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Thurman HA, Wijegunawardena G, Berthias F, Williamson DL, Wu H, Nagy G, Jensen ON, Shvartsburg AA. Multiplatform High-Definition Ion Mobility Separations of the Largest Epimeric Peptides. Anal Chem 2024; 96:2318-2326. [PMID: 38301112 DOI: 10.1021/acs.analchem.3c03079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Ion mobility spectrometry (IMS) coupled to mass spectrometry (MS) has become a versatile tool to fractionate complex mixtures, distinguish structural isomers, and elucidate molecular geometries. Along with the whole MS field, IMS/MS advances to ever larger species. A topical proteomic problem is the discovery and characterization of d-amino acid-containing peptides (DAACPs) that are critical to neurotransmission and toxicology. Both linear IMS and FAIMS previously disentangled d/l epimers with up to ∼30 residues. In the first study using all three most powerful IMS methodologies─trapped IMS, cyclic IMS, and FAIMS─we demonstrate baseline resolution of the largest known d/l peptides (CHH from Homarus americanus with 72 residues) with a dynamic range up to 100. This expands FAIMS analyses of isomeric modified peptides, especially using hydrogen-rich buffers, to the ∼50-100 residue range of small proteins. The spectra for d and l are unprecedentedly strikingly similar except for a uniform shift of the separation parameter, indicating the conserved epimer-specific structural elements across multiple charge states and conformers. As the interepimer resolution tracks the average for smaller DAACPs, the IMS approaches could help search for yet larger DAACPs. The a priori method to calibrate cyclic (including multipass) IMS developed here may be broadly useful.
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Affiliation(s)
- Hayden A Thurman
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Gayani Wijegunawardena
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Francis Berthias
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - David L Williamson
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Haifan Wu
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Gabe Nagy
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Ole N Jensen
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Alexandre A Shvartsburg
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
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2
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Pathak P, Shvartsburg AA. High-Definition Differential Ion Mobility Spectrometry with Structural Isotopic Shifts for Anionic Compounds. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023. [PMID: 37319378 DOI: 10.1021/jasms.3c00190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Differential ion mobility spectrometry (FAIMS) had emerged in the 2000s as a novel tool for postionization separations in conjunction with mass spectrometry (MS). High-definition FAIMS introduced a decade ago has enabled resolution of peptide, lipid, and other molecular isomers with minute structural variations and recently the isotopic shift analyses where the spectral pattern for stable isotopes fingerprints the ion geometry. Those studies, including all isotopic shift analyses, were in the positive mode. Here, we achieve the same high resolution for anions exemplified by phthalic acid isomers. The resolving power and magnitude of isotopic shifts are in line with the metrics for analogous haloaniline cations, establishing high-definition negative-mode FAIMS with structurally specific isotopic shifts. Different shifts (including the new 18O) remain additive and mutually orthogonal, demonstrating the generality of those properties across the elements and charge states. Expanding to common (not halogenated) organic compounds is a key step toward the broad use of FAIMS isotopic shift methodology.
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Affiliation(s)
- Pratima Pathak
- Department of Chemistry and Biochemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Alexandre A Shvartsburg
- Department of Chemistry and Biochemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
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3
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Lamont L, Hadavi D, Bowman AP, Flinders B, Cooper‐Shepherd D, Palmer M, Jordens J, Mengerink Y, Honing M, Langridge J, Porta Siegel T, Vreeken RJ, Heeren RMA. High-resolution ion mobility spectrometry-mass spectrometry for isomeric separation of prostanoids after Girard's reagent T derivatization. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2023; 37:e9439. [PMID: 36415963 PMCID: PMC10078546 DOI: 10.1002/rcm.9439] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/18/2022] [Accepted: 11/19/2022] [Indexed: 06/15/2023]
Abstract
RATIONALE Isomeric separation of prostanoids is often a challenge and requires chromatography and time-consuming sample preparation. Multiple prostanoid isomers have distinct in vivo functions crucial for understanding the inflammation process, including prostaglandins E2 (PGE2 ) and D2 (PGD2 ). High-resolution ion mobility spectrometry (IMS) based on linear ion transport in low-to-moderate electric fields and nonlinear ion transport in strong electric fields emerges as a broad approach for rapid separations prior to mass spectrometry. METHODS Derivatization with Girard's reagent T (GT) was used to overcome inefficient ionization of prostanoids in negative ionization mode due to poor deprotonation of the carboxylic acid group. Three high-resolution IMS techniques, namely linear cyclic IMS, linear trapped IMS, and nonlinear high-field asymmetric waveform IMS, were compared for the isomeric separation and endogenous detection of prostanoids present in intestinal tissue. RESULTS Direct infusion of GT-derivatized prostanoids proved to increase the ionization efficiency in positive ionization mode by a factor of >10, which enabled detection of these molecules in endogenous concentration levels. The high-resolution IMS comparison revealed its potential for rapid isomeric analysis of biologically relevant prostanoids. Strengths and weaknesses of both linear and nonlinear IMS are discussed. Endogenous prostanoid detection in intestinal tissue extracts demonstrated the applicability of our approach in biomedical research. CONCLUSIONS The applied derivatization strategy offers high sensitivity and improved stereoisomeric separation for screening of complex biological systems. The high-resolution IMS comparison indicated that the best sensitivity and resolution are achieved by linear and nonlinear IMS, respectively.
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Affiliation(s)
- Lieke Lamont
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass SpectrometryMaastricht UniversityMaastrichtThe Netherlands
| | - Darya Hadavi
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass SpectrometryMaastricht UniversityMaastrichtThe Netherlands
| | - Andrew P. Bowman
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass SpectrometryMaastricht UniversityMaastrichtThe Netherlands
| | - Bryn Flinders
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass SpectrometryMaastricht UniversityMaastrichtThe Netherlands
| | | | | | - Jan Jordens
- DSM Materials Science CenterGeleenMDThe Netherlands
| | | | - Maarten Honing
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass SpectrometryMaastricht UniversityMaastrichtThe Netherlands
| | | | - Tiffany Porta Siegel
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass SpectrometryMaastricht UniversityMaastrichtThe Netherlands
| | - Rob J. Vreeken
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass SpectrometryMaastricht UniversityMaastrichtThe Netherlands
- Janssen R&DBeerseBelgium
| | - Ron M. A. Heeren
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass SpectrometryMaastricht UniversityMaastrichtThe Netherlands
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4
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High-end ion mobility mass spectrometry: A current review of analytical capacity in omics applications and structural investigations. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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5
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Srinivasan A, Sing JC, Gingras AC, Röst HL. Improving Phosphoproteomics Profiling Using Data-Independent Mass Spectrometry. J Proteome Res 2022; 21:1789-1799. [PMID: 35877786 DOI: 10.1021/acs.jproteome.2c00172] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mass spectrometry-based profiling of the phosphoproteome is a powerful method of identifying phosphorylation events at a systems level. Most phosphoproteomics studies have used data-dependent acquisition (DDA) mass spectrometry as their method of choice. In this Perspective, we review some recent studies benchmarking DDA and DIA methods for phosphoproteomics and discuss data analysis options for DIA phosphoproteomics. In order to evaluate the impact of data-dependent and data-independent acquisition (DIA) on identification and quantification, we analyze a previously published phosphopeptide-enriched data set consisting of 10 replicates acquired by DDA and DIA each. We find that though more unique identifications are made in DDA data, phosphopeptides are identified more consistently across replicates in DIA. We further discuss the challenges of identifying chromatographically coeluting phosphopeptide isomers and investigate the impact on reproducibility of identifying high-confidence site-localized phosphopeptides in replicates.
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Affiliation(s)
- Aparna Srinivasan
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Justin C Sing
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Hannes L Röst
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
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6
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Sanders JD, Shields SW, Escobar EE, Lanzillotti MB, Butalewicz JP, James VK, Blevins MS, Sipe SN, Brodbelt JS. Enhanced Ion Mobility Separation and Characterization of Isomeric Phosphatidylcholines Using Absorption Mode Fourier Transform Multiplexing and Ultraviolet Photodissociation Mass Spectrometry. Anal Chem 2022; 94:4252-4259. [PMID: 35239318 DOI: 10.1021/acs.analchem.1c04711] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structural diversity of phospholipids plays a critical role in cellular membrane dynamics, energy storage, and cellular signaling. Despite its importance, the extent of this diversity has only recently come into focus, largely owing to advances in separation science and mass spectrometry methodology and instrumentation. Characterization of glycerophospholipid (GP) isomers differing only in their acyl chain configurations and locations of carbon-carbon double bonds (C═C) remains challenging due to the need for both effective separation of isomers and advanced tandem mass spectrometry (MS/MS) technologies capable of double-bond localization. Drift tube ion mobility spectrometry (DTIMS) coupled with MS can provide both fast separation and accurate determination of collision cross section (CCS) of molecules but typically lacks the resolving power needed to separate phospholipid isomers. Ultraviolet photodissociation (UVPD) can provide unambiguous double-bond localization but is challenging to implement on the timescales of modern commercial drift tube time-of-flight mass spectrometers. Here, we present a novel method for coupling DTIMS with a UVPD-enabled Orbitrap mass spectrometer using absorption mode Fourier transform multiplexing that affords simultaneous localization of double bonds and accurate CCS measurements even when isomers cannot be fully resolved in the mobility dimension. This method is demonstrated on two- and three-component mixtures and shown to provide CCS measurements that differ from those obtained by individual analysis of each component by less than 1%.
