate, Red 613, PerCP, TruRed, FluorX, BODIPY-FL, G-Dye100, G-Dye200, G-Dye300, G-Dye400, Cy2, Cy3, Cy3B, Cy3.5, Cy5, and Cy5.5、Cy7、TRITC、X-ローダミン、LissamineローダミンB、Texas Red、アロフィコシアニン(APC)、APC-Cy7コンジュゲート、DAPI、Hoechst 33258、SYTOX Blue、クロモマイシンA3、ミトラマイシン、YOYO-1、ACT 390、ACT 425、ACT 465、ACT 488, ACT 495, ACT 514, ACT 520, ACT 532, ACT Rho6G, ACT 550, ACT 565, ACT Rho3B, ACT Rho11, ACT Rho12, ACT Thio12, ACT Rho101, ACT 590, ACT Rho13, ACT 594, ACT 610, ACT Rho14, ACT 633, ACT 647, ACT 647N, ACT 655, ACT Oxa12, ACT 665, ACT Oxa12, ACT 665, ACT 680, ACT 700, ACT 725, ACT 740, Brilliant Violet 421、Brilliant Violet 510、Brilliant Violet 570、Brilliant Violet 605、Brilliant Violet 650、Brilliant Violet 711、Brilliant Violet 750、Brilliant Violet 785、TM-BDP、KFL-1、KFL-2、KFL-3、KFL-4、Super Bright 436、Super Bright 600、Super Bright 645、Super Bright 702、Super Bright 780、Alexa Flour 350、Alexa Flour 405、Alexa Flour 488、Alexa Flour 532、Alexa Flour 546、Alexa Flour 555、Alexa Flour 568、Alexa Flour 594、Alexa Flour 647、Alexa Flour 680、Alexa Flour 850、クマリン、Pacific Green、Oregon Green、フルオレセイン(FITC)、PE-シアニン7、ForCP-シアニン5.5, Tetramethylrhodamine (TRITC), eFlour 450, eFlour506, eFlour660, PE-eFlour 610, PerCP-eFlour 710, APC-eFlour 780, Super Bright 436, Super Bright 600, Super Bright 645, Super Bright 702, Super Bright 780, DAPI, SYTOX Green, SYTO 9, TO-PRO-3, Qdot 525, Qdot 565, Qdot 605, Qdot 655, Qdot 705, Qdot 800, R-phycoerythrin (R-PE), CFP, GFP (emGFP), RFP (tagRFP), VioBlue, VioGreen, VioBright 515, Vio 515, VioBright FITC, PE, PE-Vio The method of item 392, selected from the group consisting of 615, PerCP, PerCP-Vio 700, PE-Vio 770, APC, APC-Vio 770, 1,8-naphthalimide, Acridine Orange, SYTOX Green, TOTO-1, TO-PRO-1, TO-PRO:cyanine monomer, Thiazole Orange, CyTRAK Orange, propidium iodide (PI), LDS 751, 7-AAD, SYTOX Orange, TOTO-3, TO-PRO-3, DRAQ5, DRAQ7, Indo-1, Fluo-3, Fluo-4, DCFH, DHR, or SNARF.

[0480] 394. Fluorescent labeling is performed by any one of the methods described in items 379-390, wherein the fluorescent labeling includes a fluorescent protein.

[0481] 395. Fluorescent proteins include GFP (Y66H mutation), GFP (Y66F mutation), EBFP, EBFP2, Azurite, GFPuv, T-Sapphire, Cerulean, mCFP, mTurquoise2, ECFP, CyPet, GFP (Y66W mutation), mKeima-Red, TagCFP, AmCyan1, mTFP1, GFP (S65A mutation), Midoriishi Cyan, wild-type GFP, GFP (S65C mutation), TurboGFP, TagGFP, GFP (S65L mutation), Emerald, GFP (S65T mutation), EGFP, Azami Green, ZsGreen1, TagYFP, EYFP, Topaz, Venus, mCitrine, YPet, TurboYFP, ZsYellow1, and Kusabira. The method of item 394, wherein the monomer is Orange, mOrange, allophycocyanin (APC), mKO, TurboRFP, tdTomato, TagRFP, DsRed monomer, DsRed2 ("RFP"), mStrawberry, TurboFP602, AsRed2, mRFP1, J-Red, R-phycoerythrin (RPE), B-phycoerythrin (BPE), mCherry, HcRed1, Katusha, P3, peridinin chlorophyll (PerCP), mKate (TagFP635), TurboFP635, mPlum, or mRaspberry.

[0482] 396. Any one of the preceding methods, wherein the label comprises a reactive group specific to the amino acid type.

[0483] 397. The method of item 396, wherein the label comprises a reactive group that is specific to the R group of an amino acid.

[0484] 398. The methods of items 377-391 or 392-395, wherein the fluorescent label comprises a reactive group that is specific to a chemical modification performed on the amino acid form before or during the labeling step.

[0485] 399. The method of item 398, wherein the fluorescent label comprises a reactive group that is specific to a chemical modification performed on the amino acid-type R group before or during the labeling step.

[0486] 400. The method of item 398, wherein the fluorescent label comprises a reactive group that is specific to a chemical modification performed on the protein backbone adjacent to an amino acid-type R group before or during the labeling step.

[0487] 401. The method of items 396-400, wherein the reactive group is selected from the group consisting of NHS esters, maleimides, alkynes, azides, bromides, chlorides, fluorides, iodides, aryl bromides, aryl chlorides, aryl fluorides, aryl iodides, dienes, dienophiles, olefins, tetrazines, cyclooctin, biotin, streptavidin, isothiocyanates, active esters, sulfonyl chlorides, dialdehydes, iodoacetamides, ethylenediamines, aminoacridones, hydrazides, carboxyls, or alkoxyamines.

[0488] 402. The method of item 379, wherein the fluorescent label is a fluorescent dye.

[0489] 403. The method of item 402, wherein the fluorescent dye is a molecule that becomes fluorescent upon reaction with a fluorescent dye, a non-fluorescent dye, an amino acid type, and / or a molecule that shifts the fluorescence of a specific fluorescent amino acid type to the visible region of the spectrum.

[0490] 404. The method of item 402, wherein the fluorescent dye is a fluorescent dye, a non-fluorescent dye, a molecule that becomes fluorescent upon reaction with an amino acid-type R group, and / or a molecule that shifts the fluorescence of a specific fluorescent amino acid-type R group to the visible region of the spectrum.

[0491] 405. The method of item 403, wherein the fluorescent dye, the molecule that becomes fluorescent upon reaction with an amino type, or the molecule that shifts the fluorescence of a specific fluorescent amino acid type to the visible region of the spectrum is selected from the group consisting of 4-fluoro-7-sulfamoylbenzofurazan (ABD-F), 2,2,2-trichloroethanol (TCE), and / or ortho-phthalaldehyde (OPA), or mixtures thereof.

[0492] 406. The method of item 403, wherein the halo compound is a molecule that becomes fluorescent upon reaction with a fluorescent dye, an amino type, or a molecule that shifts the fluorescence of a specific fluorescent amino acid type to the visible region of the spectrum.

[0493] 407. The method of item 406, wherein the halo compound is selected from the group consisting of trichloroacetic acid, chloroform, trifluoroethanol, trifluoroacetic acid, fluoroform, tribromoethanol, tribromoacetic acid, bromoform, triiodoethanol, triiodoacetic acid, or iodoform.

[0494] 408. The method of item 407, wherein amino acid-type tryptophan (W) and / or tyrosine (Y) are labeled with trichloroacetic acid, chloroform, trifluoroethanol, trifluoroacetic acid, fluoroform, tribromoethanol, tribromoacetic acid, bromoform, triiodoethanol, triiodoacetic acid, or iodoform.

[0495] 409. One of the methods described in the preceding section, wherein the R group of each amino acid type is labeled.

[0496] 410. The method of item 409, wherein the labeled amino acid-type R group is the R group of a modified amino acid and / or an unmodified amino acid of the amino acid type.

[0497] 411. The R group of an unmodified A amino acid is palladium-catalyzed C(sp 3 The method of item 410, which involves activating the )-H3 bond, labeling with Pd(OAc)2 containing 1-ethynyl-4-iodobenzene, incorporating an alkyne, and then performing Cu(I)-catalyzed azido-alkyne ring addition (CuAAC) "click chemistry" with 3-azido-2H-chromium-2-one.

[0498] 412. The method of item 410, wherein the R group of an unmodified R amino acid is labeled with dopachrome.

[0499] 413. The method of item 410, wherein the R group of an unmodified N amino acid is labeled with 4-amino-3-formylphenylnitrate.

[0500] 414. The method of item 410, wherein the R group of an unmodified D amino acid is labeled with a BODIPY-based probe to which 4-(diethylamino)-2-(pyridine-2-ylmethoxy)benzaldehyde has been added.

[0501] 415. The method of item 410, wherein the R groups of modified and unmodified C amino acids are labeled with 4-aminosulfonyl-7-fluoro-2,1,3-benzoxadiazole (ABD-F) after reduction of the oxidized thiol with tris(2-carboxyethyl)phosphine (TCEP).

[0502] 416. Unmodified C amino acids (C R The method of item 410, wherein the R group of ) is labeled with 4-aminosulfonyl-7-fluoro-2,1,3-benzoxadiazole (ABD-F) or o-maleimide BODIPY or ethyl(Z)-2-(6-(ethyl((3-(trifluoromethyl)phenyl)ceranyl)amino)-3-(ethylimino)-2,7-dimethyl-3H-xanthene-9-yl)benzoate.

[0503] 417. The method of item 410, wherein the R group of an unmodified E amino acid is labeled with a BODIPY-based probe to which 4-(diethylamino)-2-(pyridine-2-ylmethoxy)benzaldehyde has been added.

[0504] 418. The method of item 410, wherein the R group of an unmodified Q amino acid is labeled with 4-amino-3-formylphenylnitrate.

[0505] 419. The method of item 410, wherein the R group of an unmodified G amino acid is labeled via alpha-CH bond functionalization to the carbonyl via reaction with H-alkynyl-Phe in the presence of CuBr (1 μM) and 10 μM tBuOOH in DCM, and subsequently with CuAAc containing 3-azido-7-methoxy-2H-chromene-2-onketone.

[0506] 420. The R group labeled with the unmodified H amino acid is 2-butyl-6-(4-((6-(((2-ethoxyethyl)amino)methyl)pyridine-2-yl)methyl)piperazine-1-yl)-1H-benzo[de]isoquinoline-1,3(2H)-dione-Cu 2+ The method of item 410, which is marked with

[0507] 421. The method of item 410, wherein the R group of an unmodified I amino acid is incorporated by a Hoffman-Loffler-Freytag reaction attempted by blue light for δ-CH functionalization of isoleucine, followed by a reaction with acetyl hypobromite anhydride catalyzed by blue LED, then an azide group is incorporated by an SN2 reaction with KN3, and then labeled with CuAAc containing 4-((7-ethynyl-2-oxo-2H-chromen-4-yl)methoxy)-4-oxobutanoic acid.

