Tandem mass spectrometry procedures

Abstract

Method for data-independent tandem mass spectrometry (MS-MS) analysis comprising the following steps: ramping or stepping in small steps a first parent ion selection mass spectrometer (MS1) to transmit a parent ion mass window with a width of at least 10 amu (1.66054e-26 kg); Establishing rapid ion transfer through a collision cell (15, 35) to induce fragmentation of parent ions, either by axial gas flow or by an axial direct current (DC) field or by a propagating radio frequency (RF) wave; Receiving families of parent and fragment ions in an orthogonal accelerator (17, 37), frequent pulsing of the orthogonal accelerator (17, 37) with a sequence of time-coded pulses; Analyzing fragment ions in a multi-reflecting time-of-flight mass spectrometer; Collecting data that is representative of the families of ancestral and Fragment ions are detected on the multi-reflecting time-of-flight mass spectrometer in a data recording format; Decoding the sequence of time-coded pulses corresponding to the parent ion mass window to form fragment spectra based on a temporal correlation in the acquired data between fragment and parent masses; and Adjusting a scan time of the ramped or stepped operation of the parent ion selection mass spectrometer (MS1) based on a time profile of a chromatographic peak width in the acquired data obtained in a preceding chromatographic separation.

Description

[0001] Tandem mass spectrometry (MS-MS) can be used to identify multiple compounds in complex mixtures. In such applications, a mixture of analytes (analyte mixture) is ionized, a parent ion species is selected at a time in a first mass spectrometer (MS1), undergoes fragmentation, usually in a CID (collision-induced dissociation) cell, and the mass spectra of fragment ions are recorded in the second-stage mass spectrometer (MS2). Because the combination of parent and fragment ion masses m1-m2 is compound-specific, MS-MS analysis can detect ultratrace levels within the reach of the chemical matrices. Triple-quadrupole MS-MS (where a CID cell is considered the second quadrupole) is widely used for drug metabolite studies, where selected and predefined combinations of m1-m2 are monitored.Recently, MS-MS instruments using quadrupoles for MS1 and time-of-flight (TOF) for MS2 have become useful for characterizing complex mixtures such as proteome mixtures. In such analyses, the quadrupole selector can be scanned across the entire mass range (usually up to 1000 amu for systems using electrospray ESI sources) in an attempt to cover the maximum number of analyte compounds, while TOF systems are often used to acquire panoramic spectra.

[0002] When analyzing complex mixtures, such as a collection of up to a million different peptides from cell lysates, Q-TOF tandems are combined with liquid chromatography (LC). Chromatography can drastically reduce sample complexity for a short time, but hundreds and thousands of compounds still coelute simultaneously. In an MS-MS instrument, the underlying analysis is performed in a limited timeframe; a full mass range analysis is typically completed within 1-3 seconds.

[0003] LC-Q-TOF acquisition methods are being developed that pursue two general strategies. In one strategy, called data-dependent acquisition (DDA), a list of major parent peaks is generated when the mixture is analyzed without fragmentation. Then, the MS1 stage is stepped between parent masses, and fragmentation is turned on (by adjusting ion energy at the entrance of the CID cell) to generate a set of fragment spectra. This analysis can generally be limited by the ability to detect parent ions in the MS1 spectrum (which, for small compounds, is obscured by a rich chemical matrix), the number of channels tracked, and a relatively small dynamic range, due to simply not having time to acquire spectra for all parent ions.

[0004] In another data-independent strategy, the MS1 stage can be run stepwise across the entire mass range, while acquiring fragment spectra for each parent mass M1, but for a very limited residence time. For example, and without limitation, with a scan time of approximately one second, a mass span of approximately 1000 amu, and an MS1 ​​window of 3 amu (usually designed to observe an isotopic cluster), a residence time of approximately 3 ms is required to acquire MS-MS spectra for the individual mass window. The combination of the short residence time and low duty cycle of a conventional orthogonal TOF MS limits the dynamic range of analyzed compounds.Such an exemplary system generally requires rapid ion transfer through the CID cell (causing about 1 ms time loss for parent ion switching) and generally a rapidly controlled and synchronized power electronics and data acquisition system.

