1
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Premathilaka SH, Westrick JA, Isailovic D. Identification of Serine-Containing Microcystins by UHPLC-MS/MS Using Thiol and Sulfoxide Derivatizations and Detection of Novel Neutral Losses. Anal Chem 2024; 96:775-786. [PMID: 38170221 DOI: 10.1021/acs.analchem.3c04047] [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: 01/05/2024]
Abstract
Microcystins (MCs) are hepatotoxic cyclic heptapeptides produced by cyanobacteria, and their structural diversity has led to the discovery of more than 300 congeners to date. However, with known amino acid combinations, many more MC congeners are theoretically possible, suggesting many remain unidentified. Herein, two novel serine (Ser)-containing MCs were putatively identified in a Lake Erie cyanobacterial harmful algal bloom (cyanoHAB), using high-resolution UHPLC-MS as well as thiol and sulfoxide derivatization procedures. These MCs contain an α,β-unsaturated carbonyl on methyl dehydroalanine (Mdha) residue that undergoes Michael addition to produce a thiol-derivatized MC. Derivatization reactions using various thiolation reagents were followed by MS/MS, and two Python codes were used for data analysis and structural elucidation of MCs. Two novel MCs containing Ser at position 1 (i.e., next to Mdha) were putatively identified as [Ser1]MC-RR and [Ser1]MC-YR. Using thiol- and sulfoxide-modified [Ser1]MCs, identifications were confirmed by the observation of specific neutral losses of the oxidized thiols or sulfoxides in CID-MS/MS spectra in both positive and negative electrospray ionization (ESI) modes. These novel neutral losses are unique for MCs with Mdha and an adjacent Ser residue. Data suggest that a gas-phase reaction occurs between oxygen from adjacent Ser residue and sulfur of the Mdha-bonded thiol or sulfoxide, which leads to the formation and detection of stable cyclic MC ions in MS/MS spectra at m/z values corresponding to the loss of oxidized thiols or oxidized sulfoxides from Ser1-containing MCs.
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Affiliation(s)
- Sanduni H Premathilaka
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio 43606, United States
| | - Judy A Westrick
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Dragan Isailovic
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio 43606, United States
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2
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Khateb H, Hook AL, Kern S, Watts JA, Singh S, Jackson D, Marinez-Pomares L, Williams P, Alexander MR. Identification of Pseudomonas aeruginosa exopolysaccharide Psl in biofilms using 3D OrbiSIMS. Biointerphases 2023; 18:031007. [PMID: 37255378 PMCID: PMC10234676 DOI: 10.1116/6.0002604] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/29/2023] [Accepted: 05/09/2023] [Indexed: 06/01/2023] Open
Abstract
Secondary ion mass spectrometry (SIMS) offers advantages over both liquid extraction mass spectrometry and matrix assisted laser desorption mass spectrometry in that it provides the direct in situ analysis of molecules and has the potential to preserve the 3D location of an analyte in a sample. Polysaccharides are recognized as challenging analytes in the mass spectrometry of liquids and are also difficult to identify and assign using SIMS. Psl is an exopolysaccharide produced by Pseudomonas aeruginosa, which plays a key role in biofilm formation and maturation. In this Letter, we describe the use of the OrbiTrap analyzer with SIMS (3D OrbiSIMS) for the label-free mass spectrometry of Psl, taking advantage of its high mass resolving power for accurate secondary ion assignment. We study a P. aeruginosa biofilm and compare it with purified Psl to enable the assignment of secondary ions specific to the Psl structure. This resulted in the identification of 17 peaks that could confidently be ascribed to Psl fragments within the biofilm matrix. The complementary approach of the following neutral loss sequences is also shown to identify multiple oligosaccharide fragments without the requirement of a biological reference sample.