[0508] 422. The method of item 410, wherein the R group of an unmodified L amino acid is incorporated by a Hoffman-Loffler-Freytag reaction attempted by blue light for δ-CH functionalization of isoleucine, followed by a reaction with acetyl hypobromite anhydride catalyzed by blue LED, then an azide group is incorporated by an SN2 reaction with KN3, and then labeled with CuAAc containing 4-((7-ethynyl-2-oxo-2H-chromen-4-yl)methoxy)-4-oxobutanoic acid.

[0509] 423. The method of item 410, wherein the R group of an unmodified K amino acid is labeled with ortho-phthalaldehyde (OPA) in the presence of β-mercaptoethanol (BME).

[0510] 424. The method of item 410, wherein the R group of an unmodified M amino acid is labeled by reaction with an alkyne containing a methionine-selective iodonium salt, followed by click chemistry with a CalFlour dye.

[0511] 425. The method of item 410, wherein the R group of an unmodified F amino acid is labeled by a palladium-catalyzed alkynylation reaction with 1 μM (bromoethinyl)triisopropylsilane containing 20 μM K2CO3 as a base and 1 μM Pd(OAc)2 containing 1 μM PivOH as an additive, followed by a reaction with CuAAc containing 3-azido-7-hydroxy-2H-chromen-2-one.

[0512] 426. The R group of an unmodified P amino acid is an amphiphilic bipolar Schiff base Zn II The method of item 410, which involves labeling with a complex.

[0513] The method of item 410, wherein the R group of an unmodified amino acid is labeled by selective conversion to an azide with TT / n-Bu4NN3 or Ph3P:2,3-dichloro-5,6-dicyanobenzoquinone (DDQ):n-Bu4NN3, followed by a reaction with Fl-DIBO.

[0514] 428. The method of item 410, wherein the R group of an unmodified T amino acid is labeled via selective conversion to an azide using TT / n-Bu4NN3 or Ph3P:2,3-dichloro-5,6-dicyanobenzoquinone (DDQ):n-Bu4NN3, followed by a reaction with Fl-DIBO.

[0515] 429. The method of item 410, wherein the R group of an unmodified W amino acid is labeled with trichloroethanol (TCE), trichloroacetic acid (TCA), chloroform, trifluoroethanol (TFE), trifluoroacetic acid (TFA), fluoroform, tribromoethanol, tribromoacetic acid (TBA), bromoform, triiodoethanol (TIE), or triiodoacetic acid (TIA), iodoform, or 2-(2-(2-methoxyethoxy)ethoxy)ethyl(E)-2-diazo-4-phenylbuta-3-enoate in the presence of Rh2(OAc)4 and tBuHNOH.

[0516] 430. The method of item 410, wherein the R group of a modified W amino acid is labeled with trichloroethanol (TCE).

[0517] 431. The method of item 410, wherein the R group of an unmodified Y amino acid is labeled with trichloroethanol (TCE), or an aryl group is incorporated ortho to the tyrosine hydroxyl group using [RhCl(PPh3)3], R2P(OAr), Ar-Br, or CsCO3.

[0518] 432. The method of item 410, wherein the R group of an unmodified V amino acid is incorporated into the valine side chain using a visible light-catalyzed [Ru(bpy)3]Cl2 catalyst and 1-azido-1l3-benzo[d][1,2]iodooxol-3(1H)-one, and then labeled via a fluorescent CuAAC reaction with 4-((7-ethynyl-2-oxo-2H-chromen-4-yl)methoxy)-4-oxobutanoic acid.

[0519] 433. The method of item 410, wherein the R group of an unmodified O amino acid is labeled via a Diels-Alder reaction with azaphthalimide.

[0520] 434. The method of item 410, wherein the R group of an unmodified U amino acid is labeled with ABD-F at pH 7.

[0521] 435. The method of item 410, wherein the R group of a modified S amino acid is labeled with BO-IMI.

[0522] 436. The method of item 410, wherein the R group of the modified T amino acid of threonine is labeled with BO-IMI.

[0523] 437. The method of item 410, wherein the R group of the modified Y amino acid is labeled with BO-IMI.

[0524] 438. The method of item 410, wherein the modified R amino acid is labeled with o-maleimide bodipy.

[0525] 439. The method of item 410, wherein a modified N amino acid is labeled with a boronic acid tosyl probe having an alkyne substituent, and then reacted with a CalFlour dye.

[0526] 440. The method of item 410, wherein a modified K amino acid is labeled with 9-fluorenylmethylchloroformate.

[0527] 441. The method of item 379, wherein the fluorescent label is a fluorescent protein or a conjugated antibody.

[0528] 442. The method of item 441, wherein the fluorescent protein is selected from the group consisting of smURFP, GFP, EGFP, Cerulean, mTurquoise, TagBFP, mCherry, mOrange, Citrine, Dronpa, dsRed, eqFP611, Dendra, EosFP, IrisFP, TagRFPs, and FbFPs.

[0529] 443. The method of item 441, wherein the conjugated antibody is a post-translationally modified monoclonal antibody.

[0530] 444. Post-translational modified monoclonal antibodies undergo phosphoserine, phosphothreonine, phosphotyrosine, phosphorylation, lysine methylation, arginine methylation, lysine acetylation, arginine acetylation, amidation, pyrrolidone carboxylic acid formation, isomerization, proline hydroxylation, lysine hydroxylation, sulfation, flavin bonding, cysteine ​​oxidation, nitrosylation, lysine acylation, cysteine ​​acylation, N-terminal acylation, lysine formylation, lysine alkylation, cysteine ​​alkylation, arginylation, amide bond formation, butyrylation, gamma-carboxylation, arginine glycosylation, asparagine glycosylation, and cy The method of item 443 for detecting stain glycosylation, hydroxylysine glycosylation, celling glycosylation, threoning glycosylation, tyrosine glycosylation, tryptophan glycosylation, malonylation, proline hydroxylation, lysine hydroxylation, tyrosine iodation, nucleotide addition, phosphorylation, adenylation, uridilylation, propionylation, pyroglutamate formation, S-glutathionylation, cysteine ​​sulfenylation, cysteine ​​sulfonylation, lysine succinylation, tyrosine sulfate, myristoylation, palmitoylation, isoprenylation, prenylation, ubiquitination, and glycation.

[0531] 445. The method of items 1-376, wherein the tag is a tandem mass tag.

[0532] 446. The method of item 445, wherein the tandem mass tag is selected from the group consisting of TMTzero, TMTduplex, TMTsimplex, TMT 10-plex, TMTpro, and TMTpro Zero.

[0533] 447. The methods of items 1-376, wherein the label is an isotope label.

[0534] 448. The method of item 447, wherein the isotope labeling is a non-radioactive isotope.

[0535] 449. The method of item 449, wherein the non-radioactive isotope labeling is selected from 2H, 13C, and / or 15N.

[0536] 450. The method of paragraph 350, wherein the detected signal is a chemiluminescent signal or a biochemiluminescent signal.

[0537] 451. The method of item 450, wherein the chemiluminescent label is N-(4-aminobutyl)-N-ethyl-isoluminol (ABEI) macrocyclic lactone.

[0538] 452. One of the methods described in items 377-451, which involves labeling two or more amino acid types using a combination of fluorescent labeling, isotope labeling, tandem mass tagging, and / or chemiluminescent labeling.

[0539] 453. The method of item 358, wherein measured labels for amino acid-type serine and threonine are deconvoluted from each other.

[0540] 454. The method of item 358, wherein measured labels for the amino acids asparagine and glutamine are deconvolved with each other.

[0541] 455. The method of item 358, wherein the measured labels for amino acid-type glutamic acid and aspartic acid are deconvolved with each other.

[0542] 456. The method of item 358, wherein measured labels for amino acid-type leucine and isoleucine are deconvolved with respect to each other.

[0543] 457. One of the preceding methods, wherein the sample is denatured before or during the labeling reaction.

[0544] 458. The method of measuring the signal of the marker, as described in item 376.

[0545] 459. One of the preceding terms by which the measured label is corrected for background noise.

[0546] 459a. The method of item 459, wherein the autofluorescence of the sample is removed.

[0547] 460. Methods of sections 447-449, wherein isotope labeling is measured by NMR and / or mass spectrometry.

[0548] 461. The method of sections 445-446, in which the tandem mass tag is measured by mass spectrometry.

[0549] 462. The method of sections 379-395 or 398-442, wherein the fluorescent label is measured by a fluorescence microscope.

[0550] 463. The method of items 379-395 or 398-442, wherein the fluorescent label is measured by a fluorometer.

[0551] 464. The method of sections 379-395 or 398-442, wherein the fluorescent label is measured by a fluorescent plate reader.

[0552] 465. The methods of sections 379-395 or 398-442, wherein the fluorescent label is measured by an instrument that performs and / or reads several fluorescent reactions in parallel or in series.

[0553] 466. The method of item 462, wherein amino acid type Y is labeled with a fluorescent label, and the fluorescent label is measured at excitation wavelengths of approximately 250 nm to approximately 380 nm and emission wavelengths of approximately 370 nm to approximately 500 nm.

[0554] 467. The method of item 462, wherein amino acid type W is labeled with a fluorescent label, and the fluorescent label is measured at excitation wavelengths of approximately 270 nm to approximately 380 nm and emission wavelengths of approximately 430 nm to approximately 600 nm.

[0555] 468. The method of item 462, wherein amino acid type K is labeled with a fluorescent label, and the fluorescent label is measured at excitation wavelengths of approximately 320 nm to approximately 415 nm and emission wavelengths of approximately 400 nm to approximately 500 nm.

[0556] 469. The method of item 462, wherein amino acid type C is labeled with a fluorescent label, and the fluorescent label is measured at excitation wavelengths of approximately 330 nm to approximately 400 nm and emission wavelengths of approximately 430 nm to approximately 580 nm.

[0557] 470. The method of item 462, wherein, from the range of excitation and emission wavelengths provided, the excitation wavelength is separated from the emission wavelength by approximately 10 nm to approximately 20 nm for each fluorescent label of each labeled amino acid type in the sample.

[0558] 471. Any one of the preceding terms, wherein the amino acid concentration of each labeled amino acid type is calculated from the measured label, and the amino acid concentration is calculated from the measured label using a calibration curve or standard that converts between the measured label of the sample and the amino acid concentration of that amino acid type in the sample.