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Affiliation(s)
- James D Sanders
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Samuel W Shields
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Edwin E Escobar
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Michael B Lanzillotti
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jamie P Butalewicz
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Virginia K James
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Molly S Blevins
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Sarah N Sipe
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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7
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Chang CH, Yeung D, Spicer V, Ogata K, Krokhin O, Ishihama Y. Sequence-Specific Model for Predicting Peptide Collision Cross Section Values in Proteomic Ion Mobility Spectrometry. J Proteome Res 2021; 20:3600-3610. [PMID: 34133192 DOI: 10.1021/acs.jproteome.1c00185] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The contribution of peptide amino acid sequence to collision cross section values (CCS) has been investigated using a dataset of ∼134 000 peptides of four different charge states (1+ to 4+). The migration data were acquired using a two-dimensional liquid chromatography (LC)/trapped ion mobility spectrometry/quadrupole/time-of-flight mass spectrometry (MS) analysis of HeLa cell digests created using seven different proteases and was converted to CCS values. Following the previously reported modeling approaches using intrinsic size parameters (ISP), we extended this methodology to encode the position of individual residues within a peptide sequence. A generalized prediction model was built by dividing the dataset into eight groups (four charges for both tryptic/nontryptic peptides). Position-dependent ISPs were independently optimized for the eight subsets of peptides, resulting in prediction accuracy of ∼0.981 for the entire population of peptides. We find that ion mobility is strongly affected by the peptide's ability to solvate the positively charged sites. Internal positioning of polar residues and proline leads to decreased CCS values as they improve charge solvation; conversely, this ability decreases with increasing peptide charge due to electrostatic repulsion. Furthermore, higher helical propensity and peptide hydrophobicity result in a preferential formation of extended structures with higher than predicted CCS values. Finally, acidic/basic residues exhibit position-dependent ISP behavior consistent with electrostatic interaction with the peptide macrodipole, which affects the peptide helicity. The MS raw data files have been deposited with the ProteomeXchange Consortium via the jPOST partner repository (http://jpostdb.org) with the dataset identifiers PXD021440/JPST000959, PXD022800/JPST001017, and PXD026087/ JPST001176.
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Affiliation(s)
- Chih-Hsiang Chang
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Darien Yeung
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
- Department of Internal Medicine, University of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
| | - Victor Spicer
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
| | - Kosuke Ogata
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Oleg Krokhin
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
- Department of Internal Medicine, University of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
- Department of Chemistry, University of Manitoba, 360 Parker Building, Winnipeg, Manitoba R3T 2N2, Canada
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
- Laboratory of Clinical and Analytical Chemistry, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
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8
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Berthias F, Baird MA, Shvartsburg AA. Differential Ion Mobility Separations of d/l Peptide Epimers. Anal Chem 2021; 93:4015-4022. [DOI: 10.1021/acs.analchem.0c05023] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Francis Berthias
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Matthew A. Baird
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Alexandre A. Shvartsburg
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
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9
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Leyva D, Jaffe R, Fernandez-Lima F. Structural Characterization of Dissolved Organic Matter at the Chemical Formula Level Using TIMS-FT-ICR MS/MS. Anal Chem 2020; 92:11960-11966. [PMID: 32786462 DOI: 10.1021/acs.analchem.0c02347] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
TIMS-FT-ICR MS is an important alternative to study the isomeric diversity and elemental composition of complex mixtures. While the chemical structure of many compounds in the dissolved organic matter (DOM) remains largely unknown, the high structural diversity has been described at the molecular level using chemical formulas. In this study, we further push the boundaries of TIMS-FT-ICR MS by performing chemical formula-based ion mobility and tandem MS analysis for the structural characterization of DOM. The workflow described is capable to mobility select (R ∼ 100) and isolate molecular ion signals (Δm/z = 0.036) in the ICR cell, using single-shot ejections after broadband ejections and MS/MS based on sustained off-resonance irradiation collision-induced dissociation (SORI-CID). The workflow results are compared to alternative TIMS-q-FT-ICR MS/MS experiments with quadrupole isolation at nominal mass (∼1 Da). The technology is demonstrated with isomeric and isobaric mixtures (e.g., 4-methoxy-1-naphthoic acid, 2-methoxy-1-naphthoic acid, decanedioic acid) and applied to the characterization of DOM. The application of this new methodology to the analysis of a DOM is illustrated by the isolation of the molecular ion [C18H18O10-H]- in the presence of other isobars at nominal mass 393. Five IMS bands were assigned to the heterogeneous ion mobility profile of [C18H18O10-H]-, and candidate structures from the PubChem database were screened based on their ion mobility and the MS/MS matching score. This approach overcomes traditional challenges associated with the similarity of fragmentation patterns of DOM samples (e.g., common neutral losses of H2O, CO2, and CH2-H2O) by narrowing down the isomeric candidate structures using the mobility domain.
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10
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Lam KHB, Le Blanc JCY, Campbell JL. Separating Isomers, Conformers, and Analogues of Cyclosporin using Differential Mobility Spectroscopy, Mass Spectrometry, and Hydrogen–Deuterium Exchange. Anal Chem 2020; 92:11053-11061. [DOI: 10.1021/acs.analchem.0c00191] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- K. H. Brian Lam
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | | | - J. Larry Campbell
- SCIEX, 71 Four Valley Drive, Concord, Ontario L4K 4 V8, Canada
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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11
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Pathak P, Baird MA, Shvartsburg AA. High-Resolution Ion Mobility Separations of Isomeric Glycoforms with Variations on the Peptide and Glycan Levels. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1603-1609. [PMID: 32501708 DOI: 10.1021/jasms.0c00183] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Glycosylation is a ubiquitous post-translational modification (PTM) that strongly affects the protein folding and function. Glycosylation patterns are impacted by many diseases, making promising biomarkers. Glycans are also the most complex PTMs, exhibiting isomers (linkage, anomers, and those with isomeric moieties). Permuted with localization variants that occur for all PTMs, these produce numerous isomeric glycoforms. Characterizing them by mass spectrometry and ion mobility spectrometry (IMS) has been a challenge. High-definition differential IMS (FAIMS) had robustly disentangled isomeric peptides involving other PTMs but was not evaluated for glycopeptides that featured multilevel isomerism. Here, we apply it to representative mucin glycopeptides with O-linked glycans: three GalNAc localization variants, a pair with α/β GalNAc anomers, and another with GalNAc/GlcNAc isomers. The first two classes were separated baseline with the resolution exceeding previous benchmarks by 10-fold, and the last pair was partly resolved. The recently demonstrated straightforward coupling to ultrahigh-resolution MS and electron-transfer dissociation makes high-definition FAIMS an attractive tool for glycoproteomics.