[0005] For the analysis of complex mixtures, prior art Q-TOF tandems can provide either only a limited number of identifications or only within a limited dynamic range. In one embodiment, the invention extends the dynamic range of analyzed compounds without limiting the list of parent masses, and does so in a data-independent and thus robust acquisition manner. WO 2012 / 035412 A2 discloses a system for storing ion spectra obtained using a tandem mass spectrometer. US 2010 0 286 927 A1 discloses a data-dependent acquisition system for mass spectrometers. WO 2010 / 136 780 A1 also relates to mass spectrometry. US 2005 / 0 242 279 A1 discloses a mass spectrometry system with a dynamic data acquisition procedure. A fast and sensitive tandem mass spectrometry analysis is known from GB 2 390 935 A.US 6166378 A describes a method for improving the signal-to-noise ratio using two mass spectrometers. WO 2004 / 046731 A2 discloses a method for analyzing amino acids, peptides, or proteins. EP 1 006 559 A2 relates to mass spectrometry including multiple mass analysis steps and a final analysis in a time-of-flight device. WO 99 / 30351 A1 provides a method and apparatus for selective collision-induced dissociation of a substance by resonance excitation of ions. WO 02 / 052259 A1 relates to methods for identifying polypeptides by simultaneously determining the mass of a subset of parent polypeptides from a population of polypeptides and the mass of fragments of the subset of parent polypeptides.WO 2011 / 143760 A1 discloses methods and systems for analyzing a peptide sample stream from a chromatography column using tandem mass spectroscopy. Finally, WO 2012 / 164378 A2 describes the use of systems and methods for bandpass filtering ions from a mass range.

[0006] According to the invention, a method according to claim 1 for data-independent tandem mass spectrometry (MS-MS) analysis is disclosed, comprising the following steps: ramping or stepping in small steps a first parent ion selection mass spectrometer (MS1) to transfer a parent ion mass window with a width of at least 10 amu (1.66054e-26 kg); establishing rapid ion transfer through a collision cell to induce fragmentation of parent ions, either by axial gas flow or by an axial direct current (DC) field or by a propagating radio frequency (RF) wave; receiving families of parent and fragment ions in an orthogonal accelerator, frequently pulsing the orthogonal accelerator with a sequence of time-coded pulses; analyzing fragment ions in a multi-reflecting time-of-flight mass spectrometer; acquiring data,representative of the families of parent and fragment ions, at the multi-reflecting time-of-flight mass spectrometer in a data recording format; decoding the sequence of time-coded pulses corresponding to the parent mass window to form fragment spectra based on a temporal correlation in the acquired data between fragment and parent masses; and adjusting a sampling time of the ramping or stepping operation of the parent ion selection mass spectrometer (MS1) based on a time profile of a chromatographic peak width of parent ions in the acquired data obtained in a preceding chromatographic separation. A method for data-independent MS-MS analysis is disclosed. The method comprises ramping or stepping in small steps through a wide (at least 10 amu) parent mass window in a first parent selection mass spectrometer (MS1).Providing rapid ion transfer through a collision cell, either by axial gas flow or by an axial DC field or by a propagating RF wave, frequently pulsing an orthogonal accelerator with a string of time-coded pulses, analyzing fragment ions in a multi-reflecting time-of-flight mass spectrometer, acquiring data in a data recording format, and decoding signal sequences corresponding to the entire parent mass scan so that fragment spectra are formed based on a temporal correlation between fragment and parent masses. BRIEF DESCRIPTION OF THE DRAWINGS

[0007] The accompanying drawings illustrate various embodiments of the present system and method and are incorporated herein by reference. The illustrated embodiments are merely examples of the present apparatus and method and do not limit the scope of the disclosure. Fig. 1 illustrates an exemplary spectrometry apparatus according to an embodiment; Fig. Figure 2 illustrates an implementation of a ramp-shaped data-independent analysis strategy; Fig. 3 illustrates an embodiment of a spectrometry device according to an embodiment; and Fig. Figure 4 illustrates a strategy for ramp-shaped data-independent analysis.

[0008] The details of one or more embodiments of the disclosure are set forth in the accompanying drawings and description below. Other aspects, features, and advantages will become apparent from the description and drawings, as well as from the claims. DETAILED DESCRIPTION

[0009] The following description of the various embodiments is merely exemplary and is in no way intended to limit the invention, its application, or uses. Based on the foregoing, it is generally understood that the nomenclature employed herein is for convenience only, and the terms used to describe the invention are to be interpreted in their broadest sense by one of ordinary skill in the art.