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Affiliation(s)
- Heba Khateb
- Advanced Materials and Healthcare Technologies Division, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom
- National Biofilms Innovation Centre, Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Andrew L Hook
- Advanced Materials and Healthcare Technologies Division, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom
| | - Stefanie Kern
- Nanoscale and Microscale Research Centre, University of Nottingham, Nottingham, United Kingdom
| | - Julie A Watts
- Nanoscale and Microscale Research Centre, University of Nottingham, Nottingham, United Kingdom
| | - Sonali Singh
- National Biofilms Innovation Centre and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Darryl Jackson
- National Biofilms Innovation Centre and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Luisa Marinez-Pomares
- National Biofilms Innovation Centre and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Paul Williams
- National Biofilms Innovation Centre, Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Morgan R Alexander
- Advanced Materials and Healthcare Technologies Division, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom
- National Biofilms Innovation Centre, Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
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3
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Estrada P, Bañares-Hidalgo Á, Pérez-Gil J. Disulfide bonds in the SAPA domain of the pulmonary surfactant protein B precursor. J Proteomics 2022; 269:104722. [PMID: 36108905 DOI: 10.1016/j.jprot.2022.104722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/31/2022] [Accepted: 09/06/2022] [Indexed: 10/14/2022]
Abstract
The disulfide bonds formed in the SAPA domain of a recombinant version of the NH2-terminal propeptide (SP-BN) from the precursor of human pulmonary surfactant protein B (SP-B) were identified through sequential digestion of SP-BN with GluC/trypsin or thermolysin/GluC, followed by mass spectrometry (MS) analysis. MS spectra allowed identification of disulfide bonds between Cys32-Cys49 and Cys40-Cys55, and we propose a disulfide connectivity pattern of 1-3 and 2-4 within the SAPA domain, with the Cys residues numbered according to their position from the N-terminus of the propeptide sequence. The peaks with m/z ∼ 2136 and ∼ 1780 in the MS spectrum of the GluC/trypsin digest were assigned to peptides 24AWTTSSLACAQGPE37 and 45QALQCR50 linked by Cys32-Cys49 and 38FWCQSLE44 and 51ALGHCLQE58 linked by Cys40-Cys55 respectively. Tandem mass spectrometry (MS/MS) analysis verified the position of the bonds. The results of the series ions, immonium ions and internal fragment ions were all compatible with the proposed 1-3/2-4 position of the disulfide bonds in the SAPA domain. This X-pattern differs from the kringle-type found in the SAPB domain of the SAPLIP proteins, where the first Cys in the sequence links to the last, the second to the penultimate and the third to the fourth one. Regarding the SAPB domain of the SP-BN propeptide, the MS analysis of both digests identified the bond Cys100-Cys112, numbered 7-8, which is coincident with the bond position in the kringle motif. SIGNIFICANCE: The SAPLIP (saposin-like proteins) family encompasses several proteins with homology to saposins (sphingolipids activator proteins). These are proteins with mainly alpha-helical folds, compact packing including well conserved disulfide bonds and ability to interact with phospholipids and membranes. There are two types of saposin-like domains termed as Saposin A (SAPA) and Saposin B (SAPB) domains. While disulfide connectivity has been well established in several SAPB domains, the position of disulfide bonds in SAPA domains is still unknown. The present study approaches a detailed proteomic study to determine disulfide connectivity in the SAPA domain of the precursor of human pulmonary surfactant-associated protein SP-B. This task has been a challenge requiring the combination of different sequential proteolytic treatments followed by MS analysis including MALDI-TOF and tandem mass MS/MS spectrometry. The determination for first time of the position of disulfide bonds in SAPA domains is an important step to understand the structural determinants defining its biological functions.
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Affiliation(s)
- Pilar Estrada
- Dept. Biochemistry and Molecular Biology, Faculty of Biology, Complutense University, 28040 Madrid, Spain
| | - Ángeles Bañares-Hidalgo
- Dept. Biochemistry and Molecular Biology, Faculty of Biology, Complutense University, 28040 Madrid, Spain
| | - Jesús Pérez-Gil
- Dept. Biochemistry and Molecular Biology, Faculty of Biology, Complutense University, 28040 Madrid, Spain.