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Affiliation(s)
- Pratima Pathak
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Matthew A Baird
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Alexandre A Shvartsburg
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
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12
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Shliaha PV, Gorshkov V, Kovalchuk SI, Schwämmle V, Baird MA, Shvartsburg AA, Jensen ON. Middle-Down Proteomic Analyses with Ion Mobility Separations of Endogenous Isomeric Proteoforms. Anal Chem 2020; 92:2364-2368. [DOI: 10.1021/acs.analchem.9b05011] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Pavel V. Shliaha
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Vladimir Gorshkov
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Sergey I. Kovalchuk
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Veit Schwämmle
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Matthew A. Baird
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Alexandre A. Shvartsburg
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Ole N. Jensen
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark
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13
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Pathak P, Baird MA, Shvartsburg AA. Structurally Informative Isotopic Shifts in Ion Mobility Spectra for Heavier Species. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:137-145. [PMID: 32881519 DOI: 10.1021/jasms.9b00018] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The isotopic molecular envelopes due to stable isotopes for most elements were a staple of mass spectrometry since its origins, often leveraged to identify and quantify compounds. However, all isomers share one MS envelope. As the molecular motion in media also depends on the isotopic composition, separations such as liquid chromatography (LC) and ion mobility spectrometry (IMS) must also feature isotopic envelopes. These were largely not observed because of limited resolution, except for the (structurally uninformative) shifts in LC upon H/D exchange. We recently found the isotopic shifts in FAIMS for small haloanilines (∼130-170 Da) to hinge on the halogen position, opening a novel route to isomer characterization. Here, we extend the capability to heavier species: dibromoanilines (DBAs, ∼250 Da) and tribromoanilines (TBAs, ∼330 Da). The 13C shifts for DBAs and TBAs vary across isomers, some changing sign. While 81Br shifts are less specific, the 2-D 13C/81Br shifts unequivocally differentiate all isomers. The trends for DBAs track those for dichloroanilines, with the 13C shift order preserved for most isomers. The peak broadening due to merged isotopomers is also isomer-specific. The absolute shifts for TBAs are smaller than those for lighter haloanilines, but differentiate isomers as well because of compressed uncertainties. These results showcase the feasibility of broadly distinguishing isomers in the more topical ∼200-300 Da range using the isotopic shifts in IMS spectra.
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Affiliation(s)
- Pratima Pathak
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Matthew A Baird
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Alexandre A Shvartsburg
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
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14
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Winter DL, Mastellone J, Kabir KMM, Wilkins MR, Donald WA. Separation of Isobaric Mono- and Dimethylated RGG-Repeat Peptides by Differential Ion Mobility-Mass Spectrometry. Anal Chem 2019; 91:11827-11833. [DOI: 10.1021/acs.analchem.9b02504] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daniel L. Winter
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Jordan Mastellone
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - K. M. Mohibul Kabir
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Marc R. Wilkins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - William A. Donald
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
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15
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Kaszycki JL, La Rotta A, Colsch B, Fenaille F, Dauly C, Kamleh A, Wu C. Separation of biologically relevant isomers on an Orbitrap mass spectrometer using high-resolution drift tube ion mobility and varied drift gas mixtures. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33 Suppl 2:3-10. [PMID: 30772932 DOI: 10.1002/rcm.8414] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 02/08/2019] [Accepted: 02/11/2019] [Indexed: 06/09/2023]
Abstract
RATIONALE Atmospheric pressure drift tube ion mobility is a powerful addition to the Orbitrap mass spectrometer enabling direct separation of isomers. Apart from offering high resolving power in a compact design, it also facilitates optimization of the separation gas, as shown here for a series of biologically relevant isomer pairs. METHODS An Excellims MA3100 High-Resolution Atmospheric Pressure Ion Mobility Spectrometer (HR-IMS) was coupled to a Thermo Scientific™ Q Exactive™ Focus hybrid quadrupole-Orbitrap™ mass spectrometer, using an Excellims Directspray™ Electrospray Ionization source and a gas mixture setup to provide various drift gases (air, CO2 and mixtures). This instrument combination was used to separate isomers of eight pairs of metabolites and gangliosides, optimizing drift gas conditions for best separation of each set. RESULTS All but one of the isomers pairs provided could be partially or fully separated by the HR-IMS-MS combination using ion mobility drift times. About half of the separated compounds showed significantly better analytical separation when analyzed in a mixture of CO2 and air rather than air or CO2 alone. Resolving power of up to 102 was achieved using the 10 cm atmospheric drift tube ion mobility add-on for the Orbitrap mass spectrometer. CONCLUSIONS The present analysis demonstrates the usefulness of using atmospheric drift tube IMS on an Orbitrap mass spectrometer to characterize the isomeric composition of samples. It also highlights the potential benefits of being able to quickly optimize the drift gas composition to selectively maximize the mobility difference for isomer separation.
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Affiliation(s)
| | | | - Benoit Colsch
- Service de Pharmacologie et d'Immunoanalyse, Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, MetaboHUB, F-91191, Gif-sur-Yvette, France
| | - François Fenaille
- Service de Pharmacologie et d'Immunoanalyse, Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, MetaboHUB, F-91191, Gif-sur-Yvette, France
| | | | | | - Ching Wu
- Excellims Corporation, Acton, MA, USA
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16
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Winter DL, Wilkins MR, Donald WA. Differential Ion Mobility–Mass Spectrometry for Detailed Analysis of the Proteome. Trends Biotechnol 2019; 37:198-213. [DOI: 10.1016/j.tibtech.2018.07.018] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/27/2018] [Accepted: 07/30/2018] [Indexed: 10/28/2022]
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17
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Affiliation(s)
- Clement
M. Potel
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Simone Lemeer
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
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18
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Leyva D, Tose LV, Porter J, Wolff J, Jaffé R, Fernandez-Lima F. Understanding the structural complexity of dissolved organic matter: isomeric diversity. Faraday Discuss 2019; 218:431-440. [DOI: 10.1039/c8fd00221e] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In the present work, the advantages of ESI-TIMS-FT-ICR MS to address the isomeric content of dissolved organic matter are studied.
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Affiliation(s)
- Dennys Leyva
- Department of Chemistry and Biochemistry
- Florida International University
- Miami
- USA
- Southeast Environmental Research Center
| | - Lilian V. Tose
- Department of Chemistry and Biochemistry
- Florida International University
- Miami
- USA
| | - Jacob Porter
- Department of Chemistry and Biochemistry
- Florida International University
- Miami
- USA
| | | | - Rudolf Jaffé
- Southeast Environmental Research Center
- Florida International University
- Miami
- USA
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry
- Florida International University
- Miami
- USA
- Biomolecular Sciences Institute
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19
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Chouinard CD, Nagy G, Smith RD, Baker ES. Ion Mobility-Mass Spectrometry in Metabolomic, Lipidomic, and Proteomic Analyses. ADVANCES IN ION MOBILITY-MASS SPECTROMETRY: FUNDAMENTALS, INSTRUMENTATION AND APPLICATIONS 2019. [DOI: 10.1016/bs.coac.2018.11.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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20
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Baird MA, Anderson GA, Shliaha PV, Jensen ON, Shvartsburg AA. Differential Ion Mobility Separations/Mass Spectrometry with High Resolution in Both Dimensions. Anal Chem 2018; 91:1479-1485. [DOI: 10.1021/acs.analchem.8b04518] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Matthew A. Baird
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Gordon A. Anderson
- GAACE, 101904 Wiser Parkway Ste 105, Kennewick, Washington 99338, United States
| | - Pavel V. Shliaha
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Ole N. Jensen
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Alexandre A. Shvartsburg
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
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21
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Tose LV, Benigni P, Leyva D, Sundberg A, Ramírez CE, Ridgeway ME, Park MA, Romão W, Jaffé R, Fernandez-Lima F. Coupling trapped ion mobility spectrometry to mass spectrometry: trapped ion mobility spectrometry-time-of-flight mass spectrometry versus trapped ion mobility spectrometry-Fourier transform ion cyclotron resonance mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:1287-1295. [PMID: 29756663 DOI: 10.1002/rcm.8165] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 03/28/2018] [Accepted: 05/03/2018] [Indexed: 05/05/2023]
Abstract
RATIONALE There is a need for fast, post-ionization separation during the analysis of complex mixtures. In this study, we evaluate the use of a high-resolution mobility analyzer with high-resolution and ultrahigh-resolution mass spectrometry for unsupervised molecular feature detection. Goals include the study of the reproducibility of trapped ion mobility spectrometry (TIMS) across platforms, applicability range, and potential challenges during routine analysis. METHODS A TIMS analyzer was coupled to time-of-flight mass spectrometry (TOF MS) and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) instruments for the analysis of singly charged species in the m/z 150-800 range of a complex mixture (Suwannee River Fulvic Acid Standard). Molecular features were detected using an unsupervised algorithm based on chemical formula and IMS profiles. RESULTS TIMS-TOF MS and TIMS-FT-ICR MS analysis provided 4950 and 7760 m/z signals, 1430 and 3050 formulas using the general Cx Hy N0-3 O0-19 S0-1 composition, and 7600 and 22 350 [m/z; chemical formula; K; CCS] features, respectively. CONCLUSIONS TIMS coupled to TOF MS and FT-ICR MS showed similar performance and high reproducibility. For the analysis of complex mixtures, both platforms were able to capture the major trends and characteristics; however, as the chemical complexity at the level of nominal mass increases with m/z (m/z >300-350), only TIMS-FT-ICR MS was able to report the lower abundance compositional trends.