[0010] While specific system and process examples are discussed, the principles described can be applied in many ways to other suitable environments.

[0011] In one embodiment, the dynamic range of a data-independent MS-MS analysis can be improved by substantially continuously ramping (or stepping, in small steps) through a wide (at least 10 amu) parent mass window in a first parent-selected mass spectrometer (MS1), effecting rapid ion transfer through a collision cell, frequently pulsing an orthogonal accelerator with a sequence of time-encoded pulses, analyzing fragment ions in a multi-reflecting time-of-flight mass spectrometer, acquiring data in a data log format, and decoding signal sequences corresponding to the entire parent mass scan.

[0012] According to Fig. 1, an exemplary apparatus 11 comprises a front-end chromatograph 12 (LC or GC), an ion source 13 for sample ionization, an analytical quadrupole analyzer 14, a CID cell 15, a multi-reflecting analyzer 16 with an orthogonal accelerator 17 driven by a generator 18 with frequently coded pulses (frequently coded pulsing), and a decoding data system 19 fed with ion signals and receiving information about the trigger pulse timing. The output profiles 12p of the chromatograph 12 are expected to have a width of substantially approximately 5-10 seconds for LC and substantially approximately 1 second for GC. In one embodiment, the quadrupole mass spectrometer 14 is ramped up at a rate of about 1000 Th / s to briefly transmit a relatively wide (essentially about 10-20 Th) mass window for selecting parent ions as shown in diagram 14p.In one embodiment, parent ions can be injected into a collision cell at substantially about 20-50 eV energy to induce fragmentation. Consequently, at the output of the CID cell 15, families of parent and fragment ions appear correlated on a timescale of approximately 1 ms. Exemplary families are represented by profiles 15p, where sharp peaks generally correspond to an individual family and broader curves generally represent a much more slowly modulating profile of the chromatography peak. In one embodiment, the entire ion beam is fed substantially continuously into the orthogonal accelerator 17. In one embodiment, the accelerator 17 is pulsed in a coded manner at an average rate of substantially about 100 kHz, with most pulse intervals being unique so that the superimposed spectrum can be decoded in the decoder 19.

[0013] Fig. Figure 2 illustrates one embodiment of a ramped data-independent analysis strategy. The upper graph 21 represents a linear ramp from the RF amplitude. In one embodiment, the DC voltage of the analytical MS1 quadrupole is scanned and linked. However, compared to a high-resolution scan (e.g., R=M), one can use either (i) a slightly smaller ratio between RF and DC or (ii) an offset DC voltage to transmit the Th mass window, which is generally wider than one. In one embodiment, the offset or ratio determines the mass width of the window 23, which is expected to be used anywhere substantially from about 1 to 100 amu, and preferably substantially from about 10 to 20 amu, as shown in graph 22. Figure 24 shows hypothetical time profiles of parent ions at the output of the CID cell 15 and Figure 25 shows time profiles for the corresponding daughter ions.When setting up the appropriate CID cell, e.g., with an axial gas flow or with an axial DC gradient, the transfer time in the CID cell is expected to be much shorter compared to the width of profiles 24 and 26, so that the corresponding fragment profiles correlate strongly in time with the parent ion profiles. A mass-dependent delay is expected to be essentially around 100 to 200 µs, which can be calibrated experimentally and then taken into account in the correlation analysis. Graph 26 shows triggers of the OA, which basically demonstrates that a large number of frequently coded starts would occur in the parent emission profile. At a finer timescale (not shown), intervals between pulses are designed to be largely unambiguous, so that mass spectrum peaks do not systematically overlap and would allow mass spectrum decoding.Frequent coded pulsing significantly increases the duty cycle of MS-MS analysis (50-100 times) and simultaneously allows rapid tracking of time profiles 24 and 25.

[0014] An example will now be described. In one embodiment, the parent ion mass scan is performed in a quadrupole mass spectrometer with a total scan time of generally about one second. The quadrupole selector is designed to have a mass window of generally about 10 amu. Each individual parent ion mass is then scanned through the quadrupole analyzer for about 10 ms. Low mass resolution quadrupoles have an ion transmission close to unity. The extended transmission of parent ions can expand the dynamic range of the tandem analysis, resulting in an overlap of multiple parent ions (with a different mass-to-charge ratio). This can be resolved by analyzing the time profiles of individual parent masses, for example, by temporal correlation between parent and fragment ions as described below.Thus, rapid tracking of profiles 24 and 25 allows setup with extended time windows for parent transmission (which increases sensitivity) without sacrificing resolution of parent ion selection.