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4
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Gao F, Tom E, Skowronska-Krawczyk D. Dynamic Progress in Technological Advances to Study Lipids in Aging: Challenges and Future Directions. FRONTIERS IN AGING 2022; 3:851073. [PMID: 35821837 PMCID: PMC9261449 DOI: 10.3389/fragi.2022.851073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 02/23/2022] [Indexed: 11/29/2022]
Abstract
Lipids participate in all cellular processes. Diverse methods have been developed to investigate lipid composition and distribution in biological samples to understand the effect of lipids across an organism’s lifespan. Here, we summarize the advanced techniques for studying lipids, including mass spectrometry-based lipidomics, lipid imaging, chemical-based lipid analysis and lipid engineering and their advantages. We further discuss the limitation of the current methods to gain an in-depth knowledge of the role of lipids in aging, and the possibility of lipid-based therapy in aging-related diseases.
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Affiliation(s)
- Fangyuan Gao
- Department of Ophthalmology, Center for Translational Vision Research, School of Medicine, UC Irvine, Irvine, CA, United States
| | - Emily Tom
- Department of Physiology and Biophysics, Department of Ophthalmology, Center for Translational Vision Research, School of Medicine, UC Irvine, Irvine, CA, United States
| | - Dorota Skowronska-Krawczyk
- Department of Ophthalmology, Center for Translational Vision Research, School of Medicine, UC Irvine, Irvine, CA, United States
- Department of Physiology and Biophysics, Department of Ophthalmology, Center for Translational Vision Research, School of Medicine, UC Irvine, Irvine, CA, United States
- *Correspondence: Dorota Skowronska-Krawczyk,
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5
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Aisporna A, Chen A, Benton HP, Galano JM, Giera M, Siuzdak G. Neutral Loss Mass Spectral Data Enhances Molecular Similarity Analysis in METLIN. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:530-534. [PMID: 35174708 PMCID: PMC10131246 DOI: 10.1021/jasms.1c00343] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Neutral loss (NL) spectral data presents a mirror of MS2 data and is a valuable yet largely untapped resource for molecular discovery and similarity analysis. Tandem mass spectrometry (MS2) data is effective for the identification of known molecules and the putative identification of novel, previously uncharacterized molecules (unknowns). Yet, MS2 data alone is limited in characterizing structurally related molecules. To facilitate unknown identification and complement the METLIN-MS2 fragment ion database for characterizing structurally related molecules, we have created a MS2 to NL converter as a part of the METLIN platform. The converter has been used to transform METLIN's MS2 data into a neutral loss database (METLIN-NL) on over 860 000 individual molecular standards. The platform includes both the MS2 to NL converter and a graphical user interface enabling comparative analyses between MS2 and NL data. Examples of NL spectral data are shown with oxylipin analogues and two structurally related statin molecules to demonstrate NL spectra and their ability to help characterize structural similarity. Mirroring MS2 data to generate NL spectral data offers a unique dimension for chemical and metabolite structure characterization.
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Affiliation(s)
- Aries Aisporna
- Scripps Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Andy Chen
- Scripps Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - H. Paul Benton
- Scripps Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Jean Marie Galano
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS, ENSCM, Université de Montpellier, France
| | - Martin Giera
- Leiden University Medical Center, Center for Proteomics and Metabolomics, Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Gary Siuzdak
- Scripps Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
- Department of Chemistry, Molecular and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
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6
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Yu F, Haynes SE, Teo GC, Avtonomov DM, Polasky DA, Nesvizhskii AI. Fast Quantitative Analysis of timsTOF PASEF Data with MSFragger and IonQuant. Mol Cell Proteomics 2020; 19:1575-1585. [PMID: 32616513 PMCID: PMC7996969 DOI: 10.1074/mcp.tir120.002048] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/21/2020] [Indexed: 01/01/2023] Open
Abstract
Ion mobility brings an additional dimension of separation to LC-MS, improving identification of peptides and proteins in complex mixtures. A recently introduced timsTOF mass spectrometer (Bruker) couples trapped ion mobility separation to TOF mass analysis. With the parallel accumulation serial fragmentation (PASEF) method, the timsTOF platform achieves promising results, yet analysis of the data generated on this platform represents a major bottleneck. Currently, MaxQuant and PEAKS are most used to analyze these data. However, because of the high complexity of timsTOF PASEF data, both require substantial time to perform even standard tryptic searches. Advanced searches (e.g. with many variable modifications, semi- or non-enzymatic searches, or open searches for post-translational modification discovery) are practically impossible. We have extended our fast peptide identification tool MSFragger to support timsTOF PASEF data, and developed a label-free quantification tool, IonQuant, for fast and accurate 4-D feature extraction and quantification. Using a HeLa data set published by Meier et al. (2018), we demonstrate that MSFragger identifies significantly (∼30%) more unique peptides than MaxQuant (1.6.10.43), and performs comparably or better than PEAKS X+ (∼10% more peptides). IonQuant outperforms both in terms of number of quantified proteins while maintaining good quantification precision and accuracy. Runtime tests show that MSFragger and IonQuant can fully process a typical two-hour PASEF run in under 70 min on a typical desktop (6 CPU cores, 32 GB RAM), significantly faster than other tools. Finally, through semi-enzymatic searching, we significantly increase the number of identified peptides. Within these semi-tryptic identifications, we report evidence of gas-phase fragmentation before MS/MS analysis.