[0559] 472. The method of item 471, wherein the calibration curve or standard is calculated from measured labels of one or more proteins or amino acids with one or more known amino acid concentrations.

[0560] 473. The method of item 471, wherein the amino acid concentration of each labeled amino acid type is calculated from the measured label, and the amino acid concentration is calculated from the measured label using a calibration curve that converts between the measured label of the sample and the amino acid concentration of that amino acid type in the sample.

[0561] 474. The method of paragraph 471, wherein the amino acid concentration of each labeled amino acid type is calculated from the measured label, and the amino acid concentration is calculated from the measured label using a standard that converts between the measured label of the sample and the amino acid concentration of that amino acid type in the sample.

[0562] 475. The method of item 473, wherein the calibration curve is calculated from measured labels of one or more proteins or one or more known amino acid concentrations.

[0563] 476. The method of paragraph 474, wherein the standard is calculated from a measured label of one known amino acid concentration of one protein or amino acid.

[0564] 477. The method of terms 471, 474, or 476, in which more than one standard generates a calibration curve.

[0565] 478. The calibration curve is nonlinear, using one of the methods described in terms 471, 472, 473, or 476.

[0566] 478a. The method of term 478, where nonlinear fitting is polynomial fitting.

[0567] 478b. The method of item 478, where the nonlinear fitting is a power law fitting.

[0568] 478c. The method of term 478, where nonlinear fitting is exponential fitting.

[0569] 478d. The method of section 478, wherein the nonlinear fitting is sigmoid fitting.

[0570] 479. The calibration curve is linear, using one of the methods described in terms 471, 472, 473, or 476.

[0571] 480. One of the methods in items 471, 472, 473, or 475, wherein the best fit for converting between the measured label and amino acid concentration is calculated for the calibration curve.

[0572] 481. The best fit for converting between the measured label and amino acid concentration is calculated for the calibration curve and is a linear fit, according to the method of item 480.

[0573] 482. The best-fit line is calculated using the method in item 481, using linear regression.

[0574] 483. The best fit is calculated using the methods of terms 471, 472, 473, or 475, using nonlinear regression.

[0575] 484. The label is a fluorescent label, and the best-fit line for the calibration curve is given by equation 5. Label value n =m n ×AA concentration n +b n Calculated using, in the formula, the indicator value n However, this is the label value for amino acid type n in AU, and m n However, this is the slope of the best-fit line at AU / amino acid concentration for amino acid type n, and AA concentration n However, this is the amino acid concentration of amino acid type n, and b n However, the label value is zero for amino acid type n, according to the method of item 481. The output of the fitting is m n and b n That is the case.

[0576] 485. The amino acid concentration of each labeled amino acid type in the sample is the reciprocal of the calibration curve, given by equation 6.

number

[0577] 486. The label is a fluorescent label, the label is a corrected background, and the best-fit line of the calibration curve is given by equation 7. Label value n =m n ×AA concentration n Calculated using, in the formula, the indicator value n However, this is the label value for amino acid type n in AU, and m n However, this is the slope of the best-fit line at AU / amino acid concentration for amino acid type n, and AA concentration n However, the amino acid concentration of amino acid type n is given by the method in item 481. The output of the fitting is m n That is the case.

[0578] 487. The amino acid concentration of each labeled amino acid type in the sample is the reciprocal of the calibration curve, given by equation 8.

number

[0579] 488. Slope m of the best-fit line for amino acid type n n However, the calibration coefficient f for amino acid type n n The method described in either section 484 or 486, which can be used to convert the amino acid concentration of a target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome to a known label value.

[0580] 489. The reciprocal of the calibration coefficient f for amino acid type n. n -1 However, the reciprocal of the slope of the best-fit line

number

[0581] 490. The method of item 488 or 489, wherein the calibration coefficient for each labeled amino acid type in the sample is determined using data from one amino acid concentration of one standard.

[0582] 491. The method of item 490, wherein the standard is a protein or amino acid.

[0583] 492. The method of item 490, wherein the reciprocal of the calibration coefficient for amino acid type n is determined by the following:

number

[0584] 493. Any one of the preceding terms, wherein the number of amino acids of each labeled amino acid type in the sample is calculated, and the number of amino acids of each labeled amino acid type in the sample is calculated by dividing the amino acid concentration by the total molar protein concentration of the sample.

[0585] 494. The method of item 493, wherein the sample is identified for the presence of the proteome, subproteome, or complex mixture of the target, and the number of amino acids of each labeled amino acid type is the average number of amino acids of each labeled amino acid type in all proteins across the proteome, subproteome, or complex mixture of the target.

[0586] 495. The method of paragraph 494, wherein the average number of amino acids is the weighted average number of amino acids of each labeled amino acid type in all proteins across the proteome, subproteome, or mixture of proteins of interest, weighted by the proportion of each protein across the proteome, subproteome, or mixture of proteins.

[0587] 496. The weighted average number of amino acids for each amino acid type is given by equation 11

number

[0588] 497.

number

[0589] 498.q i The method of section 496 or 497, wherein the expression level of the target protein i within the target proteome or subproteome is the expression level of the target protein i within the target proteome or subproteome.

[0590] 499. The method of paragraph 498, wherein the expression level of target i in the target proteome or subproteome is determined from publicly available data, including mass spectrometry or immunoassay.

[0591] 500. The method of Section 499, wherein publicly available data are public databases such as the Human Protein Atlas, Human Peptide Atlas, and / or ProteomeXchange.

[0592] 501.q is the total predicted expression level of all proteins (proteins i through c) contained within the proteome or subproteome of interest, each evaluated using publicly available protein expression data, by one of the methods in paragraphs 496 or 497.

[0593] The method of item 501, wherein 502.q is the total protein concentration of the proteome or subproteome of interest.

[0594] The method of item 502, wherein 503.q is the total protein concentration of the proteome or subproteome of interest, calculated using a method standard in the art.

[0595] 504.q i The methods of paragraphs 501 and 502, wherein q and q are determined using mRNA expression data.

[0596] 505.q i However, the method of item 504 is determined using mRNA expression data and gene-specific RNA-protein (RTP) conversion coefficients.

[0597] 506.q i The method of item 496, wherein q and can be calculated from a known structural model.

[0598] 506a.

number

number

[0599] 506b.q i =int m And, In the expression, int m However, the method of item 506a is the molar intensity of individual proteins in the sample calculated from a mass spectrometry database.

[0600] 506c.q=Σint m And, In the formula, Σint m However, the method of item 506a or 506b, which is the sum of the molar intensities of all individual proteins in the sample calculated from a mass spectrometry database.

[0601] 506d.

number

[0602] The method of item 506d, where 506e.int is a normalized intensity, raw intensity, normalized abundance, or raw abundance.

[0603] 506f.int is calculated using one of the methods from terms 506a to 506e, with label-free quantification (LFQ) being used.

[0604] 506g. The mass spectrometry database is the Proteome Xchange database, using one of the methods described in items 506a to 506d.

[0605] 506h. The database providing the molecular weight and amino acid sequence of proteins is the UniProt database, one of the methods in items 506a to 506g.

[0606] 506i. Average(Σint m ) = aΣ molar protein concentration In the formula, Σmolar protein concentration is the sum of the molar protein concentrations for all proteins in the target proteome, subproteome, or sample type, as provided by the molar concentration database, and the average (Σint m ) for all samples in the database Σint m One of the methods from terms 506a to 506c, which is the average of the values.

[0607] 506j. The molar concentration value is calculated from the Human Peptide Atlas database using the method of item 506i.

[0608] 506k. The method of item 506i, wherein the molar protein concentration values ​​for each protein in the database are calculated using an immunoassay-based technique such as an ELISA assay, or the mass protein concentration values ​​for each protein in the database are calculated using an immunoassay-based technique such as an ELISA assay and converted to molar protein concentrations using a molecular weight database for each protein, such as one accessed from the UniProt database.

[0609] The method of item 506i, wherein the molar protein concentration value for each protein in the database is calculated using aptamer-based techniques such as the Somascan assay, or the mass protein concentration value for each protein in the database is calculated using immunoassay-based techniques such as the ELISA assay and is converted to molar protein concentration using a database of molecular weights for each protein, such as those accessed from the UniProt database.

[0610] The method of any one of items 506i to 506l, wherein 506m.a is calculated for a given set of samples by:

Number

[0611] 506n. The method of item 506m, wherein the average (Σint m ) is the average of the Σint m values for all samples in the database.

[0612] 506o.

Number

Number

[0613] 506p.q i = int, and In the formula, int is the intensity of individual proteins in the sample provided by the mass spectrometry database, as in the method of item 506o.

[0614] 506q.q = Σint, The method of item 506o or 506p, wherein Σint is the sum of the intensities of all individual proteins in the sample calculated from a mass spectrometry database.

[0615] 506r.int is one of the methods from terms 506o to 506q, where 506r.int is the normalized intensity, raw intensity, normalized abundance, or raw abundance.

[0616] 506s.int is calculated using one of the methods from terms 506o to 506r, using label-free quantification (LFQ).

[0617] 506t. The mass spectrometry database is the Proteome Xchange database, according to the methods of sections 506o and 506p.

[0618] 506u. Average(Σint)=Σmass protein concentration The method of item 506n, wherein Σmassprotein concentration is the sum of massprotein concentrations for all proteins in the target proteome, subproteome, or sample type provided by a database of mass concentration values, and mean (Σint) is the average of the Σint values ​​for all samples in the database.

[0619] 506v. The method of item 506u, in which the mass protein concentration value is calculated from the Human Peptide Atlas database.

[0620] 506w. The mass protein concentration value for each protein in the database was calculated using one of the methods from items 506t to 506v, using an immunoassay-based technique such as an ELISA assay.

[0621] 506x. The mass protein concentration value for each protein in the database was calculated using one of the methods from items 506t to 506v, using an aptamer-based technique such as the Somascan assay.

[0622] 506y.a is calculated for a given set of samples by one of the following methods: terms 506u~506x.

number

[0623] 506z. The method of term 506y, where the mean (Σint) is the average of the Σint values ​​for all samples in the database.

[0624] 507. The target proteome is a virus, q i The method of item 496, where q is the number of proteins i in the structure of the virus, and q is the total number of proteins (i through c) in the structure of the virus.

[0625] 508. The method of item 507, in which the number of coronavirus spike proteins is calculated from a model of the coronavirus virus capsid.

[0626] 509. The weighted average number of amino acids for each amino acid type is given by equation 12

number

[0627] The method of paragraph 509, wherein the weight for each protein of interest within the proteome or sub-proteome of interest is equal since all proteins within the proteome or sub-proteome of interest are considered to have equal expression or proportion within the proteome or sub-proteome of interest.