[0015] In one embodiment, for a given parent ion mass, the time profile after MS1 exhibits a gate shape with a rising and falling slope of approximately 0.5 amu. After passing through the CID cell with a typical transfer time of 1 ms, the profile slopes would become flat. Profiles of different fragment masses are likely to shift within a time of 1 ms, with the time shift correlated with the fragment mass and capable of being calibrated experimentally. A given ion family (a collection of parent ions with corresponding fragment ions) would arrive at the orthogonal accelerator within a time of approximately 10 ms, which would improve sensitivity compared to conventional MS-MS strategies with a shorter residence time of 1 ms.In one embodiment, the orthogonal accelerator is pulsed (clocked) with an average period of 10 µs while being time-encoded, improving the duty cycle (and thus sensitivity) by 50–100 times compared to standard high-resolution MR-TOF operation while also improving the speed of tracking family profiles. An exemplary time-encoding sequence can be expressed in terms of pulse number (i) and time as Ti=T1+T2*i*(i+1) / 2, where T1=10 µs, T2=10 ns, and i=0,1,2,...100. Such an encoding sequence is repeated approximately every 1 ms. Data at the MR-TOF detector is acquired in a so-called data-logging manner. The signal is stripped of zeros (sparse format) and each non-zero signal piece (splash) is recorded in such a way that information about the laboratory time (e.g.The data sets can be tracked by a series of parameters, such as the number of the current pulse sequence, time of flight corresponding to the signal splash start, and sequence of non-zero signal intensities. To separate adjacent splashes, an individual data set can be terminated with zero intensity. The flux of multiple data sets corresponding to such multiple splashes can then be analyzed in a multi-core CPU or GPU. For typical ion fluxes in tandem mass spectrometers at or below 100 million ions per second (160 pA current), the data flow is expected to pass through modern signal buses (e.g., up to 800 Mbyte / sec in 8-lane PCIe) and through GPU processing. It is important that the signal includes the laboratory time information so that time profiles can be obtained for each observed m / z species in MR-TOF spectra.

[0016] Since the typical time-of-flight in multi-reflectance mass spectrometers (MR-TOF) is on the order of 1 ms and trigger pulses are 100 times more frequent, the MR-TOF signal is heavily overlaid. To extract m / z information from coded spectra, a spectral coding method is applied that is based on reconstructing signal series with knowledge of trigger-pulse intervals. An exemplary coding-decoding method is disclosed in WO 2011 / 135477 A1, which is incorporated herein by reference in its entirety. In the present numerical example, the duration of the parent ion profile is approximately 10 ms and the average pulse period is approximately 10 µs, so the signal sequence would contain up to 1000 individual ion signals. According to our own studies, the decoding algorithm is expected to cover signal series containing only 10 to 20 ions per series.In one embodiment, rare overlaps between series can be discarded in a "logical analysis" step after reconstructing individual series. Thus, within the total flux of 1E+8 ions / sec and with 1E+6 ions allowed in 10 ms profiles, the minimum obtainable signal corresponds to approximately 10 ions. The minimum interpretable tandem mass spectrum is expected to be approximately 100 ions. The total dynamic range of a data-independent analysis for all parent masses is estimated to be 1E+4 per 1 second of analysis. The dynamic range of the entire LC-MS-MS analysis is expected to be approximately 10 times higher, considering a 10-fold repetition of an MS-MS scan with a typical LC peak width of 10 seconds.

[0017] In one embodiment, the decoding step obtains information about the detected flight times and precise mass-to-charge ratios of the fragment ions, and equally importantly, parent ion masses, since typical CID fragmentation is incomplete. In a collection of short-term observed peaks, parent ion mass peaks are distinguished as those peaks corresponding to the highest molecular weight, taking into account the charge state, which in turn is determined based on the isotope spacing. For example, doubly charged ions would have a spacing of 0.5 Th, triply charged ions a spacing of 0.33 Th. If mass components are known, parent ion peaks are determined, and information about corresponding individual signal splashes is also available, allowing their time profiles to be reconstructed.Then, the correspondence between parent and fragment ions must be derived using a laboratory time correlation, which means that corresponding fragments appear simultaneously with parent ions. Although multiple profiles are likely to partially overlap, the accuracy of the temporal correlation is expected to be approximately 10% of the profile width. In other words, the accuracy of the temporal correlation is expected to be on the order of 1 ms, i.e., corresponding to 1 Th of parent ion mass. Thus, although a wider mass window (e.g., 10 Th) is allowed, accompanied by a 10-fold improvement in signal intensity, the effective resolution of the parent ion detection is 1 Th.

