Identification of unknowns using a theoretical collision cross-section

Abstract

A method for mass spectrometry, comprising: Measuring one or more first ion mobility values, collision cross sections or interaction cross sections and one or more mass-to-charge ratios of one or more analyte ions, Generating an initial list of compounds that may be the one or more analyte ions, based on the one or more measured mass-to-charge ratios; calculating or estimating one or more secondary ion mobility values, collision cross sections, or Interaction cross sections of at least some of the compounds in the first list, and: (i) Generating a second reduced list of compounds by removing compounds from the first list if the difference between the one or more measured first ion mobility values, collision cross sections or interaction cross sections and the one or more calculated or estimated second ion mobility values, collision cross sections or interaction cross sections is greater than a certain amount, and / or (ii) Providing a probability value associated with the one or more compounds in the first list, representing a probability that the one or more compounds are the one or more analytes, and reducing the Probability value if the difference between one or more measured first ion mobility values, collision cross sections or interaction cross sections and one or more calculated or estimated second ion mobility values, collision cross sections or interaction cross sections is greater than a certain amount.

Description

Field of invention

[0001] The present invention relates generally to mass spectrometry and in particular to methods for mass spectrometry and to mass spectrometers. background

[0002] Mass spectrometry (“MS”) and tandem mass spectrometry (“MS-MS”) are well-established methods for identifying unknown compounds. Precise mass measurements of molecular ions and / or fragment ions can provide information regarding the possible elemental composition and functional groups present in an unknown compound. Comparing mass spectra with library spectra can help identify compounds or structurally related compounds. This information, combined with other techniques such as optical spectroscopy or NMR, can yield a high degree of specificity in compound identification. However, these methods alone can often lead to ambiguity among various candidate compounds assigned to the unknown compound.

[0003] WO 2011 / 128703 A1 deals with a method for identifying a sample compound, which includes calculating a theoretical value of the collision cross-section for each of two or more known compounds, measuring a value of the collision cross-section for the sample compound and comparing the measured value with the theoretical values.

[0004] It is desirable to provide an improved method for mass spectrometry. Summary

[0005] According to the invention, a method for mass spectrometry and a mass spectrometer with the features of the independent claims are proposed. According to one aspect, a method for mass spectrometry is provided, comprising: Experimentally determining or measuring one or more first ion mobility values, collision cross sections or interaction cross sections and one or more masses or one or more mass-to-charge ratios of one or more analyte ions; generating a first list of possible candidate compounds corresponding to the one or more analyte ions based on the one or more determined or measured masses or the one or more first mass-to-charge ratios; calculating, estimating or determining one or more second ion mobility values, collision cross sections or interaction cross sections of at least some of the candidate compounds in the first list; and either: (i) Generating a second reduced list of possible candidate compounds by filtering or removing candidate compounds from the first list if the difference between one or more experimentally determined or measured first ion mobility values, collision cross sections or interaction cross sections and one or more calculated, estimated or determined second ion mobility values, collision cross sections or interaction cross sections is greater than a certain amount, and / or (ii) Reducing a probability value assigned to one or more possible candidate compounds in the first list if the difference between one or more experimentally determined or measured first ion mobility values, collision cross sections or interaction cross sections and one or more calculated, estimated or determined second ion mobility values, collision cross sections or interaction cross sections is greater than a predetermined amount.

[0006] One embodiment relates to a mass spectrometry method in which the collision or interaction cross sections and the masses or mass-to-charge ratios of one or more analyte ions are experimentally determined or measured, and an initial list of possible candidate compounds is compiled based on the determined or measured masses or mass-to-charge ratios. A collision or interaction cross section can then be theoretically calculated, estimated, or determined for each candidate compound in the initial list. The theoretically calculated, estimated, or determined collision or interaction cross sections are then used to filter or remove candidate compounds from the initial list or to decrease one of the probability values ​​assigned to the one or more candidate compounds in the initial list.

[0007] In this way, confidence in the identification of the connections can be advantageously increased. For example, by theoretically calculating, estimating, or determining collision cross-sections in this manner, it is not necessary to rely on experimentally determined collision cross-section values.

[0008] Furthermore, this embodiment advantageously makes efficient use of computing power, since the collision or interaction cross-section is calculated, estimated, or determined only for those connections that are present in the initial list (i.e., those that have already been identified as potential matches). This means that the calculation, estimation, or determination can effectively be performed in real time, that is, during the experimental workflow or course of the experiment.

[0009] It will therefore be evident that an improved method for mass spectrometry will be provided.

[0010] According to one embodiment, the method further comprises: experimentally determining or measuring one or more first additional physicochemical or other properties of one or more analytes, calculating, estimating or determining one or more second additional physicochemical or other properties of at least some of the candidate compounds in the first list, and either: (i) Generating the second, reduced list of possible candidate compounds by filtering or removing candidate compounds from the first list based on the difference between one or more experimentally determined or measured first additional physicochemical or other properties and one or more calculated, estimated or determined second additional physicochemical or other properties and / or (ii) Reducing a probability value belonging to one or more possible candidate compounds in the first list on the basis of the difference between one or more experimentally determined or measured first additional physicochemical or other properties and one or more calculated, estimated or determined second additional physicochemical or other properties.

[0011] According to one embodiment, the one or more additional physicochemical or other properties include a tip shape, tip width, tip skew, number of tips and / or a tip kurtosis.

[0012] According to one embodiment, the method further comprises: ionizing a sample to generate the analyte ions, or ionizing a sample to generate first ions, and then fragmenting or allowing the first ions to act or react in order to generate the analyte ions.

[0013] According to one embodiment, the step of experimentally determining or measuring the one or more first masses or mass-to-charge ratios includes a mass analysis of the analytes.

[0014] According to one embodiment, the step of experimentally determining or measuring one or more first ion mobility values, collision cross sections or interaction cross sections includes a temporary separation of at least some of the analyte ions according to their ion mobility.

[0015] According to one embodiment, the analyte ions include ions generated by a sample under first conditions and ions generated by the sample under second, different conditions.

[0016] According to one embodiment, the first conditions comprise one or more first pre-ionization, ionization and / or post-ionization conditions, and the second distinct conditions comprise one or more second distinct pre-ionization, ionization and / or post-ionization conditions.

[0017] According to one embodiment, the first and / or second conditions are selected from the group consisting of: (i) the composition and / or concentration of a salt, doping agent, derivatizing agent, reagent, shifting reagent, supercharge reagent or charge-reducing reagent added to a liquid sample prior to ionization, (ii) the composition and / or concentration of a neutral gas, doping gas, derivatizing agent gas, reagent gas, shifting reagent gas, supercharge reagent gas or charge-reducing reagent gas added to a gaseous sample or a sample in the vapor phase prior to ionization, (iii) the composition and / or concentration of a neutral gas, a reactive gas, a doping gas, a derivatizing gas, a reagent gas, a shifting reagent gas, a supercharge reagent gas or a charge-reducing reagent gas designed to interact or react with the analyte ions after ionization, and (iv) the composition and / or concentration of doping ions, derivatizing ions, reagent ions, supercharge reagents or charge-reducing reagents designed to interact or react with the analyte ions after ionization.