[0628] The method of paragraph 496 or 509, wherein a linear combination is taken for all proteins i through c in the proteome or sub-proteome of interest.

[0629] 512. The weighted average of the amino acids of each amino acid type is

Number

[0630] is a measure of the amount of protein i in the complex mixture of the protein of interest, and q is an equivalent measure of the total amount of all proteins (from protein i through c) in the complex mixture of the protein of interest, the method of paragraph 494.

Number

[0631] 514. The weighted average of the amino acids of each amino acid type is

Number

[0632] 515. The methods of paragraphs 494, 509 and 514, wherein the protein complex mixture is a mixture having 5, 6, 7, 8, 9, or 10 or more proteins.

[0633] 516. The method of paragraphs 494, 509, and 514, wherein the fraction, proportion, or composition of each protein across a proteome, subproteome, or mixture of proteomes is determined by comparing the expression level of that protein fraction with the expression levels of all proteins in the protein or mixture of proteomes.

[0634] 517. Any one of the preceding terms, wherein known labeled values ​​or amino acid concentrations of the same two or more amino acid types in one or more target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, proteomes, or mixtures of proteins, peptides, polypeptides, oligopeptides, subproteomes, or proteomes at one or more protein concentrations are calculated from the amino acid sequence of one or more target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, proteomes, or mixtures of proteins, peptides, polypeptides, oligopeptides, subproteomes, or proteomes.

[0635] 518. The method of item 517, wherein the amino acid sequence of one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, proteomes, or mixtures of proteins, peptides, polypeptides, oligopeptides, subproteomes, or proteomes of interest provides the number of amino acids of each amino acid type.

[0636] 519. The method of item 518, wherein the number of amino acids includes the number of unmodified amino acids of an amino acid type in the amino acid sequence, and the number of unmodified amino acids of an amino acid type is obtained by subtracting the number of post-translational modifications of that amino acid type from the number of occurrences of that amino acid type in the amino acid sequence.

[0637] 520. Any one of the preceding terms, in which, when calculating the number of each amino acid of two or more amino acid types contained in or within the amino acid sequence of a target protein, peptide, oligopeptide, protein complex, subproteome, or proteome, the number of amino acids of each amino acid type in the target protein is adjusted by considering post-translational modifications (PTMs) that affect the amino acid type in such a manner that they do not chemically react with the labels used for amino acid labeling.

[0638] 521. The method of paragraph 520, wherein when calculating the number of each amino acid of two or more amino acid types contained in or within the amino acid sequence of a target protein, peptide, oligopeptide, protein complex, subproteome, or proteome, the number of amino acids of each amino acid type in the target protein is adjusted by considering post-translational modifications (PTMs) that affect the R group defining the amino acid type in such a manner that they do not chemically react with the label used for amino acid labeling.

[0639] 522. Methods of paragraphs 519-521, which allow information about post-translational modifications to be obtained based on experimental results or by using predictions.

[0640] 523. The methods of paragraphs 519-522, to which the rules provided in Table 4 apply.

[0641] 524. The method of Section 523, wherein if -1 is added to the number of amino acid types in the amino acid sequence, the unmodified amino acids of the amino acid type are labeled in the sample using the labeling chemistry disclosed herein.

[0642] 525. The method of Section 523, wherein if zero is added to the number of amino acid types in the amino acid sequence, all amino acid types (both unmodified and modified amino acids) are labeled in the sample using the labeling chemistry disclosed herein.

[0643] 526. Any method in the preceding section in which the rule in section 523 does not apply when an amino acid-type modified amino acid is converted to an amino acid-type unmodified amino acid in the sample before or during the labeling reaction.

[0644] 527. The method of paragraph 495, wherein the weighted average number of each amino acid of two or more amino acid types for the proteome or subproteome of interest is calculated using publicly available proteome-wide PTM statistics.

[0645] 528. The method of paragraph 495, wherein the number of unmodified or modified amino acids is calculated for a proteome or subproteome of interest by using publicly available proteome-wide post-translational modification statistics.

[0646] 529. The method of paragraph 528, wherein proteome-wide post-translational modification statistics are filtered to provide post-translational modification frequencies specific to prokaryotes, eukaryotes, and mammals, including humans.

[0647] 530. The method of paragraph 529, wherein the virus is treated as unmodified because it does not contain a gene encoding an enzyme that performs post-translational modification.

[0648] 531. The method of paragraph 530, wherein the virus is treated such that it undergoes post-translational modifications, or a subset of post-translational modifications, that a protein in the host undergoes, in order to bypass the translational mechanism of the host cell.

[0649] 532. The method of paragraphs 528-531, wherein, in order to predict the number of unmodified amino acids of an amino acid type, or to predict the number of modified amino acids of an amino acid type, the frequency of modifications of that amino acid type is determined by summing all post-translational modifications affecting that amino acid type and dividing by the total number of amino acids in that amino acid type in the Swiss Prot database, and the post-translational modifications affecting the amino acid type are provided in paragraph 523.

[0650] 533. Modifiers for each amino acid type are provided, which may differ depending on the species of organism, by the method of section 532.

[0651] 534. The method according to any one of the prior claims, wherein the presence and / or concentration of one or more target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes is identified from information indicating known label values ​​and / or amino acid concentrations and / or the number of amino acids of two or more amino acid types that are the same as the amino acid types labeled in the sample within the one or more target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes.

[0652] 535. The method of item 534, wherein information relating to the attributes and / or protein concentration of one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest is obtained from a database, including known label values ​​for two or more amino acid types, amino acid concentrations, or the number of amino acids.

[0653] 536. The method of item 535, wherein information obtained from a database relating to the attributes and / or protein concentration of one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest, includes one or more protein sequences of each of the proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest, including known label values ​​for two or more amino acid types, amino acid concentrations, or the number of amino acids.

[0654] 537. The method of paragraph 534, 535, or 536, wherein information relating to the attributes and / or protein concentration of one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest obtained from a database includes information relating to post-translational modifications of one or more protein sequences of each of the proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest.

[0655] 538. Any one of the methods in items 534-537, wherein information relating to the attributes and / or protein concentration of one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest obtained from a database includes an identifier for each of the proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest, including known label values ​​for two or more amino acid types, amino acid concentrations, or the number of amino acids.

[0656] 539. Any one of the methods in items 534-538, wherein information relating to the attributes and / or protein concentration of one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest obtained from a database includes the names of each of the proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest, including known label values ​​for two or more amino acid types, amino acid concentrations, or the number of amino acids.

[0657] 540. Any one of the methods from items 534 to 539, wherein information relating to the attributes and / or protein concentration of one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest obtained from a database includes the lineage of each of the proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest, including known label values ​​for two or more amino acid types, amino acid concentrations, or the number of amino acids.

[0658] 541. Any one of the methods described in items 534-540, wherein information relating to the attributes and / or protein concentration of one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest obtained from a database includes taxons of each of the proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest, including known label values, amino acid concentrations, or the number of amino acids of two or more amino acid types.

[0659] 542. Any one of the methods from items 534 to 541, wherein information relating to the attributes and / or protein concentration of one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest obtained from a database includes known label values, amino acid concentrations, or the number of amino acids of two or more amino acid types, including known protein concentration ranges for each of the proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest within the sample type of interest.

[0660] 543. Any one of the methods from items 534 to 542, wherein information relating to the attributes and / or protein concentration of one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest obtained from a database includes known label values, amino acid concentrations, or number of amino acids for two or more amino acid types, including known protein concentration ranges for each of the proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest within the tissue type of interest.

[0661] 544. Any one of the methods in items 534-543, wherein information relating to the attributes and / or protein concentration of one or more target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes obtained from a database includes known protein expression data for each target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome within the target sample type.

[0662] 545. Any one of the methods in paragraphs 534-544, wherein the criterion is information relating to the attributes and / or protein concentration of each protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome of interest, such as known label values ​​of two or more amino acid types, amino acid concentrations, or the number of amino acids.

[0663] 545a. The method of item 545, wherein information relating to two or more known label values, amino acid concentrations, or number of amino acids for the attributes and / or protein concentrations of each proteome or subproteome of interest is provided as a single criterion.

[0664] 546. The method of items 1a to 1h, wherein the known label values ​​and / or amino acid concentrations of two or more amino acid types that are the same as the amino acid types labeled in each sample of one or more target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes at one or more protein concentrations, and / or the number of amino acids of two or more amino acid types that are the same as the amino acid types labeled in the sample of one or more target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes are determined from the amino acid sequence of one or more target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes.

[0665] 547. The method of paragraph 546, wherein the amino acid sequence of one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, proteomes, or mixtures of proteins, peptides, polypeptides, oligopeptides, subproteomes, or proteomes of interest is determined by protein sequencing.

[0666] 548. One of the preceding methods for obtaining from a database the known label values, amino acid concentrations, or number of amino acids of two or more identical amino acid types in one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest.

[0667] 549. Any one of the preceding methods, wherein the criterion is a known label value, amino acid concentration, or number of amino acids of two or more identical amino acid types in one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest.

[0668] 550. Any one of the preceding terms, wherein each criterion provides known labeled values ​​or amino acid concentrations of two or more identical amino acid types of each protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome of interest, depending on a common parameter of protein concentration, as a set of parametric equations or vector functions, or each criterion provides the number of amino acids of two or more identical amino acid types of each protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome of interest.

[0669] 551. Any one of the preceding terms, wherein the known label values ​​or amino acid concentrations of two or more identical amino acid types in one or more target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes at one or more protein concentrations are a function of the protein concentration of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome.

[0670] 552. The method of item 551, wherein the known label values ​​or amino acid concentrations of two or more identical amino acid types in one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest at one or more protein concentrations are a function of the total molar protein concentration of the protein, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest.

[0671] 553. The method of paragraph 551, wherein the known labeled values ​​or amino acid concentrations of one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or the same two or more amino acid types in a proteome of interest at one or more protein concentrations are a function of the peptide, oligopeptide, polypeptide, protein, or protein complex concentration, or a function of the total protein concentration in the subproteome or proteome of interest.

[0672] 554. The method of paragraph 551, wherein a known label value or amino acid concentration of one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or the same two or more amino acid types in a proteome of interest at one or more protein concentrations is a function of the total molar concentration of peptides, oligopeptides, polypeptides, proteins, or protein complexes, or a function of the total molar concentration of proteins in a subproteome or proteome of interest.

[0673] 555. The method of item 551, wherein known label values ​​or amino acid concentrations of two or more identical amino acid types of each protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome of interest are provided as vector-valued functions depending on a common parameter of protein concentration.

[0674] 556. The method of item 551, wherein known label values ​​or amino acid concentrations of two or more identical amino acid types of each target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome are provided as a vector function depending on a common parameter of protein concentration.