[0018] At the effective 1 Th parent mass separation, and based on tracking LC profiles with an accuracy of at least 10% of the chromatography peak, the overall separation efficiency of the analysis is expected to be approximately 1E+6, i.e., sufficient for proteomic analysis, where a separation factor of 100-300 comes from LC separation, a 10-fold improvement comes from accurate tracking of LC profiles (with a full scan time of 1 second and a typical LC peak width of 10 seconds), and a factor of 1000 comes from parent mass separation. The separation efficiency can be further improved by interpreting so-called chimera spectra, where overlapped fragment spectra could still be interpreted while utilizing information on accurate masses of fragment ions, which are expected to be below 1 ppm with high-resolution MR-TOF spectrometry.

[0019] The described strategy can be optimized in several ways. First, the width of the allowed window can be adjusted based on the spectral and sample complexity, so that sufficient separation is achieved while maximizing the duty cycle of the parent separation in MS1. Second, the scan speed could be optimized based on the LC peak width. For example, the method can be applied to fast separations, such as CE. Third, the scan (ramp) speed can be varied during the scan based on the local parent mass population. For example, for peptide ions, the densest m / z region lies between 400 and 600 amu, which is formed by multiply charged peptide ions. Fourth, during the parent mass scan, the fragmentation energy (i.e.The M1 scan (i.e., the energy of ion injection into the CID cell) can be scanned at a much higher rate, so that the energy microscan occurs upon passage of a single parent mass window. Fifth, the average fragmentation energy can be scanned, so that the collision energy increases at a higher parent m / z. The M1 scan is also expected to be accompanied by a ramped lens voltage increase, such as from high-frequency ion guide voltages, for optimized transmission of a current m / z range of parent ions. Such voltages can be tuned in multiple elements in the region from the ion source, through the analytical quadrupole, and up to the collision cell.

[0020] Now with reference to Fig. 3, another exemplary device 31 comprises a front-end gas chromatograph 32, an accumulating ion source 33 for sample ionization, a time-of-flight separator 34, a CID cell 35, a multi-reflecting analyzer 36 with an orthogonal accelerator 37 driven by a generator 38 with frequently coded pulses, and a decoding data system 39 fed by ion signals for obtaining information about trigger pulse times. The output profiles 32p of the chromatograph 32 are expected to have a width of substantially about 1 second. In one embodiment, the ion source 33 is a closed-loop electron impact EI source capable of storing and pulse-ejecting parent ions by applying pulses to a repeller and extraction electrodes as described in WO 2012 / 024468 A2. An ion ejection period of about 30 µs is preferably chosen.In one embodiment, the time-of-flight separator 34 is a linear time-of-flight drift region 10-20 cm long, preferably including an electrostatic lens for spatial ion focusing. Parent ion selection occurs after time gate 34g at the entrance of the CID cell 35. The time gate window is preferably set to provide a scan with approximately 10 Th mass windows within a mass span of 100 Th, the latter of which correlates with the GC retention time (RT). The limited mass span is permissible because parent mass is known to partially correlate with the GC retention time. Preferably, the parent mass window is ramped at a rate of about 1000 Th / s to scan 100 Th mass window span in 0.1 second while briefly transmitting a relatively wide (essentially about 10-20 Th) mass window to select parent ions, as shown in diagram 35p.In one embodiment, parent ions can be injected into the CID cell 37 essentially with approximately 20-50 eV energy into a collision cell to induce fragmentation. In one embodiment, the CID cell 37 is filled with helium to minimize interference with the aforementioned EI source 33 and to allow a wider range of injection energies for relatively small parent ions of semi-volatile compounds typical for GC separation. Preferably, the CID cell 37 is heated to 200-250°C to prevent surface contamination by semi-volatile analyte. The CID cell is preferably equipped with additional electrodes 34a to form an axial DC field. Preferably, the aforementioned additional electrodes 34a have a double-wedge geometry to enable a linear potential distribution, as shown in the figure inset. The axial DC field accelerates the ion flow through the CID cell to 300-500 µs.Nevertheless, short (1.5 µs) ion packets entering the 30 µs period CID cell 37 are expected to be extended and smoothed in gas collisions to approximately 300 µs, thus converting periodic pulses into a quasi-continuous ion flow. Consequently, families of parent and fragment ions correlated at a timescale of approximately 300 µs appear at the output of the CID cell 35. Exemplary families are represented by profiles 35p, where sharp peaks generally correspond to an individual family and broader curves generally show a much more slowly modulating profile of the 1-second width chromatographic peak. In one embodiment, the total ion beam is fed essentially continuously (or more accurately, quasi-continuously) into the orthogonal accelerator 37.In one embodiment, the accelerator 37 is pulsed at an average rate of substantially about 100 kHz (10 µs pulse period) in a coded manner, with most pulse intervals being unique, so that the superimposed spectra can be decoded in the decoder 39.