[0018] According to one embodiment, the first and / or second conditions are selected from the group consisting of: (i) a condition which affects the charge state of the analytes ions, (ii) a condition which affects an energy level of the analytes ions, (iii) a condition which affects the kinetic energy of the analytes ions, (iv) a condition which affects the activation energy of analytes, and (v) a condition which affects the conformal form or property of the analytes.

[0019] According to one embodiment, the first and / or second conditions are selected from the group consisting of: (i) an ionization condition of an ion source, (ii) the type of ion source used for ionizing a sample, (iii) a voltage setting of an ion source, (iv) an ionization polarity of ions produced by an ion source, (v) a flow rate of a sample being delivered to an ion source, (vi) one or more liquid chromatography conditions of a liquid chromatography system, (vii) a composition of a liquid chromatography solution or solvent and (viii) a liquid chromatography flow rate.

[0020] According to one embodiment, the first and / or second conditions are selected from the group consisting of: (i) subjecting ions to a hydrogen-deuterium exchange, (ii) one or more hydrogen-deuterium exchange conditions, (iii) Subjecting ions to activation, photoactivation, dissociation or photodissociation, (iv) one or more dissociation, photodissociation, activation and / or photoactivation conditions, (v) Subjecting ions to heating or RF heating, (vi) one or more heating or RF heating conditions, (vii) Subjecting ions to electromagnetic irradiation, microwave irradiation or laser irradiation, (viii) one or more electromagnetic irradiation, microwave irradiation or laser irradiation conditions, (ix) Subjecting the ions to fragmentation or reaction and (x) one or more fragmentation or reaction conditions.

[0021] According to one embodiment, the step of calculating, estimating or determining one or more second ion mobility values, collision cross sections or interaction cross sections of at least some of the candidate compounds in the first list includes calculating one or more second ion mobility values, collision cross sections or interaction cross sections taking into account the first conditions and / or the second conditions.

[0022] According to one embodiment, the method further comprises: Determining a first ion mobility value, collision cross-section or interaction cross-section difference between the first ion mobility values, collision cross-sections or interaction cross-sections determined or measured for the ions produced by the sample under the first conditions and the ions produced by the sample under the second, different conditions. Determining a second ion mobility value, collision cross-section, or interaction cross-section difference between the second ion mobility values, collision cross-sections, or interaction cross-sections calculated, estimated, or determined for the ions produced by the sample under the first conditions and the ions produced by the sample under the second different conditions, and either: (i) Generating the second reduced list of possible candidate compounds by filtering or removing candidate compounds from the first list based on the difference between the first ion mobility value, collision cross-section or interaction cross-section difference and the second ion mobility value, collision cross-section or interaction cross-section difference, and / or (ii) Reducing a probability value associated with one or more possible candidate compounds in the first list, based on the difference between the first ion mobility value, collision cross section or interaction cross section difference and the second ion mobility value, collision cross section or interaction cross section difference.

[0023] According to one embodiment, the step of experimentally determining or measuring one or more first ion mobility values, collision cross sections or interaction cross sections comprises experimentally determining or measuring a first ion mobility value, collision cross section or interaction cross section of at least some of the analyte ions under first experimental conditions and experimentally determining or measuring a first ion mobility value, collision cross section or interaction cross section of at least some of the analyte ions under second, different experimental conditions.and / or the step of experimentally determining or measuring one or more masses or mass-to-charge ratios includes experimentally determining or measuring a mass or mass-to-charge ratio of at least some of the analytes under first experimental conditions and experimentally determining a mass or mass-to-charge ratio of at least some of the analytes under second, different experimental conditions.

[0024] According to one embodiment, the first experimental conditions and / or the second experimental conditions are selected from the group consisting of: (i) a voltage applied to an ion-optical component, (ii) a route taken by the analyte ions through part of the mass spectrometer, (iii) the transition time of analyte ions through a part of the mass spectrometer, (iv) one or more pressures within the mass spectrometer, (v) one or more temperatures within the mass spectrometer, (vi) the composition of a gas within the mass spectrometer and (vii) the strength of an electric field inside the mass spectrometer.

[0025] According to one embodiment, the first experimental conditions and / or the second experimental conditions are selected from the group consisting of: (i) the composition of an ion mobility separation or buffer gas, (ii) the composition of one or more additives, dopants and / or reagents added to an ion mobility separation or buffer gas, (iii) the flow rate and / or direction of an ion mobility separation or buffer gas, (iv) the pressure or density number of an ion mobility separation or buffer gas, (v) the temperature within an ion mobility separation device, (vi) the strength of an electric field within an ion mobility separation device, (vii) the distance traveled by ions within an ion mobility separation device, (viii) the residence time of ions within an ion mobility separation device, (ix) the initial width of an ion pulse introduced into an ion mobility separation device and (x) the speed, amplitude or repetition pattern of a traveling DC voltage wave within an ion mobility separation device.

[0026] According to one embodiment, the step of calculating, estimating or determining one or more second ion mobility values, collision cross sections or interaction cross sections of at least some of the candidate compounds in the first list includes calculating one or more second ion mobility values, collision cross sections or interaction cross sections taking into account the first experimental conditions and / or the second experimental conditions.

[0027] According to one embodiment, the method further comprises: determining a first ion mobility value, collision cross-section or interaction cross-section difference between the first ion mobility value, collision cross-section or interaction cross-section determined or measured under the first experimental conditions and the first ion mobility value, collision cross-section or interaction cross-section determined or measured under the second experimental conditions.

[0028] Determining a second ion mobility value, collision cross-section, or interaction cross-section difference between a second ion mobility value, collision cross-section, or interaction cross-section calculated, estimated, or determined using the first experimental conditions and a second ion mobility value, collision cross-section, or interaction cross-section calculated, estimated, or determined using the second experimental conditions, and either: (i) Generating the second reduced list of possible candidate compounds by filtering or removing candidate compounds from the first list based on the difference between the first ion mobility value, collision cross-section or interaction cross-section difference and the second ion mobility value, collision cross-section or interaction cross-section difference and / or (ii) Reducing a probability value associated with one or more possible candidate compounds in the first list, based on the difference between the first ion mobility value, collision cross section or interaction cross section difference and the second ion mobility value, collision cross section or interaction cross section difference.

[0029] According to one embodiment, the step of generating the first list of possible candidate compounds corresponding to the one or more analytes, based on the one or more determined or measured masses or mass-to-charge ratios, includes using a library search to generate the first list of possible candidate compounds.