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Affiliation(s)
- Lilian V Tose
- Federal University of Espírito Santo, Petroleomic and Forensic Chemistry Laboratory, Department of Chemistry, 29075-910, Vitória, ES, Brazil
| | - Paolo Benigni
- Florida International University, Department of Chemistry and Biochemistry, Miami, FL, 33199, USA
| | - Dennys Leyva
- Florida International University, Department of Chemistry and Biochemistry, Miami, FL, 33199, USA
| | - Abigail Sundberg
- Florida International University, Department of Chemistry and Biochemistry, Miami, FL, 33199, USA
| | - César E Ramírez
- Florida International University, Department of Chemistry and Biochemistry, Miami, FL, 33199, USA
| | | | | | - Wanderson Romão
- Federal University of Espírito Santo, Petroleomic and Forensic Chemistry Laboratory, Department of Chemistry, 29075-910, Vitória, ES, Brazil
- Federal Institute of Education, Science and Technology of Espírito Santo, 29106-010, Vila Velha, ES, Brazil
| | - Rudolf Jaffé
- Florida International University, Department of Chemistry and Biochemistry, Miami, FL, 33199, USA
- Florida International University, Southeast Environmental Research Center, Miami, FL, 33199, USA
| | - Francisco Fernandez-Lima
- Florida International University, Department of Chemistry and Biochemistry, Miami, FL, 33199, USA
- Florida International University, Southeast Environmental Research Center, Miami, FL, 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL, 33199, USA
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22
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Pathak P, Baird MA, Shvartsburg AA. Identification of Isomers by Multidimensional Isotopic Shifts in High-Field Ion Mobility Spectra. Anal Chem 2018; 90:9410-9417. [DOI: 10.1021/acs.analchem.8b02057] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Pratima Pathak
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Matthew A. Baird
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Alexandre A. Shvartsburg
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
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23
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Pfammatter S, Bonneil E, McManus FP, Thibault P. Gas-Phase Enrichment of Multiply Charged Peptide Ions by Differential Ion Mobility Extend the Comprehensiveness of SUMO Proteome Analyses. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1111-1124. [PMID: 29623662 DOI: 10.1007/s13361-018-1917-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 02/07/2018] [Accepted: 02/08/2018] [Indexed: 06/08/2023]
Abstract
The small ubiquitin-like modifier (SUMO) is a member of the family of ubiquitin-like modifiers (UBLs) and is involved in important cellular processes, including DNA damage response, meiosis and cellular trafficking. The large-scale identification of SUMO peptides in a site-specific manner is challenging not only because of the low abundance and dynamic nature of this modification, but also due to the branched structure of the corresponding peptides that further complicate their identification using conventional search engines. Here, we exploited the unusual structure of SUMO peptides to facilitate their separation by high-field asymmetric waveform ion mobility spectrometry (FAIMS) and increase the coverage of SUMO proteome analysis. Upon trypsin digestion, branched peptides contain a SUMO remnant side chain and predominantly form triply protonated ions that facilitate their gas-phase separation using FAIMS. We evaluated the mobility characteristics of synthetic SUMO peptides and further demonstrated the application of FAIMS to profile the changes in protein SUMOylation of HEK293 cells following heat shock, a condition known to affect this modification. FAIMS typically provided a 10-fold improvement of detection limit of SUMO peptides, and enabled a 36% increase in SUMO proteome coverage compared to the same LC-MS/MS analyses performed without FAIMS. Graphical Abstract ᅟ.
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Affiliation(s)
- Sibylle Pfammatter
- Institute for Research in Immunology and Cancer, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, Québec, H3C 3J7, Canada
- Department of Chemistry, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, Québec, H3C 3J7, Canada
| | - Eric Bonneil
- Institute for Research in Immunology and Cancer, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, Québec, H3C 3J7, Canada
| | - Francis P McManus
- Institute for Research in Immunology and Cancer, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, Québec, H3C 3J7, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, Québec, H3C 3J7, Canada.
- Department of Chemistry, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, Québec, H3C 3J7, Canada.
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24
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Garabedian A, Baird M, Porter J, Jeanne Dit Fouque K, Shliaha PV, Jensen ON, Williams TD, Fernandez-Lima F, Shvartsburg A. Linear and Differential Ion Mobility Separations of Middle-Down Proteoforms. Anal Chem 2018; 90:2918-2925. [PMID: 29359922 PMCID: PMC6366606 DOI: 10.1021/acs.analchem.7b05224] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Comprehensive characterization of proteomes comprising the same proteins with distinct post-translational modifications (PTMs) is a staggering challenge. Many such proteoforms are isomers (localization variants) that require separation followed by top-down or middle-down mass spectrometric analyses, but condensed-phase separations are ineffective in those size ranges. The variants for "middle-down" peptides were resolved by differential ion mobility spectrometry (FAIMS), relying on the mobility increment at high electric fields, but not previously by linear IMS on the basis of absolute mobility. We now use complete histone tails with diverse PTMs on alternative sites to demonstrate that high-resolution linear IMS, here trapped IMS (TIMS), broadly resolves the variants of ∼50 residues in full or into binary mixtures quantifiable by tandem MS, largely thanks to orthogonal separations across charge states. Separations using traveling-wave (TWIMS) and/or involving various time scales and electrospray ionization source conditions are similar (with lower resolution for TWIMS), showing the transferability of results across linear IMS instruments. The linear IMS and FAIMS dimensions are substantially orthogonal, suggesting FAIMS/IMS/MS as a powerful platform for proteoform analyses.
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Affiliation(s)
- Alyssa Garabedian
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199
| | - Matthew Baird
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, KS 67260
| | - Jacob Porter
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199
| | | | - Pavel V. Shliaha
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Ole N. Jensen
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Todd D. Williams
- Mass Spectrometry Laboratory, University of Kansas, Lawrence, KS 66045
| | | | - Alexandre Shvartsburg
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, KS 67260
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25
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Pettit ME, Brantley MR, Donnarumma F, Murray KK, Solouki T. Broadband ion mobility deconvolution for rapid analysis of complex mixtures. Analyst 2018; 143:2574-2586. [DOI: 10.1039/c8an00193f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Broadband IM-MS deconvolution allows generation of IM and MS data for species that are UPLC-IM-MS unresolved.
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Affiliation(s)
| | | | | | | | - Touradj Solouki
- Department of Chemistry and Biochemistry
- Baylor University
- Waco
- USA
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26
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Kaszycki JL, Baird MA, Shvartsburg AA. Molecular Structure Characterization by Isotopic Splitting in Nonlinear Ion Mobility Spectra. Anal Chem 2017; 90:669-673. [DOI: 10.1021/acs.analchem.7b04610] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Julia L. Kaszycki
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Matthew A. Baird
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Alexandre A. Shvartsburg
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
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27
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Shvartsburg AA, Haris A, Andrzejewski R, Entwistle A, Giles R. Differential Ion Mobility Separations in the Low-Pressure Regime. Anal Chem 2017; 90:936-943. [DOI: 10.1021/acs.analchem.7b03925] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Alexandre A. Shvartsburg
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Anisha Haris
- Shimadzu Research Laboratory, Wharfside, Trafford Wharf Road, Manchester M17 1GP, United Kingdom
| | - Roch Andrzejewski
- Shimadzu Research Laboratory, Wharfside, Trafford Wharf Road, Manchester M17 1GP, United Kingdom
| | - Andrew Entwistle
- Shimadzu Research Laboratory, Wharfside, Trafford Wharf Road, Manchester M17 1GP, United Kingdom
| | - Roger Giles
- Shimadzu Research Laboratory, Wharfside, Trafford Wharf Road, Manchester M17 1GP, United Kingdom
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28
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D'Atri V, Causon T, Hernandez-Alba O, Mutabazi A, Veuthey JL, Cianferani S, Guillarme D. Adding a new separation dimension to MS and LC-MS: What is the utility of ion mobility spectrometry? J Sep Sci 2017; 41:20-67. [PMID: 29024509 DOI: 10.1002/jssc.201700919] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 09/19/2017] [Accepted: 09/19/2017] [Indexed: 12/12/2022]
Abstract
Ion mobility spectrometry is an analytical technique known for more than 100 years, which entails separating ions in the gas phase based on their size, shape, and charge. While ion mobility spectrometry alone can be useful for some applications (mostly security analysis for detecting certain classes of narcotics and explosives), it becomes even more powerful in combination with mass spectrometry and high-performance liquid chromatography. Indeed, the limited resolving power of ion mobility spectrometry alone can be tackled when combining this analytical strategy with mass spectrometry or liquid chromatography with mass spectrometry. Over the last few years, the hyphenation of ion mobility spectrometry to mass spectrometry or liquid chromatography with mass spectrometry has attracted more and more interest, with significant progresses in both technical advances and pioneering applications. This review describes the theoretical background, available technologies, and future capabilities of these techniques. It also highlights a wide range of applications, from small molecules (natural products, metabolites, glycans, lipids) to large biomolecules (proteins, protein complexes, biopharmaceuticals, oligonucleotides).