[0021] Fig. Figure 4 illustrates another exemplary strategy of a ramp-shaped data-independent analysis for the device 31 of Fig.3. The upper graph 41 shows a linear ramp of the gate selector 35g time with a long time scale corresponding to a GC retention time RT (10-30 minutes), taking into account a limited parent mass range for the respective RT. Graph 42 represents a zoom view of graph 41 on a 100 ms time scale corresponding to the ramped increase of the parent selector mass. It contains several 30 µs microscans of the time gate 35g, with the time measured relative to periodic pulses of the EI source. The permitted time window of the time gate is preferably ramped to transfer the time window 43 corresponding to approximately 10 Th and 1.5 µs time windows. Preferably, the time gate span corresponds to a mass span of 50-100 Th, based on the GC retention time, in order to improve the strain selection duty cycle to 5-10%.Each specific parent mass is then admitted for approximately 5 ms of ramp time with a temporal resolution of 20 and a mass resolution of 10. Each specific parent mass is then admitted for 1.5 µs pulses with a 30 µs period and for approximately 150 source pulses. Due to the temporal spreading in the CID cell 35, the individual pulses would be smoothed to 5 ms time profiles. Figure 44 shows hypothetical time profiles of parent ions at the output of the CID cell 35, and Figure 45 shows time profiles for the corresponding daughter ions with characteristic 5 ms peak widths. With an axial DC gradient, the transfer time in the CID cell is far shorter than the width of profiles 24 and 26, so the corresponding fragment profiles would strongly correlate in time with parent ion profiles.A mass-dependent delay of essentially 200–300 µs is expected, which can be calibrated experimentally and then taken into account in the correlation analysis. Figure 26 shows triggers of the OA at the average 10 µs period, essentially demonstrating that a large number of frequently coded starts of the OA 37 would occur during the parent emission profile. At a finer timescale (not shown), intervals between pulses are designed to be largely unambiguous, so that mass spectrum peaks do not systematically overlap and would allow mass spectrum decoding. Frequently coded pulsing significantly increases the duty cycle of the MS-MS analysis (50–100 times).Frequently coded pulsing of the OA also results in rapid tracking of time profiles 44 and 45, enabling a parent-daughter correlation with approximately 1 Th accuracy, although wider (10 Th) gates for parent masses are allowed, further improving sensitivity. In summary, compared to conventional MS-MS with high-resolution MR-TOF, the expected overall gain in sensitivity is 1000-fold, with a factor of 3 coming from a correlating parent mass range with RT, a factor of 5 to 10 from the application of wide mass windows of 10 Th, and a factor of 50 to 100 from the application of frequently coded pulsing of the OA. The detection limit is expected to be in the low femtogram range, with a dynamic range up to 1E+6, achieved with high specificity of the analysis.

[0022] Various implementations of the systems and techniques described herein may be realized in digital electronic circuits, integrated circuits, specially designed ASICs (application-specific integrated circuits), computer hardware, firmware, software, and / or combinations thereof. These various implementations may include implementation in one or more computer programs that can be executed and / or interpreted on a programmable system that may include at least one programmable processor, which may be a special-purpose or general-purpose processor, connected to receive data and instructions from a memory system and to send data and instructions to a memory system, at least one input device, and at least one output device.