[0030] According to one embodiment, the step of generating the first list of possible candidate compounds corresponding to the one or more analytes, based on the one or more determined or measured masses or mass-to-charge ratios, includes comparing one or more of the one or more determined or measured masses or mass-to-charge ratios with one or more library masses or mass-to-charge ratios.

[0031] According to one embodiment, the step of calculating, estimating or determining one or more second ion mobility values, collision cross sections or interaction cross sections includes: Determining a three-dimensional structure from at least some of the candidate compounds in the first list and Calculating one or more of the second ion mobility values, collision cross sections or interaction cross sections using the three-dimensional structure.

[0032] According to one embodiment, the step of calculating, estimating or determining one or more second ion mobility values, collision cross sections or interaction cross sections includes calculating the effects of electronic interactions of ions with a polar or polarizable ion mobility separation or buffer gas.

[0033] According to one aspect, a mass spectrometer is provided, including: a device arranged and suitable for experimentally determining or measuring one or more first ion mobility values, collision cross sections or interaction cross sections and one or more masses or mass-to-charge ratios of one or more analyte ions, and a control system arranged and suitable for this purpose. (i) to generate an initial list of possible candidate compounds corresponding to one or more analytes based on one or more determined or measured masses or mass-to-charge ratios, (ii) to calculate, estimate or determine one or more second ion mobility values, collision cross sections or interaction cross sections of at least some of the candidate compounds in the first list, and either: (iii) to generate a second reduced list of possible candidate compounds by filtering or removing candidate compounds from the first list if the difference between one or more experimentally determined or measured first ion mobility values, collision cross sections or interaction cross sections and one or more calculated, estimated or determined second ion mobility values, collision cross sections or interaction cross sections is greater than a certain amount, and / or (iv) to reduce a probability value belonging to one or more possible candidate compounds in the first list if the difference between the one or more experimentally determined or measured first ion mobility values, collision cross sections or interaction cross sections and the one or more calculated, estimated or determined second ion mobility values, collision cross sections or interaction cross sections is greater than a certain amount.

[0034] According to one embodiment, a theoretically calculated collision cross section (“CCS”) or interaction cross section for a candidate compound structure identified by mass spectrometry is compared with the measured collision cross section or interaction cross section of the ion mobility and used to filter a candidate list of possible compounds in order to add specificity to the identification of the unknown.

[0035] A list of candidate structures can be generated from mass spectral data and then filtered or classified based on a comparison of a theoretically calculated collision cross section (CCS) with a measured collision cross section (CCS). This adds a high degree of specificity to the elucidation of unknown compounds based on MS and ion mobility data.

[0036] This embodiment represents an improvement over known methods in which the collision cross-section (CCS) of target ions must be experimentally measured using pure synthesized standards of these targets. The experimental data are then used to confirm the presence of a target compound in a mixture.

[0037] The embodiment advantageously allows theoretical collision cross-section (“CCS”) or relative collision cross-section (“CCS”) measurements to be used to confirm the identity of an unknown compound without requiring standards of all proposed structures to be synthesized and measured.

[0038] According to one aspect, a method for mass spectrometry is provided, including: (a) Analyzing ions of an analyte or ions derived from an analyte using mass spectrometry and ion mobility under one or more different conditions to generate a mass-to-charge ratio and measured collision cross-section information, (b) based on at least the mass-to-charge ratio information, including a proposed elemental composition fragmentation pattern and a library search output, a candidate list of compounds proposed as the identity of the analyte is generated, (c) Calculating possible three-dimensional structures for each of the proposed candidates, including isometric structures for all possible ions that can be formed from the candidate compounds, in silico or by computer-aided simulation, (d) Calculating the collision cross-section or the interaction cross-section for each of the structures in silico and (e) Filtering the candidate list based on the calculated collision cross section to provide a more specific identification of the analyte.

[0039] The difference in the theoretical collision cross-section of the analyte under two or more physicochemical conditions can be compared with the experimentally determined collision cross-section under identical conditions to filter the candidate list.

[0040] According to another aspect, a mass spectrometer is provided, which includes a control system as described above.

[0041] According to one embodiment, the mass spectrometer can further comprise: (a) an ion source selected from the group consisting of: (i) an electrospray ionization (“ESI”) ion source, (ii) an atmospheric pressure photoionization (“APPI”) ion source, (iii) an atmospheric pressure chemical ionization (“APCI”) ion source, (iv) a matrix-assisted laser desorption ionization (“MALDI”) ion source, (v) a laser desorption ionization (“LDI”) ion source, (vi) an atmospheric pressure ionization (“API”) ion source, (vii) a desorption ionization on silicon (“DIOS”) ion source, (viii) an electron impact (“EI”) ion source, (ix) a chemical ionization (“CI”) ion source, (x) a field ionization (“FI”) ion source, (xi) a field desorption (“FD”) ion source, (xii) an inductively coupled plasma (“ICP”) ion source, (xiii) a fast atom bombardment (“FAB”) ion source (xiv) a liquid secondary ion mass spectrometry (“LSIMS”) ion source, (xv) a desorption electrospray ionization (“DESI”) ion source, (xvi) a radioactive nickel-63 ion source, (xvii) a matrix-assisted atmospheric pressure laser desorption ionization ion source, (xviii) a thermospray ion source, (xix) an atmospheric scanning glow discharge ionization (“ASGDI”) ion source, (xx) a glow discharge (“GD”) ion source, (xxi) an impactor ion source, (xxii) a real-time direct analysis (“DART”) ion source, (xxiii) a laser spray ionization (“LSI”) ion source, (xxiv) a sonic spray ionization (“SSI”) ion source, (xxv) a matrix-assisted inlet ionization (“MAII”) ion source, (xxvi) a solvent-assisted inlet ionization (“SAII”) ion source (xxvii) a desorption electrospray ionization (“DESI”) ion source and (xxviii) a laser ablation electrospray ionization (“LAESI”) ion source and / or (b) one or more continuous or pulsed ion sources and / or (c) one or more ion guides or conduits and / or (d) one or more ion mobility separation devices and / or one or more field-asymmetric ion mobility spectrometer devices and / or (e) one or more ion traps or one or more ion trap areas and / or (f) one or more collision, fragmentation or reaction cells selected from the group consisting of: (i) a collision-induced dissociation (“CID”) fragmentation device, (ii) a surface-induced dissociation (“SID”) fragmentation device, (iii) an electron transfer dissociation (“ETD”) fragmentation device, (iv) an electron capture dissociation (“ECD”) fragmentation device, (v) an electron collision or impact dissociation fragmentation device, (vi) a photoinduced dissociation (“PID”) fragmentation device, (vii) a laser-induced dissociation fragmentation device, (viii) an infrared radiation-induced dissociation device, (ix) a dissociation device induced by ultraviolet radiation, (x) a nozzle wiper interface fragmentation device, (xi) a fragmentation device in a source, (xii) a collision-induced dissociation fragmentation device in a source, (xiii) a thermal or temperature source fragmentation device, (xiv) a fragmentation device induced by an electric field, (xv) a fragmentation device induced by a magnetic field, (xvi) an enzyme digestion or enzyme degradation fragmentation device, (xvii) an ion-ion reaction fragmentation device, (xviii) an ion-molecule reaction fragmentation device, (xix) an ion-atom reaction fragmentation device, (xx) an ion-metastable ion reaction fragmentation device, (xxi) an ion-metastable molecule reaction fragmentation device, (xxii) an ion-metastable atom reaction fragmentation device, (xxiii) an ion-ion reaction device for reacting ions to form adducts or productions, (xxiv) an ion-molecule reaction device for reacting ions to form adducts or productions, (xxv) an ion-atom reaction device for reacting ions to form adducts or productions, (xxvi) an ion-metastable ion reaction device for reacting ions to form adducts or productions, (xxvii) an ion-metastable molecule reaction device for reacting ions to form adducts or productions, (xxviii) an ion-metastable atom reaction device for reacting ions to form adducts or productions and (xxix) an electron ionization dissociation (“EID”) fragmentation device and / or (g) a mass analyzer selected from the group consisting of: (i) a quadrupole mass analyzer, (ii) a 2D or linear quadrupole mass analyzer, (iii) a Paul or 3D quadrupole mass analyzer, (iv) a Penning trap mass analyzer, (v) an ion trap mass analyzer, (vi) a magnetic sector mass analyzer, (vii) an ion cyclotron resonance (“ICR”) mass analyzer, (viii) a Fourier transform ion cyclotron resonance (“FTICR”) mass analyzer, (ix) an electrostatic mass analyzer designed to generate an electrostatic field having a quadro-logarithmic potential distribution, (x) an electrostatic Fourier transform mass analyzer, (xi) a Fourier transform mass analyzer, (xii) a time-of-flight mass analyzer, (xiii) an orthogonal acceleration time-mass analyzer, and (xiv) a linear acceleration-time-mass analyzer and / or (h) one or more energy analyzers or electrostatic energy analyzers and / or (i) one or more ion detectors and / or (j) one or more mass filters selected from the group consisting of: (i) a quadrupole mass filter, (ii) a 2D or linear quadrupole ion trap, (iii) a Paul or 3D quadrupole ion trap, (iv) Penning ion trap, (v) an ion trap, (vi) a magnetic sector mass filter, (vii) a time-of-flight mass filter and (viii) a Vienna filter and / or (k) a device or ion gate for pulsing ions and / or (l) a device for converting a substantially continuous ion beam into a pulsed ion beam.