[0675] 557. The method of item 551, wherein known label values ​​or amino acid concentrations of two or more identical amino acid types of each protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome of interest are provided as vector functions depending on a common parameter of the total moles of the protein, peptide, oligopeptide, polypeptide, or protein complex, or the total molar protein concentration within the subproteome or proteome of interest.

[0676] 558. The method of paragraphs 555-557, wherein the direction of a vector providing amino acid concentrations of two or more of the same amino acid types in each of the target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes is the number or weighted average number of amino acids of each amino acid type in each of the target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes.

[0677] 559. The method of paragraph 558, wherein the direction of a vector that provides the amino acid concentrations of two or more of the same amino acid types in each of the target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes is the number or weighted average number of amino acids of each amino acid type in each of the proteins, peptides, oligopeptides, polypeptides, or protein complexes.

[0678] 560. The vectors of the methods of items 555-559, starting at the origin if the label values ​​for all amino acid types are background-corrected in the sample, or starting at points (n pairs) that provide background values ​​for each of the n amino acid types labeled and measured in the sample if the label values ​​for each / any amino acid type are not background-corrected in the sample.

[0679] 561. The methods of sections 555-559, wherein the vector is bounded by upper and lower limits of protein concentrations available from known or calculated protein expression data.

[0680] 562. The vector function corresponding to the common parameter of protein concentration is vector function 1.

number

[0681] 563. A vector function that depends on a common parameter of protein concentration.

number

[0682] 564. A vector function that depends on a common parameter of protein concentration.

number

[0683] 565. The vector function corresponding to the common parameter of protein concentration is vector function 2.

number

[0684] 566. A vector function that depends on a common parameter of protein concentration.

number

[0685] 567. The vector function corresponding to the common parameter of protein concentration is vector function 3.

number

[0686] 568. A vector function that depends on a common parameter of protein concentration.

number

[0687] 569. The vector function corresponding to the common parameter of protein concentration is vector function 4.

number

[0688] 570. A vector function that depends on a common parameter of protein concentration.

number

[0689] 571. A vector function that depends on a common parameter of protein concentration.

number

[0690] The method of item 546, wherein known label values ​​or amino acid concentrations of two or more of the same amino acid types in one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest at one or more protein concentrations are calculated from one or more amino acid sequences of one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest using a set of parametric equations.

[0691] 573. The method of paragraph 572, wherein a set of parametric equations is bounded by upper and lower limits of protein concentrations available from known or calculated protein expression data.

[0692] 574. The set of parametric equations corresponding to the common parameter of protein concentration is set of parametric equations 1.

number

[0693] 575. A set of parametric equations depending on a common parameter of protein concentration,

number

[0694] 576. The set of parametric equations corresponding to the common parameter of protein concentration is set 2 of parametric equations.

number

[0695] 577. A set of parametric equations depending on a common parameter of protein concentration,

number

[0696] 578. The set of parametric equations corresponding to the common parameter of protein concentration is set 3 of parametric equations.

number

[0697] 579. A set of parametric equations depending on a common parameter of protein concentration,

number

[0698] 580. A vector function that depends on a common parameter of protein concentration.

number

[0699] 581. A vector function that depends on a common parameter of protein concentration.

number

[0700] The method of item 572, wherein known label values ​​or amino acid concentrations of two or more identical amino acid types in one or more proteins, peptides, oligopeptides, polypeptides, or protein complexes are calculated from the amino acid sequence of one or more proteins, peptides, oligopeptides, polypeptides, or protein complexes using a set of parametric equations 1 or 3, or a vector function 1 or 3.

[0701] 583. The method of item 572, wherein known label values ​​or amino acid concentrations of two or more identical amino acid types in one or more proteomes or subproteomes of interest are calculated from the amino acid sequence of one or more proteomes or subproteomes of interest using a set of parametric equations 2 or 4, or vector functions 2 or 4.

[0702] 584. The method described in item 549, where the criteria are obtained from a database.

[0703] 585. Any one of the preceding items, wherein step e) identifies the presence and / or concentration and / or amount of one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest in a sample if the measured label, amino acid concentration, or number of each labeled amino acid type in the sample is the same as, or less than, the known label value, amino acid concentration, or number of amino acids of the same two or more amino acid types labeled in the sample in one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest.

[0704] 586. The method of paragraph 585, wherein the tolerance is the order statistic of the minimum distance between the measured label, amino acid concentration, or number of labeled amino acid types in a sample and the known label value, amino acid concentration, or number of amino acids of the same amino acid type in the protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome of interest, and the k-th order statistic is the k-th smallest value.

[0705] 587. The method of paragraph 585, wherein the tolerance is a distance threshold between the measured label, amino acid concentration, or number of labeled amino acid types in a sample and a known label value, amino acid concentration, or number of amino acids of the same amino acid type in the protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome of interest.

[0706] 588. The method of item 587, wherein the distance between the measured label, amino acid concentration, or number of labeled amino acid types in a sample and the known label value, amino acid concentration, or number of amino acids of the same amino acid type in each protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome of interest is a Euclidean distance measurement.

[0707] 589. The method of paragraph 585, wherein the tolerance is the minimum distance between the measured label, amino acid concentration, or number of labeled amino acid types in a sample and the known label value, amino acid concentration, or number of amino acids of the same amino acid type in the protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome of interest.

[0708] 590. Euclidean distance measurement is given by equation 17

number

[0709] 591. The method of item 585, wherein the tolerance includes a user-specified tolerance multiplied by the values ​​of labels for two or more amino acid types measured for the sample, the amino acid concentrations, or the number of amino acids.

[0710] 592. The method of item 585, wherein the tolerance includes a user-specified tolerance multiplied by the values ​​of labels for two or more amino acid types measured for the sample, the amino acid concentrations, or the square root of the sum of the squares of the number of amino acids.

[0711] 593. The method of item 585, in which the tolerance is provided from the user-specified tolerance and multiplied by the square root of the square of the sample value, reflecting the distance calculation. This is given by equation 8.

number

[0712] 594. The method of paragraph 593, wherein the user-specified tolerance φ is 0.001, 0.002, 0.003, 0.004, 0.005, 0.006, 0.007, 0.008, 0.009, 0.01, 0.02, 0.03, 0.04, 0.05, 0.06, 0.07, 0.08, 0.09, or 0.10.

[0713] 595. The method of item 585, where, if a sample is suspected to contain k types of target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes, the tolerance is the k-th order statistic of the distances calculated for all of the target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes.

[0714] 596. If a sample is suspected to contain k types of target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes, the distances are sorted and the tolerance is the k-th smallest distance, by the method of item 585.

[0715] 597. Step e) comprises comparing the measured label of each labeled amino acid type in the sample with known label values ​​of the same two or more amino acid types of one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest at one or more protein concentrations, wherein the known label values ​​of two or more amino acid types of one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest at one or more protein concentrations are calculated from experimental information relating to one or more amino acid sequences and / or post-translational modifications of one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest using a vector function or a set of parametric equations, one of the methods in the preceding terms.

[0716] 598. Step e) comprises comparing the amino acid concentration of each labeled amino acid type in a sample with the amino acid concentrations of the same two or more amino acid types of one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest at one or more protein concentrations, wherein the amino acid concentrations of two or more amino acid types of one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest at one or more protein concentrations are calculated from experimental information relating to one or more amino acid sequences and / or post-translational modifications of one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest using a vector function or a set of parametric equations, one of the methods in the preceding terms.

[0717] 599. A method from any one of the preceding items, wherein step e) comprises comparing the number of amino acids of each labeled amino acid type in a sample with the number of amino acids of the same two or more amino acid types in one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest, wherein the number of amino acids of two or more amino acid types in one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest is calculated from experimental information relating to one or more amino acid sequences and / or post-translational modifications of one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest.

[0718] 600. A method from any one of the preceding clauses, wherein step e) comprises comparing the measured label, amino acid concentration, and / or number of amino acids of each labeled amino acid type in a sample with known label values ​​or amino acid concentrations of the same two or more amino acid types in one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest at one or more protein concentrations, or using an n-dimensional space, the number of amino acids of the same two or more amino acid types in one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest.

[0719] 601. Step e) comprises comparing the measured label, amino acid concentration, and / or number of amino acids of each labeled amino acid type in the sample as a function of protein concentration to known label values ​​or amino acid concentrations of the same two or more amino acid types in one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest, or to the number of amino acids of the same two or more amino acid types in one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest using an n-dimensional space, and the protein concentration One of the preceding terms, wherein known label values ​​or amino acid concentrations of two or more identical amino acid types in one or more target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes, as a function of , provide a line or curve in n-dimensional space which can optionally be bounded by known protein expression levels in a biological sample, and the number of amino acids of two or more identical amino acid types in one or more target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes, provides a point in n-dimensional space.

[0720] 602. The method of item 601, wherein two types of amino acids are labeled in the sample, and the n-dimensional space is a two-dimensional space.

[0721] 603. The method of item 601, wherein three types of amino acids are labeled in the sample, and the n-dimensional space is a 3-dimensional space.

[0722] 604. The method of item 601, wherein four types of amino acids are labeled in the sample, and the n-dimensional space is a 4-dimensional space.

[0723] The method of item 601, wherein 605.5 types of amino acids are labeled in the sample, and the n-dimensional space is a 5-dimensional space.

[0724] The method of item 601, wherein 606 types of amino acids are labeled in the sample, and the n-dimensional space is a 6-dimensional space.

[0725] The method of item 601, wherein 607.7 types of amino acids are labeled in the sample, and the n-dimensional space is a 7-dimensional space.

[0726] The method of item 601, wherein 608.8 types of amino acids are labeled in the sample, and the n-dimensional space is an 8-dimensional space.

[0727] The method of item 601, wherein 609.9 types of amino acids are labeled in the sample, and the n-dimensional space is a 9-dimensional space.

[0728] 610. The method of item 601, wherein 10 types of amino acids are labeled in the sample, and the n-dimensional space is a 10-dimensional space.

[0729] 611. The method of item 601, wherein 11 types of amino acids are labeled in the sample, and the n-dimensional space is an 11-dimensional space.

[0730] 612. The method of item 601, wherein 12 types of amino acids are labeled in the sample, and the n-dimensional space is a 12-dimensional space.

[0731] 613. The method of item 601, wherein 13 types of amino acids are labeled in the sample, and the n-dimensional space is a 13-dimensional space.

[0732] 614. The method of item 601, wherein 14 types of amino acids are labeled in the sample, and the n-dimensional space is a 14-dimensional space.

[0733] 615. The method of item 601, wherein 15 types of amino acids are labeled in the sample, and the n-dimensional space is a 15-dimensional space.

[0734] The method of item 601, wherein 616 types of amino acids are labeled in the sample, and the n-dimensional space is a 16-dimensional space.