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Affiliation(s)
- Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Sarah E Haynes
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Guo Ci Teo
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Dmitry M Avtonomov
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Daniel A Polasky
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.
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7
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Powell T, Knight MJ, O'Hara J, Burkitt W. Discovery of a Photoinduced Histidine-Histidine Cross-Link in an IgG4 Antibody. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1233-1240. [PMID: 32392057 DOI: 10.1021/jasms.0c00076] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A novel histidine-histidine (His-His) photooxidative cross-link has been identified in an IgG4 antibody. It was formed between the side chain of a histidine residue of the antibody and histidine from the formulation buffer. The structure of the cross-link was elucidated using high performance liquid chromatography (HPLC) hyphenated to tandem mass spectrometry (MS/MS) with higher energy collisional dissociation (HCD). The cross-link was found in multiple conformations, as the location of the oxygen varied. Furthermore, the extent of cross-link formation was shown to correlate with the amount of light the antibody was exposed to as well as the solvent accessibility of each modification site.
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Affiliation(s)
- Thomas Powell
- Biomolecular Formulation and Characterization Sciences, UCB Group, Slough, SL3WE, United Kingdom
| | - Michael J Knight
- Biomolecular Formulation and Characterization Sciences, UCB Group, Slough, SL3WE, United Kingdom
| | - John O'Hara
- Biomolecular Formulation and Characterization Sciences, UCB Group, Slough, SL3WE, United Kingdom
| | - William Burkitt
- Biomolecular Formulation and Characterization Sciences, UCB Group, Slough, SL3WE, United Kingdom
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8
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Abstract
Reversible protein phosphorylation is a key regulatory posttranslational modification that plays a significant role in major cellular signaling processes. Phosphorylation events can be systematically identified, quantified, and localized on protein sequence using publicly available bioinformatic tools. Here we present the software tools commonly used by the phosphoproteomics community, discuss their underlying principles of operation, and provide a protocol for large-scale phosphoproteome data analysis using the MaxQuant software suite.
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9
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Trahan C, Oeffinger M. Targeted cross-linking-mass spectrometry determines vicinal interactomes within heterogeneous RNP complexes. Nucleic Acids Res 2015; 44:1354-69. [PMID: 26657640 PMCID: PMC4756821 DOI: 10.1093/nar/gkv1366] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 11/24/2015] [Indexed: 02/06/2023] Open
Abstract
Proteomic and RNomic approaches have identified many components of different ribonucleoprotein particles (RNPs), yet still little is known about the organization and protein proximities within these heterogeneous and highly dynamic complexes. Here we describe a targeted cross-linking approach, which combines cross-linking from a known anchor site with affinity purification and mass spectrometry (MS) to identify the changing vicinity interactomes along RNP maturation pathways. Our method confines the reaction radius of a heterobifunctional cross-linker to a specific interaction surface, increasing the probability to capture low abundance conformations and transient vicinal interactors too infrequent for identification by traditional cross-linking-MS approaches, and determine protein proximities within RNPs. Applying the method to two conserved RNA-associated complexes in Saccharomyces cerevisae, the mRNA export receptor Mex67:Mtr2 and the pre-ribosomal Nop7 subcomplex, we identified dynamic vicinal interactomes within those complexes and along their changing pathway milieu. Our results therefore show that this method provides a new tool to study the changing spatial organization of heterogeneous dynamic RNP complexes.