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Affiliation(s)
- Valentina D'Atri
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Tim Causon
- Division of Analytical Chemistry, Department of Chemistry, University of Natural Resources and Life Sciences (BOKU Vienna), Vienna, Austria
| | - Oscar Hernandez-Alba
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC, Université de Strasbourg, CNRS, Strasbourg, France
| | - Aline Mutabazi
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Jean-Luc Veuthey
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Sarah Cianferani
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC, Université de Strasbourg, CNRS, Strasbourg, France
| | - Davy Guillarme
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
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29
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Borovcová L, Hermannová M, Pauk V, Šimek M, Havlíček V, Lemr K. Simple area determination of strongly overlapping ion mobility peaks. Anal Chim Acta 2017; 981:71-79. [DOI: 10.1016/j.aca.2017.05.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 05/01/2017] [Accepted: 05/05/2017] [Indexed: 10/19/2022]
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30
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Zheng X, Wojcik R, Zhang X, Ibrahim YM, Burnum-Johnson KE, Orton DJ, Monroe ME, Moore RJ, Smith RD, Baker ES. Coupling Front-End Separations, Ion Mobility Spectrometry, and Mass Spectrometry For Enhanced Multidimensional Biological and Environmental Analyses. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2017; 10:71-92. [PMID: 28301728 PMCID: PMC5627998 DOI: 10.1146/annurev-anchem-061516-045212] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Ion mobility spectrometry (IMS) is a widely used analytical technique for rapid molecular separations in the gas phase. Though IMS alone is useful, its coupling with mass spectrometry (MS) and front-end separations is extremely beneficial for increasing measurement sensitivity, peak capacity of complex mixtures, and the scope of molecular information available from biological and environmental sample analyses. In fact, multiple disease screening and environmental evaluations have illustrated that the IMS-based multidimensional separations extract information that cannot be acquired with each technique individually. This review highlights three-dimensional separations using IMS-MS in conjunction with a range of front-end techniques, such as gas chromatography, supercritical fluid chromatography, liquid chromatography, solid-phase extractions, capillary electrophoresis, field asymmetric ion mobility spectrometry, and microfluidic devices. The origination, current state, various applications, and future capabilities of these multidimensional approaches are described in detail to provide insight into their uses and benefits.
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Affiliation(s)
- Xueyun Zheng
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352;
| | - Roza Wojcik
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352;
| | - Xing Zhang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Anschutz Medical Campus, University of Colorado, Denver, Colorado 80045
| | - Yehia M Ibrahim
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352;
| | - Kristin E Burnum-Johnson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352;
| | - Daniel J Orton
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352;
| | - Matthew E Monroe
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352;
| | - Ronald J Moore
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352;
| | - Richard D Smith
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352;
| | - Erin S Baker
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352;
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31
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Shliaha PV, Baird MA, Nielsen MM, Gorshkov V, Bowman AP, Kaszycki JL, Jensen ON, Shvartsburg AA. Characterization of Complete Histone Tail Proteoforms Using Differential Ion Mobility Spectrometry. Anal Chem 2017; 89:5461-5466. [PMID: 28406606 PMCID: PMC5436587 DOI: 10.1021/acs.analchem.7b00379] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Histone proteins are subject to dynamic post-translational modifications (PTMs) that cooperatively modulate the chromatin structure and function. Nearly all functional PTMs are found on the N-terminal histone domains (tails) of ∼50 residues protruding from the nucleosome core. Using high-definition differential ion mobility spectrometry (FAIMS) with electron transfer dissociation, we demonstrate rapid baseline gas-phase separation and identification of tails involving monomethylation, trimethylation, acetylation, or phosphorylation in biologically relevant positions. These are by far the largest variant peptides resolved by any method, some with PTM contributing just 0.25% to the mass. This opens the door to similar separations for intact proteins and in top-down proteomics.
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Affiliation(s)
- Pavel V Shliaha
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, and Center for Epigenetics, University of Southern Denmark , DK-5230 Odense M, Denmark
| | - Matthew A Baird
- Department of Chemistry, Wichita State University , 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Mogens M Nielsen
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, and Center for Epigenetics, University of Southern Denmark , DK-5230 Odense M, Denmark
| | - Vladimir Gorshkov
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, and Center for Epigenetics, University of Southern Denmark , DK-5230 Odense M, Denmark
| | - Andrew P Bowman
- Department of Chemistry, Wichita State University , 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Julia L Kaszycki
- Department of Chemistry, Wichita State University , 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, and Center for Epigenetics, University of Southern Denmark , DK-5230 Odense M, Denmark
| | - Alexandre A Shvartsburg
- Department of Chemistry, Wichita State University , 1845 Fairmount, Wichita, Kansas 67260, United States
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32
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Liao R, Zheng D, Nie A, Zhou S, Deng H, Gao Y, Yang P, Yu Y, Tan L, Qi W, Wu J, Li E, Yi W. Sensitive and Precise Characterization of Combinatorial Histone Modifications by Selective Derivatization Coupled with RPLC-EThcD-MS/MS. J Proteome Res 2017; 16:780-787. [PMID: 28034318 DOI: 10.1021/acs.jproteome.6b00788] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Deciphering the combinatorial histone codes has been a long-standing interest in the epigenetics field, which requires the reliable and robust characterization of the post-translational modifications (PTMs) coexisting on histones. To this end, weak cation exchange hydrophilic interaction liquid chromatography is commonly used in middle-down liquid chromatography-mass spectrometry approaches for online separation of variously modified histone peptides. Here we provide a novel strategy that combines the selective histone peptide derivatization using N-hydroxysuccinimide propionate ester with reversed-phase liquid chromatography (RPLC) for the robust, sensitive, and reliable characterization of combinatorial histone PTMs. Derivatization amplifies the subtle physical differences between similarly modified histone peptides, thereby allowing baseline separation of these peptides by standard RPLC. Also, the sensitivity of MS is enhanced greatly by derivatization due to the increased peptide hydrophobicity and concentrated charge-state envelope during electrospray ionization. Furthermore, we systematically optimized the dual electron transfer and higher energy collision dissociation and achieved near-complete peptide sequence coverage in MS/MS spectra, allowing highly precise and reliable PTM identification. Using this method, we identified 311 and 293 combinations of histone H3 PTMs from the lymphoma cells Karpas-422 with/without drug treatment, confirming the advantages of our method in serving as a platform for profiling combinatorial histone PTMs.
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Affiliation(s)
- Rijing Liao
- Xuhui Central Hospital, Shanghai Clinical Center, Chinese Academy of Sciences , Shanghai 200031, China
| | - Dan Zheng
- Novartis Institutes for BioMedical Research (China) Co., Ltd. , 4218 Jinke Road, Shanghai 201203, China
| | - Aiying Nie
- Thermo Fisher Scientific (China) Co., Ltd. , Building 6, No. 27 Xin Jinqiao Road, Shanghai 201206, China
| | - Shaolian Zhou
- Novartis Institutes for BioMedical Research (China) Co., Ltd. , 4218 Jinke Road, Shanghai 201203, China
| | - Haibing Deng
- Novartis Institutes for BioMedical Research (China) Co., Ltd. , 4218 Jinke Road, Shanghai 201203, China
| | - Yuan Gao
- Novartis Institutes for BioMedical Research (China) Co., Ltd. , 4218 Jinke Road, Shanghai 201203, China
| | - Pengyuan Yang
- Department of Chemistry, Fudan University , 220 Handan Road, Shanghai 200433, China
| | - Yanyan Yu
- Novartis Institutes for BioMedical Research (China) Co., Ltd. , 4218 Jinke Road, Shanghai 201203, China
| | - Lin Tan
- Novartis Institutes for BioMedical Research (China) Co., Ltd. , 4218 Jinke Road, Shanghai 201203, China
| | - Wei Qi
- Novartis Institutes for BioMedical Research (China) Co., Ltd. , 4218 Jinke Road, Shanghai 201203, China
| | - Jiaxi Wu
- Xuhui Central Hospital, Shanghai Clinical Center, Chinese Academy of Sciences , Shanghai 200031, China
| | - En Li
- Novartis Institutes for BioMedical Research (China) Co., Ltd. , 4218 Jinke Road, Shanghai 201203, China
| | - Wei Yi
- Novartis Institutes for BioMedical Research (China) Co., Ltd. , 4218 Jinke Road, Shanghai 201203, China
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33
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Baird MA, Shvartsburg AA. Localization of Post-Translational Modifications in Peptide Mixtures via High-Resolution Differential Ion Mobility Separations Followed by Electron Transfer Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:2064-2070. [PMID: 27644938 PMCID: PMC7063994 DOI: 10.1007/s13361-016-1498-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 08/28/2016] [Accepted: 08/31/2016] [Indexed: 05/02/2023]
Abstract
Precise localization of post-translational modifications (PTMs) on proteins and peptides is an outstanding challenge in proteomics. While electron transfer dissociation (ETD) has dramatically advanced PTM analyses, mixtures of localization variants that commonly coexist in cells often require prior separation. Although differential or field asymmetric waveform ion mobility spectrometry (FAIMS) achieves broad variant resolution, the need for standards to identify the features has limited the utility of approach. Here we demonstrate full a priori characterization of variant mixtures by high-resolution FAIMS coupled to ETD and the procedures to systematically extract the FAIMS spectra for all variants from such data. Graphical Abstract ᅟ.