[0735] 617. The method of item 601, wherein 17 types of amino acids are labeled in the sample, and the n-dimensional space is a 17-dimensional space.

[0736] 618. The method of item 601, wherein 18 types of amino acids are labeled in the sample, and the n-dimensional space is an 18-dimensional space.

[0737] 619. The method of item 601, wherein 19 types of amino acids are labeled in the sample, and the n-dimensional space is a 19-dimensional space.

[0738] The method of item 601, wherein 620.20 types of amino acids are labeled in the sample, and the n-dimensional space is a 20-dimensional space.

[0739] The method of item 601, wherein 621 types of amino acids are labeled in the sample, and the n-dimensional space is a 21-dimensional space.

[0740] The method of item 601, wherein 622.22 types of amino acids are labeled in the sample, and the n-dimensional space is a 22-dimensional space.

[0741] The method of item 601, wherein 623.23 types of amino acids are labeled in the sample, and the n-dimensional space is a 23-dimensional space.

[0742] The method of item 601, wherein 624.24 types of amino acids are labeled in the sample, and the n-dimensional space is a 24-dimensional space.

[0743] The method of item 601, wherein 625.25 types of amino acids are labeled in the sample, and the n-dimensional space is a 25-dimensional space.

[0744] The method of item 601, wherein 626.26 types of amino acids are labeled in the sample, and the n-dimensional space is a 26-dimensional space.

[0745] The method of item 601, wherein 627.27 types of amino acids are labeled in the sample, and the n-dimensional space is a 27-dimensional space.

[0746] The method of item 601, wherein 628.28 types of amino acids are labeled in the sample, and the n-dimensional space is a 28-dimensional space.

[0747] The method of item 601, wherein 629.29 types of amino acids are labeled in the sample, and the n-dimensional space is a 29-dimensional space.

[0748] The method of item 601, wherein 630.30 types of amino acids are labeled in the sample, and the n-dimensional space is a 30-dimensional space.

[0749] The method of item 601, wherein 631 types of amino acids are labeled in the sample, and the n-dimensional space is a 31-dimensional space.

[0750] The method of item 601, wherein 632.32 types of amino acids are labeled in the sample, and the n-dimensional space is a 32-dimensional space.

[0751] The method of item 601, wherein 633.33 types of amino acids are labeled in the sample, and the n-dimensional space is a 33-dimensional space.

[0752] The method of item 601, wherein 634.34 types of amino acids are labeled in the sample, and the n-dimensional space is a 34-dimensional space.

[0753] The method of item 601, wherein 635.35 types of amino acids are labeled in the sample, and the n-dimensional space is a 35-dimensional space.

[0754] The method of item 601, wherein 636.36 types of amino acids are labeled in the sample, and the n-dimensional space is a 36-dimensional space.

[0755] The method of item 601, wherein 637.37 types of amino acids are labeled in the sample, and the n-dimensional space is a 37-dimensional space.

[0756] The method of item 601, wherein 638.38 types of amino acids are labeled in the sample, and the n-dimensional space is a 38-dimensional space.

[0757] The method of item 601, wherein 639.39 types of amino acids are labeled in the sample, and the n-dimensional space is a 39-dimensional space.

[0758] The method of item 601, wherein 640.40 types of amino acids are labeled in the sample, and the n-dimensional space is a 40-dimensional space.

[0759] 641. The method of item 585, wherein if a single protein concentration value exists, the one or more target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes are identified in the sample if the values ​​of labels or amino acid concentrations of two or more amino acid types measured in the sample are the same as, or less than or equal to the tolerance values ​​of known labels or amino acid concentrations of two or more amino acid types provided by a reference function for one or more target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes, provided that a reference function for one or more target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes is provided that a single protein concentration value exists.

[0760] 642. The method of item 585, wherein the protein concentration of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome identified in the sample is the same as, or less than or equal to, the values ​​of the labels or amino acid concentrations of two or more amino acid types provided by a reference function for the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome identified in the sample.

[0761] 643. The method of item 642, wherein the amount of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome protein identified in the sample is obtained by multiplying the protein concentration of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome protein identified in the sample by the volume of the sample.

[0762] 644. Any one of the preceding terms, wherein the presence of a target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome is identified in a sample if the amino acid concentrations of two or more amino acid types measured for the sample are the same as the amino acid concentrations of the same two or more corresponding amino acid types provided for the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome by its reference vector function or set of parametric equations.

[0763] 645. The method of item 228, where, if a single solution of protein concentration t exists, the solution for t is the protein concentration of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome identified in the sample, and the sample point lies on the baseline.

[0764] 646. The method of item 585, wherein a single protein concentration value exists, and the values ​​of labels or amino acid concentrations of two or more amino acid types measured in the sample are less than or equal to the tolerance of the values ​​of labels or amino acid concentrations of two or more amino acid types provided by a reference function for one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest, provided that one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest are identified in the sample.

[0765] 647. The method of item 234, wherein the distance between the values ​​of labels or amino acid concentrations of two or more amino acid types measured in a sample and the values ​​of labels or amino acid concentrations of two or more amino acid types known by a reference function for one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest is calculated.

[0766] 648. The method of paragraph 647, wherein the minimum distance between the values ​​of labels or amino acid concentrations of two or more amino acid types measured in a sample and the values ​​of labels or amino acid concentrations of two or more amino acid types known by a reference function for one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest is calculated by finding a point on a reference line where the distance between the sample point and the reference line is perpendicular.

[0767] 649. The point on the reference line at which the distance between the sample point and the reference line is perpendicular is found by providing a general vector equation for the vector between the sample point and the reference line, taking the dot product of this vector and the direction vector of the reference line, setting the dot product to a value equal to 0, and solving for the protein concentration i, which is the protein concentration on the reference line that results in a point at which the distance from the sample point is perpendicular, as in the method of section 648.

[0768] 650. The method of item 649, wherein the amino acid concentration or label value for each amino acid type at this protein concentration on the baseline is calculated, the distance between this point and the sample point is calculated and compared with the tolerance.

[0769] 651. The method of item 650, wherein, if the distance is less than or equal to the tolerance, the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome is present in the sample at a protein concentration at which the distance is perpendicular.

[0770] 652. The method of paragraph 647, wherein if more than one protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome of interest is identified in the sample, a mixture of the protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome of interest is identified in the sample, and the relative composition of each component in the mixture is inversely proportional to the distance between the value measured for the sample and the value provided for each identified component of the mixture.

[0771] 653. The method of paragraph 652, wherein the relative composition of each component in the mixture is determined by inversely normalizing the distance between the sample and each component by the maximum distance between the sample and any given component.

[0772] 654. The method of paragraph 653, wherein the inverse normalized distance of each component is divided by the sum of the inverse normalized distances of all components to provide the relative composition of each component in the mixture.

[0773] 655. The method of item 652, wherein the relative composition of each component in a mixture is multiplied by the protein concentration of each protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome of interest, to provide the concentration of each protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome of interest in the mixture.

[0774] 656. Any one of the preceding terms, wherein the known label values, amino acid concentrations, or number of amino acids of two or more identical amino acid types in the target subproteome or proteome is a weighted average based on the known label values, amino acid concentrations, or number of amino acids of each amino acid type based on all amino acid sequences contained in the target proteome or subproteome.

[0775] 657. Any one of the preceding terms, wherein the number of amino acids of two or more of the same amino acid type in the target subproteome or proteome is the weighted average of the number of amino acids of each amino acid type in all amino acid sequences contained within the target proteome or subproteome.

[0776] 658. The method of paragraph 656, wherein known label values ​​or amino acid concentrations of two or more identical amino acid types in the target subproteome or proteome are calculated using a weighted average of the number of amino acids of each amino acid type in all amino acid sequences contained in the target proteome or subproteome.

[0777] 659. Step e) comprises removing any protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome of interest from a sample, wherein the measured label, amino acid concentration, and number of each amino acid type refer to any duplicate protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome of interest, according to any one of the preceding provisions.

[0778] 660. A method from any one of the preceding clauses, wherein step e) identifies the presence and / or concentration and / or amount of one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes in a sample if the measured label, amino acid concentration, or number of each labeled amino acid type in the sample is the same as, or less than or equal to, the known label value, amino acid concentration, or number of the same two or more amino acid types in one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest, and the identified concentration is within the protein concentration threshold values ​​(c1, c2) based on the known concentration levels of one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes in the sample of interest.

[0779] 661. The method of sections 233-238, wherein the minimum distance between a sample point and any point on a vector corresponding to a target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome is found by the dot product of the vector between the sample point and the direction of the vector corresponding to the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome, wherein only the direction of the vector corresponding to the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome is considered.

[0780] 662. The methods of paragraphs 564, 566, and 568, wherein, when calculating the dot product, the vector corresponding to the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome is treated as unbounded or bounded only at the origin.

[0781] The method of items 1a-1h, wherein 663.3 types of amino acid types are labeled in the sample, and the measured label, amino acid concentration, or number of amino acids for each of the three types of labeled amino acid types in the sample is compared with the known label values, amino acid concentrations, or number of amino acids for the same three types of amino acid types of 200 or fewer proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest.

[0782] 664.3 amino acid types are labeled in the sample, and one of the methods from items 1a to 1h is used to compare the measured label, amino acid concentration, or number of amino acids for each of the three labeled amino acid types in the sample with the known label values, amino acid concentration, or number of amino acids for the same three amino acid types in a proteome or subproteome of interest of 9000 types or less.

[0783] 665. Any one of the preceding items, wherein the target proteome or subproteome has fewer than 4000 types of proteins.

[0784] 666. One of the preceding methods, provided the sample is not sequenced, to identify a target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome via the sequence of amino acids in the sample.

[0785] 667. Any one of the preceding methods for determining the presence and / or concentration and / or amount of a target protein, peptide, polypeptide, oligopeptide, subproteome, or mixture of proteomes in a sample, without requiring the separation of the sample into individual protein components.

[0786] 668. One of the methods from items 1 to 350, wherein step a) comprises isolating the protein component from the sample before labeling.

[0787] 669. The method of item 668, wherein protein components are isolated using centrifugation, filtration, electrophoresis, or chromatography.

[0788] 670. The method of chromatographic isolation, accompanied by HPLC, as described in item 669.

[0789] 671. Any one of the preceding methods, performed in bulk.

[0790] 672. Steps d) and e) are performed in any one of the preceding terms using the classifier.

[0791] 673. A method, either of items 472 or 475, wherein the same proportion of amino acids of the amino acid type used to generate the calibration curve are labeled in the sample as are labeled in any / all proteins and / or amino acids.