[0042] The mass spectrometer may also include either: (i) a C-trap and a mass analyzer comprising an outer drum-like electrode and a coaxial inner spindle-like electrode forming an electrostatic field with a quadro-logarithmic potential distribution, wherein in a first operating mode ions are transferred to the C-trap and then injected into the mass analyzer, and wherein in a second operating mode ions are transferred to the C-trap and then to a collision cell or an electron transfer dissociation device, wherein at least some ions are fragmented into fragment ions, and wherein the fragment ions are then transferred to the C-trap before being injected into the mass analyzer, and / or (ii) a stacked ring ion guide comprising a plurality of electrodes, each having an opening through which ions are transferred in use, and in which the distance between the electrodes increases over the length of the ion path, and in which the openings in the electrodes in an upstream section of the ion guide have a first diameter, and in which the openings in the electrodes in a downstream section of the ion guide have a second diameter which is smaller than the first diameter, and in which opposite phases of an alternating or RF voltage are applied in use to successive electrodes.

[0043] According to one embodiment, the mass spectrometer may further comprise a device that is arranged and designed to apply an alternating or RF voltage to the electrodes. The alternating or RF voltage may have an amplitude selected from the group consisting of: (i) <50V Spitze-Spitze , (ii) 50 to 100V Spitze-Spitze , (iii) 100 to 150V Spitze-Spitze , (iv) 150-200V Spitze-Spitze , (v) 200-250V Spitze-Spitze , (vi) 250-300V Spitze-Spitze , (vii) 300-350V Spitze-Spitze , (viii) 350-400V Spitze-Spitze , (ix) 400-450V Spitze-Spitze , (x) 450-500V Spitze-Spitze , and (xi) >500V Spitze-Spitze .

[0044] The alternating or RF voltage can have a frequency selected from the group consisting of: (i) <100kHz, (ii) 100-200kHz (iii) 200-300kHz, (iv) 300–400kHz, (v) 400-500kHz, (vi) 0.5–1.0MHz, (vii) 1.0–1.5MHz, (viii) 1.5–2.0MHz (ix) 2.0–2.5MHz, (x) 2.5-3.0MHz, (xi) 3.0–3.5MHz, (xii) 3.5–4.0MHz, (xiii) 4.0–4.5MHz, (xiv) 4.5-5.0MHz, (xv) 5.0-5.5MHz, (xvi) 5.5-6.0MHz, (xvii) 6.0-6.5MHz, (xviii) 6.5-7.0MHz, (xix) 7.0-7.5MHz, (xx) 7.5-8.0MHz, (xxi) 8.0-8.5MHz, (xxii) 8.5-9.0MHz, (xxiii) 9.0-9.5MHz, (xxiv) 9.5-10.0MHz and (xxv) >10.0MHz.

[0045] The mass spectrometer may also include a chromatography or other separation device upstream of an ion source. According to one embodiment, the chromatography separation device comprises a liquid chromatography or gas chromatography device. According to another embodiment, the separation device may include: (i) a capillary electrophoresis (“CE”) separation device, (ii) a capillary electrochromatography (“CEC”) separation device, (iii) an essentially solid ceramic-based multilayer microfluidic substrate (“ceramic tile”) separating device or (iv) a chromatographic separation device for a supercritical fluid.

[0046] The mass spectrometer may include a chromatography detector.

[0047] The chromatography detector may include a destructive chromatography detector selected from the group consisting of: (i) a flame ionization detector (“FID”), (ii) an aerosol-based detector or a nanoquantity analyte detector (“NQAD”), (iii) a photometric flame detector (FPD), (iv) an atomic emission detector (AED), (v) a nitrogen-phosphorus detector (“NPD”) and (vi) an evaporating light scattering detector (“ELSD”).

[0048] Additionally or alternatively, the chromatography detector may include a non-destructive chromatography detector, which may be selected from the group consisting of: (i) a fixed or variable wavelength UV detector, (ii) a thermal conductivity detector (“TCD”), (iii) a fluorescence detector, (iv) an electron capture detector (“ECD”), (v) a conductivity monitor, (vi) a photoionization detector (“PID”), (vii) a refractive index detector (“RID”), (viii) a radio waveform detector and (ix) a chiral detector.

[0049] Ion guidance can be maintained at a pressure selected from the group consisting of: (i) <0.0001mbar, (ii) 0.0001-0.001mbar, (iii) 0.001-0.01 mbar, (iv) 0.01-0.1 mbar, (v) 0.1-1mbar, (vi) 1-10mbar, (vii) 10-100 mbar, (viii) 100-1000 mbar and (ix) >1000mbar.