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Affiliation(s)
- Matthew A Baird
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, KS, 67260-0051, USA
| | - Alexandre A Shvartsburg
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, KS, 67260-0051, USA.
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34
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Pfammatter S, Bonneil E, Thibault P. Improvement of Quantitative Measurements in Multiplex Proteomics Using High-Field Asymmetric Waveform Spectrometry. J Proteome Res 2016; 15:4653-4665. [PMID: 27723353 DOI: 10.1021/acs.jproteome.6b00745] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Quantitative proteomics using isobaric reagent tandem mass tags (TMT) or isobaric tags for relative and absolute quantitation (iTRAQ) provides a convenient approach to compare changes in protein abundance across multiple samples. However, the analysis of complex protein digests by isobaric labeling can be undermined by the relative large proportion of co-selected peptide ions that lead to distorted reporter ion ratios and affect the accuracy and precision of quantitative measurements. Here, we investigated the use of high-field asymmetric waveform ion mobility spectrometry (FAIMS) in proteomic experiments to reduce sample complexity and improve protein quantification using TMT isobaric labeling. LC-FAIMS-MS/MS analyses of human and yeast protein digests led to significant reductions in interfering ions, which increased the number of quantifiable peptides by up to 68% while significantly improving the accuracy of abundance measurements compared to that with conventional LC-MS/MS. The improvement in quantitative measurements using FAIMS is further demonstrated for the temporal profiling of protein abundance of HEK293 cells following heat shock treatment.
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Affiliation(s)
- Sibylle Pfammatter
- Institute for Research in Immunology and Cancer, ‡Department of Chemistry, Université de Montréal , C.P. 6128, Succursale centre-ville, Montréal, Québec H3C 3J7, Canada
| | - Eric Bonneil
- Institute for Research in Immunology and Cancer, ‡Department of Chemistry, Université de Montréal , C.P. 6128, Succursale centre-ville, Montréal, Québec H3C 3J7, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, ‡Department of Chemistry, Université de Montréal , C.P. 6128, Succursale centre-ville, Montréal, Québec H3C 3J7, Canada
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35
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Harper B, Neumann EK, Stow SM, May JC, McLean JA, Solouki T. Determination of ion mobility collision cross sections for unresolved isomeric mixtures using tandem mass spectrometry and chemometric deconvolution. Anal Chim Acta 2016; 939:64-72. [PMID: 27639144 PMCID: PMC5744691 DOI: 10.1016/j.aca.2016.07.031] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 07/24/2016] [Accepted: 07/26/2016] [Indexed: 01/23/2023]
Abstract
Ion mobility (IM) is an important analytical technique for determining ion collision cross section (CCS) values in the gas-phase and gaining insight into molecular structures and conformations. However, limited instrument resolving powers for IM may restrict adequate characterization of conformationally similar ions, such as structural isomers, and reduce the accuracy of IM-based CCS calculations. Recently, we introduced an automated technique for extracting "pure" IM and collision-induced dissociation (CID) mass spectra of IM overlapping species using chemometric deconvolution of post-IM/CID mass spectrometry (MS) data [J. Am. Soc. Mass Spectrom., 2014, 25, 1810-1819]. Here we extend those capabilities to demonstrate how extracted IM profiles can be used to calculate accurate CCS values of peptide isomer ions which are not fully resolved by IM. We show that CCS values obtained from deconvoluted IM spectra match with CCS values measured from the individually analyzed corresponding peptides on uniform field IM instrumentation. We introduce an approach that utilizes experimentally determined IM arrival time (AT) "shift factors" to compensate for ion acceleration variations during post-IM/CID and significantly improve the accuracy of the calculated CCS values. Also, we discuss details of this IM deconvolution approach and compare empirical CCS values from traveling wave (TW)IM-MS and drift tube (DT)IM-MS with theoretically calculated CCS values using the projected superposition approximation (PSA). For example, experimentally measured deconvoluted TWIM-MS mean CCS values for doubly-protonated RYGGFM, RMFGYG, MFRYGG, and FRMYGG peptide isomers were 288.8 Å(2), 295.1 Å(2), 296.8 Å(2), and 300.1 Å(2); all four of these CCS values were within 1.5% of independently measured DTIM-MS values.
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Affiliation(s)
- Brett Harper
- Institute of Biomedical Studies, Baylor University, Waco, TX 76798, USA
| | - Elizabeth K Neumann
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76798, USA
| | - Sarah M Stow
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA; Vanderbilt Institute of Chemical Biology, Nashville, TN 37235, USA; Vanderbilt Institute for Integrative Biosystems Research and Education, Nashville, TN 37235, USA; Center for Innovative Technology, Nashville, TN 37235, USA
| | - Jody C May
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA; Vanderbilt Institute of Chemical Biology, Nashville, TN 37235, USA; Vanderbilt Institute for Integrative Biosystems Research and Education, Nashville, TN 37235, USA; Center for Innovative Technology, Nashville, TN 37235, USA
| | - John A McLean
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA; Vanderbilt Institute of Chemical Biology, Nashville, TN 37235, USA; Vanderbilt Institute for Integrative Biosystems Research and Education, Nashville, TN 37235, USA; Center for Innovative Technology, Nashville, TN 37235, USA
| | - Touradj Solouki
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76798, USA.
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36
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Glover MS, Dilger JM, Acton MD, Arnold RJ, Radivojac P, Clemmer DE. Examining the Influence of Phosphorylation on Peptide Ion Structure by Ion Mobility Spectrometry-Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:786-94. [PMID: 26860087 PMCID: PMC5750047 DOI: 10.1007/s13361-016-1343-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 01/12/2016] [Accepted: 01/15/2016] [Indexed: 05/12/2023]
Abstract
Ion mobility spectrometry-mass spectrometry (IMS-MS) techniques are used to study the general effects of phosphorylation on peptide structure. Cross sections for a library of 66 singly phosphorylated peptide ions from 33 pairs of positional isomers, and unmodified analogues were measured. Intrinsic size parameters (ISPs) derived from these measurements yield calculated collision cross sections for 85% of these phosphopeptide sequences that are within ±2.5% of experimental values. The average ISP for the phosphoryl group (0.64 ± 0.05) suggests that in general this moiety forms intramolecular interactions with the neighboring residues and peptide backbone, resulting in relatively compact structures. We assess the capability of ion mobility to separate positional isomers (i.e., peptide sequences that differ only in the location of the modification) and find that more than half of the isomeric pairs have >1% difference in collision cross section. Phosphorylation is also found to influence populations of structures that differ in the cis/trans orientation of Xaa-Pro peptide bonds. Several sequences with phosphorylated Ser or Thr residues located N-terminally adjacent to Pro residues show fewer conformations compared to the unmodified sequences.
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Affiliation(s)
- Matthew S Glover
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Jonathan M Dilger
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
- Spectrum Warfare Systems Department, NSWC Crane Division, Crane, IN, 47522, USA
| | - Matthew D Acton
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Randy J Arnold
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
- AB SCIEX, Vaughan, ON, L4K 4V8, Canada
| | - Predrag Radivojac
- Department of Computer Science and Informatics, Indiana University, Bloomington, IN, 47405, USA
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA.