[0792] 674. A method, either of items 472 or 476, wherein the sample is labeled with amino acids of the same amino acid type as those labeled in any protein used as a standard.

[0793] 675. A method, either of items 472 or 476, wherein the sample is labeled with amino acids of the same amino acid type as is labeled in any amino acid used as a standard.

[0794] 676. One of the methods of items 472 and 475, wherein the sample is labeled with the same proportion of amino acids of the same amino acid type as that labeled in any / all proteins and / or amino acids used to generate the calibration curve.

[0795] 677. One of the methods from items 472 and 476, wherein the sample is labeled with the same proportion of amino acids of the amino acid type ±5% as those labeled in any protein used as a standard.

[0796] 678. One of the methods from items 472 and 476, wherein the sample is labeled with an amino acid of the same proportion ±5% as the amino acid used as a standard, in which amino acids of the amino acid type are used.

[0797] 679. One of the methods of items 472 and 475, wherein the sample is labeled with the same proportion of amino acids of the same amino acid type as that labeled in any / all proteins and / or amino acids used to generate the calibration curve, in which case the sample is labeled.

[0798] 680. One of the methods from items 472 and 476, wherein the sample is labeled with the same proportion of amino acids of the amino acid type ±10% as those labeled in any protein used as a standard.

[0799] 681. One of the methods from items 472 and 476, wherein the sample is labeled with an amino acid of the same proportion ±10% as the amino acid used as a standard, in which amino acids of the amino acid type are used.

[0800] 682. The method of section 225 or 545, wherein the amino acid concentrations of two or more amino acid types in a sample are compared with the amino acid concentrations of the same two or more amino acid types in one or more target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes, and the amino acid concentrations of the same two or more amino acid types in one or more target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes are the experimental standard.

[0801] 683. The method of item 682, wherein the same proportion of amino acids of the amino acid type used to generate calibration curves and any experimental standards are labeled in the sample as are used to label any / all proteins and / or amino acids.

[0802] 684. The method of item 682, wherein the same proportion of amino acids of the same amino acid type as those labeled in any protein used as a standard and optional experimental reference are labeled in the sample.

[0803] 685. The method of item 682, wherein amino acids of the same amino acid type as those labeled in any amino acid used as a standard are labeled in the sample and any experimental standard.

[0804] 686. The method of item 682, wherein ±5% of the same proportions of amino acid types as those labeled in any / all proteins and / or amino acids used to create a calibration curve are labeled in the sample and any experimental standard.

[0805] 687. Any one of the methods in item 682, wherein the sample and any experimental standard are labeled with an amino acid of the same proportion ±5% as that labeled in any protein used as a standard.

[0806] 688. The method of item 682, wherein the sample and any experimental standard are labeled with an amino acid of the same proportion ±5% as the amino acid labeled in any amino acid used as a standard.

[0807] 689. The method of item 682, wherein ±10% of amino acids of the same proportion as those labeled in any / all proteins and / or amino acids used to create a calibration curve are labeled in the sample and any experimental standard.

[0808] 690. Any one of the methods in item 682, wherein the sample and any experimental standard are labeled with an amino acid of the same proportion ±10% as that labeled in any protein used as a standard.

[0809] 691. The method of item 682, wherein the sample and any experimental standard are labeled with an amino acid of the same proportion ±10% as the amino acid labeled in any amino acid used as a standard.

[0810] 692. The method of item 682, wherein amino acids of the same amino acid type are labeled in the sample and any experimental standard.

[0811] 693. The method of item 682, wherein amino acids of the same proportion ±5% are labeled in the sample and any experimental standard.

[0812] 694. The method of item 682, wherein amino acids of the same proportion ±5% are labeled in the sample and any experimental standard.

[0813] 695. The method of item 682, wherein amino acids of the same proportion ±5% are labeled in the sample and any experimental standard.

[0814] 696. The method of item 682, wherein amino acids of the same proportion ±10% amino acid type are labeled in the sample and any experimental standard.

[0815] 697. The method of item 682, wherein amino acids of the same proportion ±10% amino acid type are labeled in the sample and any experimental standard.

[0816] 698. The method of item 682, wherein amino acids of the same proportion ±10% amino acid type are labeled in the sample and any experimental standard.

[0817] 699. The method of item 1c, wherein the bacterial proteome is Salmonella and / or E. coli.

[0818] 700. The method of item 1d, wherein the target viral proteome is the SARS-CoV-2 proteome.

[0819] 701. The method of item 1d, wherein the target viral proteome is a zoonotic viral proteome.

[0820] 702. The method of item 1d, wherein the target viral proteome is the HIV proteome.

[0821] 703. The method of item 1f, wherein a target human protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome is used for the early detection of cancer.

[0822] 704. The method described in item 1g for determining whether the infection is zoonotic. [Brief explanation of the drawing]

[0823] Embodiments of the present invention will be described below with reference to the accompanying drawings.

[0824] [Figure 1] A schematic diagram is shown illustrating how the calculated unique signatures for target protein-A, target protein-B, target protein-C, and target protein-D vary as a function of the protein concentration of each target protein. A reference vector is provided for each target protein, and each point on the reference vector corresponds to the unique protein concentration of the target protein (e.g., 1 μM, black circle). The shortest distance from the sample point (white square) to each reference line is calculated to identify the presence of target protein-B in the sample. The concentration of target protein-B in the sample is the protein concentration of target protein-B that provided that shortest distance (e.g., 0.5 μM). [Figure 2] The reference lines in n-dimensional space are shown. Set 1 of parametric equations provides the following reference lines for BSA, LYZ, and TTR. Sample points are indicated by white circles. The method of the present invention involves determining the presence and / or concentration and / or amount of a target protein / protein complex in a sample based on a comparison of the distances between the sample points and each reference line. [Figure 3]This shows the unique signatures of the pathogenic proteome. (a) All 7,581 bacterial reference proteomes analyzed have unique signatures for known label values, amino acid concentrations, or average amino acid numbers across all proteins in the bacterial reference proteome. (b) Enlarged images showing the wide-ranging distribution of the average number of amino acids of two or more amino acid types within any average protein sequence. (c) All 9,377 viral reference proteomes analyzed have unique signatures for known label values, amino acid concentrations, or average amino acid numbers across all proteins in the viral reference proteome. (d) All 16,958 bacterial and viral reference proteomes analyzed have unique signatures for known label values, amino acid concentrations, or average amino acid numbers across all proteins in the bacterial and viral reference proteome. This makes it possible to identify the entire proteome in a sample without separation. [Figure 4] By analyzing the probability distribution of the leading digit in a set of numbers following Benford's Law, we demonstrate that the amino acid types in human plasma proteomes follow a predicted distribution. [Figure 5] Analysis of the probability distribution of the leading digits in a set of numbers following Benford's Law shows that the average number of amino acids across proteins, peptides, oligopeptides, polypeptides, and protein subunits in the viral proteome deviates from the expected distribution, suggesting increased variability in this dataset compared to the human proteome. [Figure 6] Analysis of the probability distribution of the leading digits in a set of numbers following Benford's Law shows that the average number of amino acids across proteins, peptides, oligopeptides, polypeptides, and protein subunits in the bacterial proteome deviates from the expected distribution, suggesting increased variability in this dataset compared to the human proteome. [Figure 7]This demonstrates that identifying the order of amino acids within a protein sequence in the human proteome is less efficient than identifying only the number of amino acids within the protein sequence. Identifying the order of two types of amino acids within a protein sequence does not add any additional information compared to identifying the order of only one type of amino acid within the protein sequence. [Figure 8] This demonstrates the effect of constraining baselines to known protein concentration ranges within the human plasma proteome. (a) Baseline for all 3263 proteins, peptides, oligopeptides, polypeptides, and protein complexes within the human plasma proteome. (b) Bounded baseline for all 3263 proteins, peptides, oligopeptides, polypeptides, and protein complexes within the human plasma proteome; the baselines are bounded by known concentration ranges of these proteins, peptides, oligopeptides, polypeptides, and protein complexes within the human plasma proteome. [Figure 9] The method of the present invention allows access to and, with and without using protein concentration information compared to known protein concentration boundaries, the occurrence of a criterion referencing more than one protein of interest has been quantified across human plasma proteomes for various amino acid type combinations (C and W, K and W, K and Y, K and S, K and P, L and S, L and K, E and L, G and L, CK and W, CK and Y, LK and S, EG and K, EG and S, REP and T, and QLK and V). [Figure 10] Without applying any bounding or constraints to protein concentration or other classifications, when two amino acid types are labeled and compared, all criteria are distinguishable and specifically map to the target protein within most of the clinically relevant proteomes and subproteomes considered (SARS-CoV-2, HIV, Epstein-Barr, glioma), and do not correspond to multiple target proteins within the clinically relevant proteomes and subproteomes. [Figure 11](a) For protein sequences in human plasma proteome and (b) human salivary proteome, we will compare the information provided by all combinations of two amino acid types with the specificity of the standard. [Figure 12] This demonstrates that all reference bacterial proteomes (7581 reference proteomes) have an average number of amino acids within two amino acid types across the proteins in that proteome, which is distinct from all other average numbers of amino acids within two amino acid types across proteins in all other proteomes. [Figure 13] To label only two specific amino acid types within a target proteome, we demonstrate that bacterial and viral proteomes cluster together according to their lineage. Here, labeling of K and W amino acid types is provided, and clustering within the orders Corynebacteriaceae, Legionellales, Bacillales, Streptomycetaceae, and Mycoplasmataceae is shown. [Figure 14] This document describes the process for an unknown mixture of proteins. The properties of the mixture are unknown, and the protein concentrations in the mixture are also unknown. [Figure 15] State-of-the-art scaling methods still require knowledge of whether proteins are folded or unfolded and do not account for partial intrinsic dysregulation, thus demonstrating that hydrodynamic radius cannot be predicted based solely on protein sequence. [Figure 16] A schematic diagram showing the reaction between the amino acid forms of (a) tryptophan (W), (b) tyrosine (Y), (c) reduced cysteine ​​(CR), (d) cysteine ​​(C), and (e) lysine (K) and a fluorescent dye or a molecule that becomes fluorescent upon reaction with the shown amino acid forms. [Figure 17] The patient samples are shown compared to the SARS-CoV-2 and influenza A baselines for (a) C and K, (b) C and W, and (C) K and W. [Figure 18]This shows a calibration curve for converting background-corrected fluorescence intensity KFI from K amino acid forms in arbitrary units (AU) to amino acid concentrations [K] of K amino acid forms in μM. Nonlinear regression revealed that a polynomial fitting to the calibration curve was obtained with R² = 0.9987. [Figure 19] This shows a calibration curve for converting background-corrected fluorescence intensity C FI from C amino acid forms in arbitrary units (AU) to amino acid concentrations [C] in μM. Nonlinear regression revealed that a polynomial fit to the calibration curve was obtained with R² = 0.9886. [Figure 20] This shows a calibration curve for converting background-corrected fluorescence intensity W FI from W amino acid forms in arbitrary units (AU) to amino acid concentrations [W] of W amino acid forms in μM. Nonlinear regression revealed that a polynomial fitting to the calibration curve was obtained with R² = 0.9886. [Figure 21] When the average measured amino acid concentrations across three technical replicas of each experimentally measured patient PPP sample are plotted in N-dimensional space (4-dimensional space), the data will form a line in N-dimensional space, as predicted by the concept of the present invention. This conceptual line is shown by drawing a line through the dataset. To calculate the actual position and equation of the baseline defining the target PPP proteome, the K, C, W, and Y components of the vector function defining the target PPP proteome were experimentally calculated in the figure below. [Figure 22] This section describes how the coefficients (direction) of the K component of the experimental baseline were calculated for the target PPP and PRP proteomes. The measured amino acid molar concentrations of amino acid type K in μM were plotted against the measured total protein concentrations in μg / mL for each target proteome, and linear regression was performed. The linear regression was constrained to pass through the origin. [Figure 23]This section describes how the coefficients (directions) of the C component of the experimental baseline were calculated for the target PPP and PRP proteomes. The measured molar concentrations of amino acid type C in μM were plotted against the measured total protein concentrations in μg / mL for each target proteome, and linear regression was performed. The linear regression was constrained to pass through the origin. [Figure 24] This section describes how the coefficients (direction) of the W component of the experimental baseline were calculated for the target PPP and PRP proteomes. The measured amino acid molar concentrations of amino acid type W in μM were plotted against the measured total protein concentrations in μg / mL for each target proteome, and linear regression was performed. The linear regression was constrained to pass through the origin. [Figure 25] This section describes how the coefficients (direction) of the Y component of the experimental baseline were calculated for the target PPP and PRP proteomes. The measured amino acid mol...