[0050] According to one embodiment, analyte ions can be subjected to electron transfer dissociation (“ETD”) fragmentation in an electron transfer dissociation fragmentation device. The analyte ions can be caused to interact with ETD reagents within an ion guide or fragmentation device.

[0051] According to one embodiment, in order to effect electron transfer dissociation, either: (a) Analyzes fragmented or induced to dissociate and form product or fragment ions upon interaction with reagents, and / or (b) Transfer electrons from one or more reagent anions or negatively charged ions to one or more of a plurality of charged analyte cations or positively charged ions, whereupon at least some of the plurality of charged analyte cations or positively charged ions are induced to dissociate and form product or fragment ions, and / or (c) Analyte ions fragmented or induced to dissociate and form product or fragment ions upon interaction with neutral reagent gas molecules or atoms or a nonionic reagent gas, and / or (d) Transfer electrons from one or more neutral, nonionic or uncharged base gases or vapors to one or more of a plurality of charged analyte ions or positively charged ions, whereupon at least some of the plurality of charged analyte cations or positively charged ions are induced to dissociate and form product or fragment ions, and / or (e) Transfer electrons from one or more neutral, non-ionic or uncharged superbase reagent gases or vapors to one or more of the majority of charged analyte cations or positively charged ions, whereupon at least some of the majority of charged analyte cations or positively charged ions are induced to dissociate and form product or fragment ions, and / or (f) Transfer electrons from one or more neutral, non-ionic or uncharged alkali metal gases or vapors to one or more of the majority of charged analyte cations or positively charged ions, whereupon at least some of the majority of charged analyte cations or positively charged ions are induced to dissociate and form product or fragment ions, and / or (g) Transferring electrons from one or more neutral, non-ionic or uncharged gases, vapors or atoms to one or more of a plurality of charged analyte cations or positively charged ions, whereupon at least some of the plurality of charged analyte cations or positively charged ions are induced to dissociate and form product or fragment ions, wherein the one or more neutral, non-ionic or uncharged gases, vapors or atoms are selected from the group consisting of: (i) sodium vapor or atoms, (ii) lithium vapor or atoms, (iii) potassium vapor or atoms, (iv) rubidium vapor or atoms, (v) cesium vapor or atoms, (vi) Francione vapor or atoms, (vii) C 60 -vapor or atoms and (viii) Magnesium vapor or atoms.

[0052] The multiply charged analyte cations or positively charged ions can include peptides, polypeptides, proteins, or biomolecules.

[0053] According to one embodiment, in order to effect electron transfer dissociation, (a) Reagent anions or negatively charged ions derived from a polyaromatic hydrocarbon or a substituted polyaromatic hydrocarbon and / or (b) the reagent anions or negatively charged ions derived from the group consisting of: (i) Antrhracenes, (ii) 9,10 Diphenyl-anthracene, (iii) Naphthalenes, (iv) Fluorine, (v) Phenathrene, (vi) Pyrenees, (vii) Fluoranthene, (viii) Chrysen, (ix) Triphenylene, (x) Perylene, (xi) Acridine, (xii) 2,2' Dipyridyl, (xiii) 2,2' Biquinoline, (xiv) 9-anthracenecarboninitrile, (xv) Dibenzothiophene, (xvi) 1,10'-Phenanthroline, (xvii) 9' Anthracene carbonitrile and (xviii) anthraquinone and / or (c) the reagent ions or negatively charged ions include azobenzene anions or azobenzene radical anions.

[0054] According to one embodiment, the process or method of electron transfer dissociation fragmentation comprises an interaction of analyte ions with reagent ions, wherein the reagent ions include dicyanobenzene, 4-nitrotoluene or azulene. Brief description of the drawings

[0055] Several exemplary embodiments will now be described, merely as examples and with reference to the accompanying drawings, in which Fig. 1 shows a flowchart illustrating an exemplary implementation, and Fig. 2 shows a flowchart illustrating a further example. Detailed description

[0056] One embodiment is directed to a method in which one or more first ion mobility values, collision cross sections or interaction cross sections and one or more masses or mass-to-charge ratios of one or more analyte ions are experimentally determined or measured, and a first list of possible candidate compounds corresponding to the one or more analyte ions is generated on the basis of the one or more determined or measured masses or mass-to-charge ratios.

[0057] One or more second ion mobility values, collision cross sections, or interaction cross sections of at least some of the candidate compounds in the first list can then be theoretically calculated, for example, by using the mass spectrometer's control system, and they can be used during the experimental workflow or process. A second, reduced list of possible candidate compounds can be generated by filtering or removing candidate compounds from the first list based on the difference between the one or more experimentally determined or measured first ion mobility values, collision cross sections, or interaction cross sections and the one or more calculated, estimated, or determined second ion mobility values, collision cross sections, or interaction cross sections, or a probability value.The value belonging to one or more possible candidate compounds in the first list is increased, decreased, or left unchanged based on the difference between one or more experimentally determined or measured first ion mobility values, collision cross sections, or interaction cross sections and one or more calculated, estimated determined second ion mobility values, collision cross sections, or interaction cross sections.

[0058] Ion mobility can provide fundamental information regarding the size and shape of an ion in the gas phase, yielding a measurement of a collision cross section (CCS). Given a proposed compound identity, three-dimensional gas-phase structures can be theoretically calculated from the ions formed by the compound. Molecular mechanisms and quantum chemical modeling techniques can be applied to accomplish this. Commercially available software, such as a Gaussian model (www.gaussian.com), can be used for this purpose. According to one embodiment, these structures can be calculated for a variety of different experimental conditions, such as drift gas compositions, and for a variety of positional isomers, stereoisomers, protomers, chiral isomers, etc., of the compound.These isomers all have the same elemental composition and are therefore difficult to identify by mass spectrometry alone.

[0059] Once structures have been proposed, the collision cross-section can be calculated using software such as MobCal from Indiana University. Reference is made to: AAShvartsburg and MF Jarrold, An Exact Hard Spheres Scattering Model for the Mobilities of Polyatomic Ions, Chem. Phys. Lett. 1996, 261, 86-91.

[0060] A method for the theoretical calculation of collision cross sections for organometallic compounds is disclosed in Rapid Commun. Mass Spectrom. 2009, 23: 3563-3569, “Use of ion mobility mass spectrometry and a collision cross section algorithm to study an organometallic ruthenium anticancer complex and its adducts with a DNA oligonucleotide.” The purpose of this paper is to understand the structure of these compounds rather than to assist in the identification of unknown compounds; however, the applied methods for the theoretical calculation of a collision cross section (“CCS”) are applicable to and can be used in embodiments of the present disclosure.