[0023] These computer programs (also known as programs, software, software applications, or code) contain machine instructions for a programmable processor and may be implemented in a high-level procedural and / or object-oriented programming language and / or in an assembly / machine language. As used herein, the terms "machine-readable medium" and "computer-readable medium" refer to any computer program product, apparatus, and / or device (e.g., magnetic disks, optical disks, memory, programmable logic devices (PLDs)) for providing a programmable processor with machine instructions and / or data, including a machine-readable medium that receives machine instructions as machine-readable signals. The term "machine-readable signal" refers to any signal for sending machine instructions and / or data to a programmable processor.

[0024] Implementations of the subject matter and functional operations described in this specification may be implemented in digital electronic circuits or in computer software, firmware, or hardware, including the structures disclosed in this specification and their structural equivalents, or in combinations of one or more thereof. Furthermore, the subject matter described in this specification may also be implemented as one or more computer program products, i.e., one or more modules of computer program instructions encoded on a computer-readable medium for execution by data processing devices or for controlling the operation thereof. The computer-readable medium may be a machine-readable storage device, a machine-readable storage substrate, a memory device, a composition of matter effecting a machine-readable propagated signal, or a combination of one or more thereof.The terms "data processing apparatus," "computing device," and "computing processor" encompass all devices, devices, and machines for processing data, including, for example, a programmable processor, a computer, or multiple processors or computers. In addition to hardware, the device may also contain code that creates an execution environment for the computer program in question, e.g., code that creates processor firmware, a protocol stack, a database management system, an operating system, or a combination of one or more thereof. A propagated signal is an artificially generated signal, e.g., a machine-generated electrical, optical, or electromagnetic signal, that is generated to encode information for transmission to a suitable receiving device.

[0025] A computer program (also known as an application, program, software, software application, script, or code) can be written in any form of programming language, including compiled or interpreted languages, and can be deployed in any form, including as a stand-alone program or as a module, component, subroutine, or other unit suitable for use in a computing environment. A computer program is not necessarily a file on a file system. A program may be stored in part of a file containing other programs or data (e.g., one or more scripts stored in a markup language document), in a single file dedicated to the program in question, or in multiple coordinated files (e.g., files storing one or more modules, subprograms, or pieces of code).A computer program can be used in such a way that it is executed on one computer or on several computers located at one location or distributed over several locations and connected to one another by a communications network.

[0026] The processes and logic sequences described in this specification can be executed by one or more programmable processors executing one or more computer programs to perform functions by acting on input data and generating outputs. The processes and logic sequences can also be executed and devices implemented as special-purpose logic circuits, e.g., an FPGA (field-programmable gate array) or an ASIC (application-specific integrated circuit).

[0027] Processors suitable for executing a computer program include, for example, both general-purpose and special-purpose microprocessors, as well as one or more processors of any type of digital computer. In general, a computer receives instructions and data from a read-only memory or a random access memory, or both. The essential elements of a computer are a processor for executing instructions, and one or more memory devices for storing instructions and data. In general, a computer also includes, or is operatively coupled to, receive data from or transfer data to, or both, one or more mass storage devices for storing data, e.g., magnetic disks, magneto-optical disks, or optical disks. However, a computer need not have such devices. In addition, a computer may be embedded in another device, e.g.,a mobile phone, a personal digital assistant (PDA), a mobile audio player, a GPS (Global Positioning System) receiver, to name just a few. Computer-readable media suitable for storing computer program instructions and data includes all forms of non-volatile memory, media, and memory devices, including, for example, semiconductor memory devices, e.g., EPROM, EEPROM, and flash memory devices; magnetic disks, e.g., internal hard disks or removable disks; magneto-optical disks; and CD-ROM and DVD-ROM disks. Processor and memory may be supplemented by, or integrated with, special-purpose logic circuitry.

[0028] To provide interaction with a user, one or more aspects of the disclosure may be implemented on a computer having a display device, e.g., a CRT (cathode ray tube), LCD (liquid crystal display) monitor, or a touch screen, for displaying information to the user, and optionally a keyboard and pointing device, e.g., a mouse or trackball, with which the user can provide input to the computer. Other types of devices may also be used to enable interaction with a user; e.g., feedback may be given to the user in any form of sensory feedback, e.g., visual feedback, audible feedback, or tactile feedback; and input from the user may be received in any form, including auditory, voice, or tactile input.Additionally, a computer may interact with a user by sending documents to and receiving documents from a device used by the user; for example, by sending web pages to a web browser on a client device of the user in response to requests received from the web browser.