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37
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Cooper HJ. To What Extent is FAIMS Beneficial in the Analysis of Proteins? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:566-77. [PMID: 26843211 PMCID: PMC4792363 DOI: 10.1007/s13361-015-1326-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 12/08/2015] [Accepted: 12/10/2015] [Indexed: 05/11/2023]
Abstract
High field asymmetric waveform ion mobility spectrometry (FAIMS), also known as differential ion mobility spectrometry, is emerging as a tool for biomolecular analysis. In this article, the benefits and limitations of FAIMS for protein analysis are discussed. The principles and mechanisms of FAIMS separation of ions are described, and the differences between FAIMS and conventional ion mobility spectrometry are detailed. Protein analysis is considered from both the top-down (intact proteins) and the bottom-up (proteolytic peptides) perspective. The roles of FAIMS in the analysis of complex mixtures of multiple intact proteins and in the analysis of multiple conformers of a single protein are assessed. Similarly, the application of FAIMS in proteomics and targeted analysis of peptides are considered.
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Affiliation(s)
- Helen J Cooper
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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38
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Ollikainen E, Bonabi A, Nordman N, Jokinen V, Kotiaho T, Kostiainen R, Sikanen T. Rapid separation of phosphopeptides by microchip electrophoresis-electrospray ionization mass spectrometry. J Chromatogr A 2016; 1440:249-254. [PMID: 26931427 DOI: 10.1016/j.chroma.2016.02.063] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 02/19/2016] [Accepted: 02/22/2016] [Indexed: 01/12/2023]
Abstract
Protein phosphorylation is a significant biological process, but separation of phosphorylated peptide isomers is often challenging for many analytical techniques. We developed a microchip electrophoresis (MCE) method for rapid separation of phosphopeptides with on-chip electrospray ionization (ESI) facilitating online sample introduction to the mass spectrometer (MS). With the method, two monophosphorylated positional isomers of insulin receptor peptide (IR1A and IR1B) and a triply phosphorylated insulin receptor peptide (IR3), all with the same amino acid sequence, were separated from the nonphosphorylated peptide (IR0) in less than one minute. For efficient separation of the positional peptide isomers from each other derivatization with 9-fluorenylmethyl reagents (either chloroformate, Fmoc-Cl, or N-succinimidyl carbonate, Fmoc-OSu) was required before the analysis. The derivatization improved not only the separation of the monophosphorylated positional peptide isomers in MCE, but also identification of the phosphorylation site based on MS/MS.
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Affiliation(s)
- Elisa Ollikainen
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5E, 00014 University of Helsinki, Finland
| | - Ashkan Bonabi
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5E, 00014 University of Helsinki, Finland
| | - Nina Nordman
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5E, 00014 University of Helsinki, Finland
| | - Ville Jokinen
- Department of Materials Science and Engineering, School of Chemical Technology, Aalto University, Finland, Micronova, Tietotie 3, 02150, Finland
| | - Tapio Kotiaho
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5E, 00014 University of Helsinki, Finland; Laboratory of Analytical Chemistry, Department of Chemistry, University of Helsinki, A. I. Virtasen aukio 1, 00014 University of Helsinki, Finland
| | - Risto Kostiainen
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5E, 00014 University of Helsinki, Finland
| | - Tiina Sikanen
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5E, 00014 University of Helsinki, Finland.
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39
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Bonneil E, Pfammatter S, Thibault P. Enhancement of mass spectrometry performance for proteomic analyses using high-field asymmetric waveform ion mobility spectrometry (FAIMS). JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:1181-1195. [PMID: 26505763 DOI: 10.1002/jms.3646] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Revised: 08/18/2015] [Accepted: 08/19/2015] [Indexed: 06/05/2023]
Abstract
Remarkable advances in mass spectrometry sensitivity and resolution have been accomplished over the past two decades to enhance the depth and coverage of proteome analyses. As these technological developments expanded the detection capability of mass spectrometers, they also revealed an increasing complexity of low abundance peptides, solvent clusters and sample contaminants that can confound protein identification. Separation techniques that are complementary and can be used in combination with liquid chromatography are often sought to improve mass spectrometry sensitivity for proteomics applications. In this context, high-field asymmetric waveform ion mobility spectrometry (FAIMS), a form of ion mobility that exploits ion separation at low and high electric fields, has shown significant advantages by focusing and separating multiply charged peptide ions from singly charged interferences. This paper examines the analytical benefits of FAIMS in proteomics to separate co-eluting peptide isomers and to enhance peptide detection and quantitative measurements of protein digests via native peptides (label-free) or isotopically labeled peptides from metabolic labeling or chemical tagging experiments.
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Affiliation(s)
- Eric Bonneil
- Institute for Research in Immunology and Cancer, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, Québec, H3C 3J7, Canada
| | - Sibylle Pfammatter
- Institute for Research in Immunology and Cancer, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, Québec, H3C 3J7, Canada
- Department of Chemistry, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, Québec, H3C 3J7, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, Québec, H3C 3J7, Canada
- Department of Chemistry, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, Québec, H3C 3J7, Canada
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40
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Lermyte F, Sobott F. Electron transfer dissociation provides higher-order structural information of native and partially unfolded protein complexes. Proteomics 2015; 15:2813-22. [DOI: 10.1002/pmic.201400516] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 03/13/2015] [Accepted: 06/15/2015] [Indexed: 12/31/2022]
Affiliation(s)
- Frederik Lermyte
- UA-VITO Center for Proteomics; University of Antwerp; Antwerp Belgium
- Biomolecular & Analytical Mass Spectrometry group; Department of Chemistry; University of Antwerp; Antwerp Belgium
| | - Frank Sobott
- UA-VITO Center for Proteomics; University of Antwerp; Antwerp Belgium
- Biomolecular & Analytical Mass Spectrometry group; Department of Chemistry; University of Antwerp; Antwerp Belgium
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41
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Sarsby J, Griffiths RL, Race AM, Bunch J, Randall EC, Creese AJ, Cooper HJ. Liquid Extraction Surface Analysis Mass Spectrometry Coupled with Field Asymmetric Waveform Ion Mobility Spectrometry for Analysis of Intact Proteins from Biological Substrates. Anal Chem 2015; 87:6794-800. [DOI: 10.1021/acs.analchem.5b01151] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Joscelyn Sarsby
- School
of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Rian L. Griffiths
- School
of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Alan M. Race
- National Physical
Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, United Kingdom
| | - Josephine Bunch
- National Physical
Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, United Kingdom
- School
of Pharmacy, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Elizabeth C. Randall
- School
of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Andrew J. Creese
- School
of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Helen J. Cooper
- School
of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
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42
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Hanozin E, Morsa D, De Pauw E. Energetics and structural characterization of isomers using ion mobility and gas-phase H/D exchange: Learning from lasso peptides. Proteomics 2015; 15:2823-34. [DOI: 10.1002/pmic.201400534] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 03/03/2015] [Accepted: 03/17/2015] [Indexed: 12/29/2022]
Affiliation(s)
- Emeline Hanozin
- Mass Spectrometry Laboratory, Department of Chemistry; University of Liege; Liege Belgium
| | - Denis Morsa
- Mass Spectrometry Laboratory, Department of Chemistry; University of Liege; Liege Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, Department of Chemistry; University of Liege; Liege Belgium
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43
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Benigni P, Thompson CJ, Ridgeway ME, Park MA, Fernandez-Lima F. Targeted high-resolution ion mobility separation coupled to ultrahigh-resolution mass spectrometry of endocrine disruptors in complex mixtures. Anal Chem 2015; 87:4321-5. [PMID: 25818070 PMCID: PMC4867114 DOI: 10.1021/ac504866v] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Traditional separation and detection of targeted compounds from complex mixtures from environmental matrices requires the use of lengthy prefractionation steps and high-resolution mass analyzers due to the large number of chemical components and their large structural diversity (highly isomeric). In the present work, selected accumulation trapped ion mobility spectrometry (SA-TIMS) is coupled to Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) for direct separation and characterization of targeted endocrine-disrupting compounds (EDC) from a complex environmental matrix in a single analysis. In particular, targeted identification based on high-resolution mobility (R ∼ 70-120) and ultrahigh-resolution mass measurements (R > 400 000) of seven commonly targeted EDC and their isobars (e.g., bisphenol A, (Z)- and (E)-diethylstilbestrol, hexestrol, estrone, α-estradiol, and 17-ethynylestradiol) is shown from a complex mixture of water-soluble organic matter (e.g., Suwannee River Fulvic Acid Standard II) complemented with reference standard measurements and theoretical calculations (<3% error).
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Affiliation(s)
- Paolo Benigni
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | | | - Mark E. Ridgeway
- Bruker Daltonics Inc., Billerica, Massachusetts 01821, United States
| | - Melvin A. Park
- Bruker Daltonics Inc., Billerica, Massachusetts 01821, United States
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
- Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
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44
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Pettit ME, Harper B, Brantley MR, Solouki T. Collision-energy resolved ion mobility characterization of isomeric mixtures. Analyst 2015. [DOI: 10.1039/c5an00940e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Existing instrumental resolving power limitations in ion mobility spectrometry (IMS) often restrict adequate characterization of unresolved or co-eluting chemical isomers.