[0061] Other approaches can be employed, including estimating the effect on the measured collision cross-section of long-range interactions between the ion and the neutral drift gas, for example, to calculate an "interaction cross-section" in effect. These effects can be caused by the presence of a polarizable drift gas or pulsable drift media containing gas-phase neutral elements with a permanent dipole moment. The interaction of polarizable or polar neutral elements with ions depends on the electronic structure of the ions (local or mass dipole moments, etc.), which can be highly specific for a given structure.

[0062] According to one embodiment, the calculated collision cross-section (“CCS”) is compared with the measured collision cross-section (“CCS”) and used to filter a candidate list of possible connections in order to add specificity to the identification of unknown connections and / or to add additional confidence to the identification of connections.

[0063] According to one embodiment, isomeric forms of unknown compounds can also be identified. If more than one isomeric form is present, for example, several ion mobility peaks with the same elemental composition and exact mass, and often very similar fragmentation patterns, can be experimentally generated. The calculated absolute or relative collision cross-section (CCS) values ​​can be compared with the measured collision cross-section (CCS) values ​​and the order in which these peaks elute from an ion mobility separator, and they can be used to assign and relatively quantify the different isomeric forms.

[0064] According to one embodiment, the presence or absence of these isomeric forms can itself be used to add specificity to the identification of the analyte in conjunction with the theoretical modeling.

[0065] For example, protomers (or ions containing other charge carriers that can be localized to more than one site on the ion) are another form of isomer that can be very specific for certain candidate compounds, and they can be used in one embodiment to aid identification.

[0066] According to one embodiment, in order to add even more specificity to the method, the mass-to-load ratio and the collision cross-section (“CCS”) can be measured under different conditions, and the difference between the calculated collision cross-section (“CCS”) and the measured collision cross-section (“CCS”) is compared.

[0067] According to one embodiment, an unknown composition can be analyzed using two or more drift gas mixtures, and the difference in the collision cross-section (“CCS”), determined experimentally and theoretically, can be compared.

[0068] Polar or polarizable drift (buffer) gases, or drift gases containing polar dopants, can be used to provide drift time shifts that are highly specific for a given ionic structure. This is due to extensive electronic interactions between the drift media and the analytes, which are specific to both the electronic structure of the analyte ion and the drift media molecules.

[0069] Theoretical calculations can be used to provide the absolute collision cross-section (CCS) or interaction cross-section and / or the magnitude of an expected displacement in the apparent collision cross-section (CCS) in various drift media. This information can be used to add specificity to connection identification.

[0070] Additionally or alternatively, in one embodiment the analyte ion can be modified, for example by changing the solution, and / or the gas phase chemistry can allow two or more independent measurements of the mass-to-charge ratio and the ion mobility for the same unknown compound.

[0071] According to one embodiment, for the same analyte, the collision cross section (“CCS”) of a protonated ion can be very different from that of a transformed ion or an ion with a different charge carrier or adduct or derivatization modification. This change may be related to the stereochemistry or the electronic structure of the ion, and again it is the experimentally observed collision cross section (“CCS”) difference that can be compared with the theoretically calculated difference to add specificity to the identification of the unknown compound.

[0072] According to one embodiment, activating an ion to increase its internal temperature by an arbitrary or known amount can induce unfolding or a transition between conformational states. In another embodiment, lasers or other energy sources can be used to excite ions before and / or during ion mobility separation. The change in the apparent collision cross-section (CCS) can be compared to a theoretically calculated value, for example, at the increased temperature, to add more specificity to analyte identification.

[0073] According to one embodiment, charging and / or charge reduction techniques can be applied to change the charge state of the ion; they can make it possible to compare two experimental and two theoretical collision cross section (“CCS”) values ​​based on calculated candidate structures.

[0074] In some cases, the same species can exist in more than one charge state. The difference in the experimental and theoretically calculated collision cross section (CCS) for candidate compounds in these charge states can be used in a single experiment to filter the candidate list.

[0075] Fig. Figure 1 shows a flowchart illustrating an exemplary implementation. In step 1, analyte ions are analyzed, for example, using mass spectrometry and ion mobility spectrometry. The analyte can be introduced directly into an analyzer or via a chromatographic separation device. The mass spectrometry and ion mobility devices can be separate instruments or integrated within the same instrument, in which case a nested dataset of ion mobility versus mass-to-charge ratio can be generated.

[0076] In steps 2 and 3, both the mass-to-charge ratio and the mobility collision cross-section (CCS) for the unknown analyte can be recorded. Depending on various embodiments, mass spectrometry (MS) or tandem mass spectrometry (MS-MS) spectral data, or data with further isolation and fragmentation (MS) stages, can be recorded.

[0077] In step 4, a list of candidate compounds can be generated using mass-to-charge ratio information. This can be done by considering possible elementary compounds based on accurate mass measurements and / or one or more library search outputs. The list may include compounds or isomers of compounds that are consistent with the mass-to-charge ratio information and that could correspond to the unknown analyte.

[0078] Thus, according to one embodiment, one or more accurate mass or mass-to-charge ratio measurements are used to generate a restricted list of possible elemental compounds that can be ordered by isotope ratio calculations (for example, based on the proposed elemental composition).

[0079] This information, along with any other data (such as fragment ion intensity, precise mass, isotopic ratios, etc.), can then be fed into a library to generate candidate structures. This means that, according to one embodiment, the first list of (plausible) candidate structures can be determined by using one or more precise masses or mass-to-charge ratios and one or more possible elemental compositions, together with chemical knowledge, for example, to predict plausible functional groups, substructures, and adducts.

[0080] In step 5, a theoretical collision cross-section value can be calculated for each candidate connection using the methods described above. In step 6, the calculated collision cross-section value can then be compared with the measured collision cross-section value, and the difference between these two values ​​can be used to either filter or classify the candidate list. According to one embodiment, this can be done by excluding connections that have a theoretical collision cross-section (CCS) that differs significantly from the measured collision cross-section (CCS), and / or by ordering or classifying the list of candidates solely according to the collision cross-section (CCS), and / or by combining the collision cross-section (CCS) and mass-to-load ratio information.

[0081] Fig. Figure 2 shows another embodiment. The embodiment of Fig. 2 is the one in Fig. The embodiment shown in Figure 1 is similar. However, in this embodiment, the mass-to-charge ratio and the collision cross-section (“CCS”) for the same analyte are measured under two separate known conditions. According to one embodiment, for example, the same analyte can be measured with different charge carriers and / or with a different mobility-separation drift gas.

[0082] Thus, in steps 1a and 1b, a compound can be analyzed under two or more different pre-ionization, ionization, post-ionization, and / or experimental or measurement conditions. In steps 2a, 2b, 3a, and 3b, two or more sets of mass-to-charge ratio and collision cross-section (CCS) data are / can be recorded, and candidate compounds can be suggested based on the mass-to-charge ratio data (step 4).