Claims

1. A method for identifying the presence and / or concentration and / or amount of one or more target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes in a sample, wherein the method is a) Labeling three or more amino acid types in the sample, wherein the amino acid type is defined by the R group of the amino acid, b) Measuring the labeling of each labeled amino acid type in the sample, e) Identifying the presence and / or concentration and / or amount of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome in the sample by comparing the measured label and / or amino acid concentration of each labeled amino acid type in the sample with known label values ​​and / or amino acid concentrations of the same three or more amino acid types labeled in each sample of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome at one or more concentrations, or by comparing the number of the amino acids of each labeled amino acid type in the sample with the number of known amino acids of the same three or more amino acid types labeled in the sample of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome, The comparison described above is performed using an n-dimensional space corresponding to n types of labeled amino acid forms.

2. The method according to claim 1, wherein the three or more amino acid types are selected from the group consisting of alanine (A), arginine (R), asparagine (N), aspartic acid (D), cysteine ​​(C), glutamic acid (E), glutamine (Q), glycine (G), histidine (H), isoleucine (I), leucine (L), lysine (K), methionine (M), phenylalanine (F), proline (P), pyrrolidine (O), selenocysteine ​​(U), serine (S), threonine (T), tryptophan (W), tyrosine (Y), and valine (V), or synthetic amino acids, and any combination thereof.

3. The method according to claim 1 or 2, wherein the three or more amino acid types include modified amino acids and / or unmodified amino acids of the amino acid type.

4. The method according to claim 3, wherein the modified amino acid of the amino acid type is a post-translation modified amino acid of the amino acid type.

5. The method according to claim 3 or 4, wherein the modified amino acid of the amino acid type is labeled independently of the unmodified amino acid of the amino acid type.

6. The method according to any one of claims 1 to 5, wherein the amino acid-type R group is labeled.

7. The method according to any one of claims 1 to 6, wherein the sign provides a signal.

8. The method according to any one of claims 1 to 6, wherein the label is a fluorescent label.

9. The method according to claim 7, wherein the fluorescent label is a molecule that becomes fluorescent upon reaction with a fluorescent dye, a fluorogenic dye, and / or an amino acid type.

10. The method according to any one of claims 1 to 9, wherein the amino acid concentration of each labeled amino acid type in the sample is calculated from the measured label, and the amino acid concentration is calculated from the measured label using the measured label of one or more proteins or amino acids, using a calibration curve or standard that converts between the measured label of the sample and the amino acid concentration of the amino acid type in the sample.

11. The method according to any one of claims 1 to 10, wherein the number of each labeled amino acid type of the amino acid in the sample is calculated, and the number of each labeled amino acid type of the amino acid in the sample is calculated by dividing the concentration of the amino acid type of the amino acid in the sample by the total molar concentration of the sample.

12. The method according to any one of claims 1 to 11, wherein information indicating the presence and / or concentration of one or more target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes, is obtained from a database, wherein information indicating the known label values ​​and / or amino acid concentrations and / or number of amino acids for three or more amino acid types that are the same as the amino acid type labeled in the sample is obtained.

13. The method according to any one of claims 1 to 12, wherein the reference is information indicating the presence and / or concentration of each of the target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes, including known label values ​​for three or more amino acid types that are the same as the amino acid type labeled in the sample, and / or amino acid concentrations and / or the number of amino acids.

14. The method according to claim 13, wherein the criteria provide, in accordance with a common parameter of concentration, the known label values ​​and / or amino acid concentrations of three or more amino acid types that are the same as the amino acid types labeled in each of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome sample, as a set of parametric equations or vector functions, and / or the criteria provide the number of the amino acids of three or more amino acid types that are the same as the amino acid types labeled in each of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome sample.

15. The method according to any one of claims 1 to 14, wherein step e) identifies the presence and / or concentration and / or amount of the one or more target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes in the sample if the measured label, amino acid concentration, or number of amino acids of each labeled amino acid type in the sample is the same as, or less than or equal to, the known label value, amino acid concentration, or number of amino acids of the same three or more amino acid types labeled in the sample of the one or more target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes.

16. The method according to claim 15, wherein if there exists a single concentration value such that the measured labels and / or amino acid concentrations of three or more amino acid types measured in the sample are the same as, or less than, the values ​​of known labels and / or amino acid concentrations of the same three or more amino acid types that are labeled in the sample of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome, then the presence and / or concentration of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome is identified in the sample.

17. The method according to any one of claims 1 to 16, wherein the amount of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome identified in the sample is obtained by multiplying the concentration of the target protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome identified in the sample by the volume of the sample.

18. The method according to any one of claims 15 or 16, wherein step e) of the method further comprises calculating a minimum distance between the measured label and / or amino acid concentration and / or number of amino acids of the labeled amino acid type of the sample and three or more known label values ​​and / or amino acid concentrations and / or number of amino acids of the same amino acid type as the amino acid type labeled in each of the sample of the protein, peptide, oligopeptide, polypeptide, protein complex, subproteome, or proteome of the target, and comparing the tolerance with the calculated minimum distance.

19. The method according to claim 15, 16, or 18, wherein the tolerance includes a user-specified tolerance, or if the sample is suspected to contain c distinct proteins, peptides, protein complexes, subproteomes, or proteomes of interest, and the distances are regular, the tolerance is the c-th smallest value of the distance.

20. The method according to any one of claims 1 to 19, wherein the known label values ​​and / or amino acid concentrations and / or number of amino acids of three or more amino acid types, which are the same as the amino acid types labeled in the sample, are calculated from experimental information relating to one or more amino acid sequences of the one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of the target, and / or post-translational modifications of the one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of the target, in one or more concentrations, the known label values ​​and / or amino acid concentrations and / or number of amino acids of three or more amino acid types, which are the same as the amino acid types labeled in the sample.

21. The method according to claim 1, wherein step e) includes comparing the measured level of each of the three or more labeled amino acid types in the sample with the known label value of each of the three or more amino acid types that are the same as the labeled amino acid types in the sample of one or more target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes at one or more concentrations; or comparing the amino acid concentration of each of the labeled amino acid types in the sample with the amino acid concentration of the three or more amino acid types that are the same as the labeled amino acid types in the sample of one or more target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes at one or more concentrations; or comparing the number of amino acids of each of the three or more labeled amino acid types in the sample with the number of amino acids of the three or more amino acid types that are the same as the labeled amino acid types in the sample of one or more target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes.

22. The method according to any one of claims 1 to 21, wherein the known label values ​​and / or amino acid concentrations and / or number of amino acids for three or more amino acid types that are the same as the amino acid type labeled in the sample in the target proteome or subproteome is a weighted average of the known label values, amino acid concentrations, or number of amino acids for each amino acid type among all amino acid sequences contained in the target proteome or subproteome.

23. The method according to any one of claims 1 to 22, wherein the target proteome and / or subproteome is the HIV proteome and / or its subproteome, and / or the SARS-CoV-2 proteome and / or its subproteome, and / or the zoonotic proteome and / or its subproteome, and / or the host response to the infectious proteome and / or its subproteome, and / or the cancer proteome and / or its subproteome.

24. The method according to any one of claims 1 to 23, wherein the method includes identifying the presence and / or concentration and / or amount of one or more cancer proteomes and / or cancer subproteomes of interest in the sample.

25. The method according to any one of claims 1 to 24, wherein step (e) comprises comparing the measured label and / or amino acid concentration of each labeled amino acid type in the sample with the known label values ​​and / or amino acid concentrations of the same three or more amino acid types labeled in each sample of one or more proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes of interest at one or more concentrations, using a machine learning classifier.

26. A method for detecting cancer, which identifies the presence and / or concentration and / or amount of one or more target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes in a sample, wherein the method is a) Labeling three or more amino acid types in the sample, wherein the amino acid type is defined by the R group of the amino acid, b) Measuring the labeling of each labeled amino acid type in the sample, e) Identifying the presence and / or concentration and / or amount of one or more cancer-related target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes in the sample by comparing the measured label and / or amino acid concentration of each labeled amino acid type in the sample with known label values ​​and / or amino acid concentrations of the same three or more amino acid types labeled in each sample of one or more cancer-related target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes at one or more concentrations, or by using an n-dimensional space corresponding to n labeled amino acid types to compare the number of the amino acids of each labeled amino acid type in the sample with the number of known amino acids of the same three or more amino acid types labeled in the sample of one or more cancer-related target proteins, peptides, oligopeptides, polypeptides, protein complexes, subproteomes, or proteomes in the sample, The comparison described above is performed using an n-dimensional space corresponding to n types of labeled amino acid forms.

27. c) calculating the amino acid concentration of each labeled amino acid type from the measured labels and / or d) calculating the number of amino acids of each labeled amino acid type, the method according to any one of claims 1 to 26.

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