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Affiliation(s)
| | - Brett Harper
- Institute of Biomedical Studies
- Baylor University
- Waco
- USA
| | | | - Touradj Solouki
- Department of Chemistry and Biochemistry
- Baylor University
- Waco
- USA
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45
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Griffiths RL, Dexter A, Creese AJ, Cooper HJ. Liquid extraction surface analysis field asymmetric waveform ion mobility spectrometry mass spectrometry for the analysis of dried blood spots. Analyst 2015. [DOI: 10.1039/c5an00933b] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
LESA mass spectrometry coupled with high field asymmetric waveform ion mobility spectrometry (FAIMS) for the analysis of dried blood spots.
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Affiliation(s)
| | - Alex Dexter
- School of Biosciences
- University of Birmingham
- Edgbaston
- UK
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46
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Harper B, Miladi M, Solouki T. Loss of internal backbone carbonyls: additional evidence for sequence-scrambling in collision-induced dissociation of y-type ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1716-1729. [PMID: 25070583 DOI: 10.1007/s13361-014-0955-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Revised: 05/14/2014] [Accepted: 06/19/2014] [Indexed: 06/03/2023]
Abstract
It is shown that y-type ions, after losing C-terminal H2O or NH3, can lose an internal backbone carbonyl (CO) from different peptide positions and yield structurally different product fragment ions upon collision-induced dissociation (CID). Such CO losses from internal peptide backbones of y-fragment ions are not unique to a single peptide and were observed in four of five model peptides studied herein. Experimental details on examples of CO losses from y-type fragment ions for an isotopically labeled AAAAHAA-NH2 heptapeptide and des-acetylated-α-melanocyte-stimulating hormone (dα-MSH) (SYSMEHFRWGKPV-NH2) are reported. Results from isotope labeling, tandem mass spectrometry (MS(n)), and ion mobility-mass spectrometry (IM-MS) confirm that CO losses from different amino acids of m/z-isolated y-type ions yield structurally different ions. It is shown that losses of internal backbone carbonyls (as CID products of m/z-isolated y-type ions) are among intermediate steps towards formation of rearranged or permutated product fragment ions. Possible mechanisms for generation of the observed sequence-scrambled a-"like" ions, as intermediates in sequence-scrambling pathways of y-type ions, are proposed and discussed.
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Affiliation(s)
- Brett Harper
- Institute of Biomedical Studies, Baylor University, Waco, TX, 76798, USA
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47
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Menlyadiev MR, Tadjimukhamedov FK, Tarassov A, Wollnik H, Eiceman GA. Low-mobility-pass filter between atmospheric pressure chemical ionization and electrospray ionization sources and a single quadrupole mass spectrometer: computational models and measurements. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:135-142. [PMID: 24285398 DOI: 10.1002/rcm.6762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 10/04/2013] [Accepted: 10/07/2013] [Indexed: 06/02/2023]
Abstract
RATIONALE Mixtures of ions produced in sources at atmospheric pressure, including chemical ionization (APCI) and electrospray ionization (ESI) can be simplified at or near ambient pressure using ion mobility based filters. METHODS A low-mobility-pass filter (LMPF) based on a simple mechanical design and simple electronic control was designed, modeled and tested with vapors of 2-hexadecanone in an APCI source and with spray of peptide solutions in an ESI source. The LMPF geometry was planar and small (4 mm wide × 13 mm long) and electric control was through a symmetric waveform in low kHz with amplitude between 0 and 10 V. RESULTS Computational models established idealized performance for transmission efficiency of ions of several reduced mobility coefficients over the range of amplitudes and were matched by computed values from ion abundances in mass spectra. The filter exhibited a broad response function, equivalent to a Bode Plot in electronic filters, suggesting that ion filtering could be done in blocks ~50 m/z units wide. CONCLUSIONS The benefit of this concept is that discrimination against ions of high mobility is controlled by only a single parameter: waveform amplitude at fixed frequency. The effective removal of high mobility ions, those of low mass-to-charge, can be beneficial for applications with ion-trap-based mass spectrometers to remove excessive levels of solvent or matrix ions.
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Affiliation(s)
- Marlen R Menlyadiev
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM, 88003, USA
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48
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Masyuko R, Lanni EJ, Sweedler JV, Bohn PW. Correlated imaging--a grand challenge in chemical analysis. Analyst 2013; 138:1924-39. [PMID: 23431559 PMCID: PMC3718397 DOI: 10.1039/c3an36416j] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Correlated chemical imaging is an emerging strategy for acquisition of images by combining information from multiplexed measurement platforms to track, visualize, and interpret in situ changes in the structure, organization, and activities of interesting chemical systems, frequently spanning multiple decades in space and time. Acquiring and correlating information from complementary imaging experiments has the potential to expose complex chemical behavior in ways that are simply not available from single methods applied in isolation, thereby greatly amplifying the information gathering power of imaging experiments. However, in order to correlate image information across platforms, a number of issues must be addressed. First, signals are obtained from disparate experiments with fundamentally different figures of merit, including pixel size, spatial resolution, dynamic range, and acquisition rates. In addition, images are often acquired on different instruments in different locations, so the sample must be registered spatially so that the same area of the sample landscape is addressed. The signals acquired must be correlated in both spatial and temporal domains, and the resulting information has to be presented in a way that is readily understood. These requirements pose special challenges for image cross-correlation that go well beyond those posed in single technique imaging approaches. The special opportunities and challenges that attend correlated imaging are explored by specific reference to correlated mass spectrometric and Raman imaging, a topic of substantial and growing interest.
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Affiliation(s)
- Rachel Masyuko
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
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49
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Creese AJ, Shimwell NJ, Larkins KPB, Heath JK, Cooper HJ. Probing the complementarity of FAIMS and strong cation exchange chromatography in shotgun proteomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:431-43. [PMID: 23400772 PMCID: PMC3586169 DOI: 10.1007/s13361-012-0544-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 11/08/2012] [Accepted: 11/11/2012] [Indexed: 05/25/2023]
Abstract
High field asymmetric waveform ion mobility spectrometry (FAIMS), also known as differential ion mobility spectrometry, coupled with liquid chromatography tandem mass spectrometry (LC-MS/MS) offers benefits for the analysis of complex proteomics samples. Advantages include increased dynamic range, increased signal-to-noise, and reduced interference from ions of similar m/z. FAIMS also separates isomers and positional variants. An alternative, and more established, method of reducing sample complexity is prefractionation by use of strong cation exchange chromatography. Here, we have compared SCX-LC-MS/MS with LC-FAIMS-MS/MS for the identification of peptides and proteins from whole cell lysates from the breast carcinoma SUM52 cell line. Two FAIMS approaches are considered: (1) multiple compensation voltages within a single LC-MS/MS analysis (internal stepping) and (2) repeat LC-MS/MS analyses at different and fixed compensation voltages (external stepping). We also consider the consequence of the fragmentation method (electron transfer dissociation or collision-induced dissociation) on the workflow performance. The external stepping approach resulted in a greater number of protein and peptide identifications than the internal stepping approach for both ETD and CID MS/MS, suggesting that this should be the method of choice for FAIMS proteomics experiments. The overlap in protein identifications from the SCX method and the external FAIMS method was ~25% for both ETD and CID, and for peptides was less than 20%. The lack of overlap between FAIMS and SCX highlights the complementarity of the two techniques. Charge state analysis of the peptide assignments showed that the FAIMS approach identified a much greater proportion of triply-charged ions.
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Affiliation(s)
- Andrew J. Creese
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Neil J. Shimwell
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, B15 2TT UK
- Present Address: School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Katherine P. B. Larkins
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - John K. Heath
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Helen J. Cooper
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, B15 2TT UK
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50
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Stedwell CN, Patrick AL, Gulyuz K, Polfer NC. Screening for Phosphorylated and Nonphosphorylated Peptides by Infrared Photodissociation Spectroscopy. Anal Chem 2012; 84:9907-12. [DOI: 10.1021/ac3023058] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Corey N. Stedwell
- Department of Chemistry, University of Florida, Post Office Box 117200, Gainesville, Florida
32611, United States
| | - Amanda L. Patrick
- Department of Chemistry, University of Florida, Post Office Box 117200, Gainesville, Florida
32611, United States
| | - Kerim Gulyuz
- Department of Chemistry, University of Florida, Post Office Box 117200, Gainesville, Florida
32611, United States
| | - Nicolas C. Polfer
- Department of Chemistry, University of Florida, Post Office Box 117200, Gainesville, Florida
32611, United States
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