[0083] A theoretical collision cross section (CCS) under these two different conditions can be calculated in steps 5a and 5b, and it can be compared with the measured collision cross section (CCS) values ​​under the corresponding condition. These two values ​​can then be used, as described above, to filter or classify the candidate connection list in steps 6a and 6b. The final filtered list is generated in step 7.

[0084] After a theoretical collision cross section or interaction cross section for a given ion structure has been calculated under a given set of conditions in various embodiments, it can be added to a database of theoretical cross sections and used to check the candidate structures without requiring a recalculation of the theoretical collision cross section (“CCS”) or the interaction cross section.

[0085] In one embodiment, a mass or mass-to-charge ratio difference and / or an ion mobility, collision cross-section, or interaction cross-section difference between ions generated or measured under different analytical conditions can be used to filter or classify the first list. In particular, according to one embodiment, the drift time difference of analyte ions that are caused to temporarily separate in the presence of buffer gases of different compositions can be measured and calculated and used to filter or classify the first list. This approach according to one embodiment is particularly advantageous in that it is significantly more robust to changes in the conditions or states of the ion mobility separation device than using a measurement of the absolute drift time.As a result, the procedure according to this embodiment leads to a significant improvement in precision and accuracy.

[0086] According to one embodiment, one or more additional physicochemical or other properties of the one or more analyte ions, such as ion mobility peak shape, ion mobility peak width, ion mobility peak tilt, number of ion mobility peaks, and / or ion mobility peak kurtosis, can also be calculated and experimentally determined or measured in a manner as described above and then used to filter the initial list or to modify the one or more likely values. For example, the shape and number of ion mobility peaks associated with each analyte ion can be used to aid characterization.This can be applied to techniques such as hydrogen-deuterium exchange, where the (mass-to-charge ratio) isotope pattern between deuterated and non-deuterated samples can be compared to work out how many exchangeable hydrogen atoms are in the sample.

[0087] In one embodiment, properties of one or more experimentally determined or measured ion peaks, such as width, tilt, or kurtosis, can be determined, for example, by applying a peak shape fitting. The corresponding theoretical values ​​can be calculated, for example, by considering them in the device parameters and states (resolution, etc.) in the calculations, in order to determine one or more expected peak shapes.