[0029] One or more aspects of the disclosure may be implemented in a computing system that has a backend component, e.g., a data server, or that has a middleware component, e.g., an application server, or that has a frontend component, e.g., a client computer having a graphical user interface or a web browser through which a user can interact with an implementation of the subject matter described in this specification, or any combination of one or more of such backend, middleware, or frontend components. The components of the system may be connected to any form or medium of digital data communication, e.g., a communications network. Examples of communications networks include a local area network ("LAN") and a wide area network ("WAN"), an internetwork (e.g., the Internet), and peer-to-peer networks (e.g., ad hoc peer-to-peer networks).

[0030] The computing system may include clients and servers. A client and server are generally located remotely from each other and typically interact over a communications network. The relationship between client and server arises due to computer programs running on the respective computers, which have a client-server relationship with each other. In some implementations, a server transmits data (e.g., an HTML page) to a client device (e.g., for displaying data on and receiving user input from a user interacting with the client device). Data generated at the client device (e.g., as a result of user interaction) may be received by the client device at the server.

[0031] While this specification contains numerous specific details, these are not intended to limit the scope of the disclosure or what is claimed, but rather to describe features specific to particular implementations of the disclosure. Certain features described in this specification in connection with separate implementations may also be implemented in combination in a single implementation. Conversely, various features described in connection with a single implementation may also be implemented in multiple implementations separately or in any suitable subcombination.Furthermore, while features were described above as acting in certain combinations and even initially claimed as such, one or more features from a claimed combination may, in some cases, be removed from the combination and the claimed combination may be directed to a subcombination or a variation of a subcombination.

[0032] Likewise, while operations are described in a particular order in the drawings, this should not be understood to mean that it is necessary that such operations be performed in the particular order shown or in a sequential order, or that all of the illustrated operations be performed to achieve desirable results. In certain situations, multitasking and parallel processing may be advantageous. Furthermore, the separation of various system components in the embodiments described above should not be understood to mean that such separation is necessary in all embodiments, but rather to mean that the described program components and systems may generally be integrated together into a single software product or packaged into multiple software products.

[0033] A number of implementations have been described. However, it will be understood that various modifications may be made without departing from the spirit and scope of the disclosure. Accordingly, other implementations are within the scope of the following claims. For example, the acts recited in the claims may be performed in a different order while still achieving desirable results.

Claims

[1] Method for data-independent tandem mass spectrometry (MS-MS) analysis, which comprises the following steps: ramping or stepping in small steps a first parent ion selection mass spectrometer (MS1) to transmit a parent ion mass window with a width of at least 10 amu (1.66054e-26 kg); Establishing rapid ion transfer through a collision cell (15, 35) to induce fragmentation of parent ions, either by axial gas flow or by an axial direct current (DC) field or by a propagating radio frequency (RF) wave; Receiving families of parent and fragment ions in an orthogonal accelerator (17, 37), frequent pulsing of the orthogonal accelerator (17, 37) with a sequence of time-coded pulses; Analyzing fragment ions in a multi-reflecting time-of-flight mass spectrometer; Collecting data that is representative of the families of ancestral and Fragment ions are on the multi-reflecting time-of-flight mass spectrometer in a data recording format; Decoding the sequence of time-coded pulses corresponding to the parent ion mass window to form fragment spectra based on a temporal correlation in the acquired data between fragment and parent masses; and Adjusting a scan time of the ramped or stepped operation of the parent ion selection mass spectrometer (MS1) based on a time profile of a chromatographic peak width in the acquired data obtained in a preceding chromatographic separation. [2] The method of claim 1, further comprising the upstream chromatographic separation in a gas chromatography (12, 32) or liquid chromatography (12), wherein the scan time of the ramped or stepped operation of the parent ion selection mass spectrometer (MS1) is adjusted to be at least three times faster than the time profile of the chromatographic peak width, and wherein a mass span of the parent ion mass window is adjusted according to an expected mass span that correlates with the time profile of the chromatographic peak width. [3] The method of claim 1, wherein ramping or stepping the parent ion selection mass spectrometer (MS1) comprises ramping or stepping a quadrupole mass spectrometer (14) or a time-of-flight mass spectrometer (34) following a pulsed release of ion packets from an ion source (13, 33).

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