Claims

[1] A method for mass spectrometry comprising: Measuring one or more first ion mobility values, collision cross sections or interaction cross sections and one or more mass-to-charge ratios of one or more analyte ions, Generating an initial list of compounds that may be the one or more analyte ions, based on the one or more measured mass-to-charge ratios; calculating or estimating one or more secondary ion mobility values, collision cross sections, or Interaction cross sections of at least some of the compounds in the first list, and: (i) Generating a second reduced list of compounds by removing compounds from the first list if the difference between the one or more measured first ion mobility values, collision cross sections or interaction cross sections and the one or more calculated or estimated second ion mobility values, collision cross sections or interaction cross sections is greater than a certain amount, and / or (ii) Providing a probability value associated with the one or more compounds in the first list, representing a probability that the one or more compounds are the one or more analytes, and reducing the Probability value if the difference between one or more measured first ion mobility values, collision cross sections or interaction cross sections and one or more calculated or estimated second ion mobility values, collision cross sections or interaction cross sections is greater than a certain amount. [2] A method as claimed in claim 1, further comprising: Measuring one or more first additional physicochemical or other properties of one or more analyte ions, calculating or estimating one or more second additional physicochemical or other properties of at least some of the compounds in the first list, and: (i) Generating the second, reduced list of compounds by removing compounds from the first list based on the difference between the one or more measured first additional physicochemical or other properties and the one or more calculated or estimated second additional physicochemical or other properties and / or (ii) Reducing the probability value attributable to the one or more compounds in the first list on the basis of the difference between the one or more measured first additional physicochemical or other properties and the one or more calculated or estimated second additional physicochemical or other properties. [3] A method as claimed in claim 2, wherein the one or more additional physicochemical or other properties include a tip shape, tip width, tip tilt, number of tips and / or tip kurtosis. [4] A method as claimed in any preceding claim, further comprising: Ionizing a sample to generate the analyte ions, or ionizing a sample to generate initial ions, and then fragmenting or reacting the initial ions to generate the analyte ions. [5] A method as claimed in any preceding claim, wherein the step of measuring one or more first mass-to-charge ratios comprises a mass analysis of the analytes. [6] A method as claimed in any preceding claim, wherein the step of measuring one or more first ion mobility values, collision cross sections or interaction cross sections comprises a temporary separation of at least some of the analyte ions according to their ion mobility. [7] A method as claimed in any preceding claim, wherein the analyte ions comprise ions produced by a sample under first conditions and ions produced by the sample under second, different conditions. [8] A method as claimed in claim 7, wherein the first conditions comprise one or more first pre-ionization, ionization and / or post-ionization conditions and the second distinct conditions comprise one or more second distinct pre-ionization, ionization and / or post-ionization conditions. [9] A method as claimed in claim 7 or 8, wherein the first and / or second conditions are selected from the group consisting of: (i) the composition and / or concentration of a salt, doping agent, derivatizing agent, reagent, shifting reagent, supercharge reagent or charge-reducing agent added to a liquid sample prior to ionization, (ii) the composition and / or concentration of a neutral gas, doping gas, derivatizing agent gas, reagent gas, shifting reagent gas, supercharge reagent gas or charge-reducing reagent gas added to a gaseous sample or a sample in the vapor phase prior to ionization, (iii) the composition and / or concentration of a neutral gas, a reactive gas, a doping gas, a derivatizing gas, a reagent gas, a shifting reagent gas, a supercharge reagent gas or a charge-reducing reagent gas designed to interact or react with the analyte ions after ionization, and (iv) the composition and / or concentration of doping ions, derivatizing ions, reagent ions, supercharge reagents or charge-reducing reagents designed to interact or react with the analyte ions after ionization. [10] A method as claimed in claim 7, 8 or 9, wherein the first and / or second conditions are selected from the group consisting of: (i) a condition which affects the charge state of the analytes ions, (ii) a condition which affects an energy level of the analytes ions, (iii) a condition which affects the kinetic energy of the analytes ions, (iv) a condition which affects the activation energy of the analytes, and (v) a condition which affects the conformal property of the analytes. [11] A method as claimed in any one of claims 7 to 10, wherein the first and / or second conditions are selected from the group consisting of: (i) an ionization condition of an ion source, (ii) the type of ion source used for ionizing a sample, (iii) a voltage setting of an ion source, (iv) an ionization polarity of ions produced by an ion source, (v) a flow rate of a sample being delivered to an ion source, (vi) one or more liquid chromatography conditions of a liquid chromatography system, (vii) a composition of a liquid chromatography solution or solvent and (viii) a liquid chromatography flow rate. [12] A method as claimed in any one of claims 7 to 11, wherein the first and / or second conditions are selected from the group consisting of: (i) subjecting ions to a hydrogen-deuterium exchange, (ii) one or more hydrogen-deuterium exchange conditions, (iii) Subjecting ions to activation, photoactivation, dissociation or photodissociation, (iv) one or more dissociation, photodissociation, activation and / or photoactivation conditions, (v) Subjecting ions to heating or RF heating, (vi) one or more heating or RF heating conditions, (vii) Subjecting ions to electromagnetic irradiation, microwave irradiation or laser irradiation, (viii) one or more electromagnetic irradiation, microwave irradiation or laser irradiation conditions, (ix) Subjecting the ions to fragmentation or reaction and (x) one or more fragmentation or reaction conditions. [13] A method as claimed in any one of claims 7 to 12, wherein the step of calculating or estimating one or more second ion mobility values, collision cross sections or interaction cross sections of at least some of the compounds in the first list comprises calculating one or more second ion mobility values, collision cross sections or interaction cross sections taking into account the first conditions and / or the second conditions. [14] A method as claimed in any one of claims 7 to 13, the method further comprising: determining a first ion mobility value, collision cross-section or interaction cross-section difference between the first ion mobility values, collision cross-sections or interaction cross-sections measured for the ions produced by the sample under the first conditions and the ions produced by the sample under the second, different conditions; determining a second ion mobility value, collision cross-section or interaction cross-section difference between the second ion mobility values, collision cross-sections or interaction cross-sections calculated or estimated for the ions produced by the sample under the first conditions and the ions produced by the sample under the second, different conditions; and: (i) Generating the second reduced list of compounds by removing compounds from the first list based on the difference between the first ion mobility value, collision cross-section or interaction cross-section difference and the second ion mobility value, collision cross-section or interaction cross-section difference, and / or (ii) Reducing a probability value associated with one or more compounds in the first list on the basis of the difference between the first ion mobility value, collision cross section or interaction cross section difference and the second ion mobility value, collision cross section or interaction cross section difference. [15] A method as claimed in any preceding claim, wherein the step of measuring one or more first ion mobility values, collision cross sections or interaction cross sections comprises measuring a first ion mobility value, collision cross section or interaction cross section of at least some of the analytes under first experimental conditions and measuring a first ion mobility value, collision cross section or interaction cross section of at least some of the analytes under second, different experimental conditions, and / or the step of measuring one or more mass-to-charge ratios comprises measuring a mass-to-charge ratio of at least some of the analytes under first experimental conditions and measuring a mass-to-charge ratio of at least some of the analytes under second, different experimental conditions. [16] A method as claimed in claim 15, wherein the first experimental conditions and / or the second experimental conditions are selected from the group consisting of: (i) a voltage applied to an ion-optical component, (ii) a route taken by the analyte ions through part of the mass spectrometer, (iii) the transition time of analyte ions through a part of the mass spectrometer, (iv) one or more pressures within the mass spectrometer, (v) one or more temperatures within the mass spectrometer, (vi) the composition of a gas within the mass spectrometer and (vii) the strength of an electric field inside the mass spectrometer. [17] A method as claimed in claim 15 or 16, wherein the first experimental conditions and / or the second experimental conditions are selected from the group consisting of: (i) the composition of an ion mobility separation or buffer gas, (ii) the composition of one or more additives, dopants and / or reagents added to an ion mobility separation or buffer gas, (iii) the flow rate and / or direction of an ion mobility separation or buffer gas, (iv) the pressure or density number of an ion mobility separation or buffer gas, (v) the temperature within an ion mobility separation device, (vi) the strength of an electric field within an ion mobility separation device, (vii) the distance traveled by ions within an ion mobility separation device, (viii) the residence time of ions within an ion mobility separation device, (ix) the initial width of an ion pulse introduced into an ion mobility separation device and (x) the speed, amplitude or repetition pattern of a traveling DC voltage wave within an ion mobility separation device. [18] A method as claimed in any one of claims 15 to 17, wherein the step of calculating or estimating one or more second ion mobility values, collision cross sections or interaction cross sections of at least some of the compounds in the first list comprises calculating one or more second ion mobility values, collision cross sections or interaction cross sections taking into account the first experimental conditions and / or the second experimental conditions. [19] A method as claimed in any one of claims 15 to 18, further comprising: Determining a first ion mobility value, collision cross-section or interaction cross-section difference between the first ion mobility value measured under the first experimental conditions, collision cross-section or interaction cross-section and the one under the second experimental conditions measured first ion mobility value, collision cross-section or interaction cross-section, Determining a second ion mobility value, collision cross-section or interaction cross-section difference between a second ion mobility value, collision cross-section or calculated or estimated using the first experimental conditions Interaction cross-section and a second ion mobility value, collision cross-section or interaction cross-section calculated or estimated using the second experimental conditions and: (i) Generating the second reduced list of compounds by removing compounds from the first list based on the difference between the first ion mobility value, collision cross-section or interaction cross-section difference and the second ion mobility value, collision cross-section or interaction cross-section difference and / or (ii) Reducing a probability value associated with one or more compounds in the first list, based on the difference between the first ion mobility value, collision cross section or interaction cross section difference and the second ion mobility value, collision cross section or interaction cross section difference. [20] A method as claimed in any preceding claim, wherein the step of generating the first list of compounds which may be the one or more analytes, based on the one or more measured mass-to-charge ratios, comprises using a library search to generate the first list of compounds. [21] A method as claimed in any preceding claim, wherein the step comprises calculating or estimating one or more second ion mobility values, collision cross sections or interaction cross sections: Determining a three-dimensional structure from at least some of the compounds in the first list and calculating one or more of the second ion mobility values, collision cross sections or Interaction cross-sections using the three-dimensional structure. [22] A method as claimed in any preceding claim, wherein the step of calculating or estimating one or more second ion mobility values, collision cross sections or interaction cross sections comprises calculating the effects of electronic interactions of ions with a polar or polarizable ion mobility separation or buffer gas. [23] A mass spectrometer comprising: a device that is arranged and suitable to determine one or more first ion mobility values, collision cross-sections or interaction cross-sections and one or to measure multiple mass-to-charge ratios of one or more analyte ions, and a control system which is arranged and suitable for this purpose, to generate an initial list of compounds that could be one or more analyte ions, based on one or more measured mass-to-charge ratios, to calculate or estimate one or more second ion mobility values, collision cross sections or interaction cross sections of at least some of the compounds in the first list, and: (i) to generate a second reduced list of compounds by removing compounds from the first list if the difference between the one or more measured first ion mobility values, collision cross sections or interaction cross sections and the one or more calculated or estimated second ion mobility values, collision cross sections or interaction cross sections is greater than a certain amount, and / or (ii) to provide a probability value associated with one or more compounds in the first list, representing a probability that the one or more compounds are the one or more analyte ions, and to decrease the probability value if the difference between the one or more measured first ion mobility values, collision cross sections or interaction cross sections and the one or more calculated or estimated second ion mobility values, collision cross sections or interaction cross sections is greater than a certain amount.

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