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Affiliation(s)
- Christian Trahan
- Department for Systems Biology, Institut de recherches cliniques de Montréal, Montréal, Québec H2W 1R7, Canada Département de biochimie, Faculté de médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Marlene Oeffinger
- Department for Systems Biology, Institut de recherches cliniques de Montréal, Montréal, Québec H2W 1R7, Canada Département de biochimie, Faculté de médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada Division of Experimental Medicine, Faculty of Medicine, McGill University, Montréal, Québec H3A 1A3, Canada
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10
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Erickson BK, Jedrychowski MP, McAlister GC, Everley RA, Kunz R, Gygi SP. Evaluating multiplexed quantitative phosphopeptide analysis on a hybrid quadrupole mass filter/linear ion trap/orbitrap mass spectrometer. Anal Chem 2015; 87:1241-9. [PMID: 25521595 PMCID: PMC4303329 DOI: 10.1021/ac503934f] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
![]()
As
a driver for many biological processes, phosphorylation remains
an area of intense research interest. Advances in multiplexed quantitation
utilizing isobaric tags (e.g., TMT and iTRAQ) have the potential to
create a new paradigm in quantitative proteomics. New instrumentation
and software are propelling these multiplexed workflows forward, which
results in more accurate, sensitive, and reproducible quantitation
across tens of thousands of phosphopeptides. This study assesses the
performance of multiplexed quantitative phosphoproteomics on the Orbitrap
Fusion mass spectrometer. Utilizing a two-phosphoproteome model of
precursor ion interference, we assessed the accuracy of phosphopeptide
quantitation across a variety of experimental approaches. These methods
included the use of synchronous precursor selection (SPS) to enhance
TMT reporter ion intensity and accuracy. We found that (i) ratio distortion
remained a problem for phosphopeptide analysis in multiplexed quantitative
workflows, (ii) ratio distortion can be overcome by the use of an
SPS-MS3 scan, (iii) interfering ions generally possessed a different
charge state than the target precursor, and (iv) selecting only the
phosphate neutral loss peak (single notch) for the MS3 scan still
provided accurate ratio measurements. Remarkably, these data suggest
that the underlying cause of interference may not be due to coeluting
and cofragmented peptides but instead from consistent, low level background
fragmentation. Finally, as a proof-of-concept 10-plex experiment,
we compared phosphopeptide levels from five murine brains to five
livers. In total, the SPS-MS3 method quantified 38 247 phosphopeptides,
corresponding to 11 000 phosphorylation sites. With 10 measurements
recorded for each phosphopeptide, this equates to more than 628 000
binary comparisons collected in less than 48 h.
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Affiliation(s)
- Brian K Erickson
- Harvard Medical School , Department of Cell Biology, Boston, Massachusetts 02115, United States
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11
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Strategies in protein sequencing and characterization: Multi-enzyme digestion coupled with alternate CID/ETD tandem mass spectrometry. Anal Chim Acta 2015; 854:106-17. [DOI: 10.1016/j.aca.2014.10.053] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 10/28/2014] [Accepted: 10/30/2014] [Indexed: 12/14/2022]
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12
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Kelstrup CD, Frese C, Heck AJR, Olsen JV, Nielsen ML. Analytical utility of mass spectral binning in proteomic experiments by SPectral Immonium Ion Detection (SPIID). Mol Cell Proteomics 2014; 13:1914-24. [PMID: 24895383 PMCID: PMC4125726 DOI: 10.1074/mcp.o113.035915] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Unambiguous identification of tandem mass spectra is a cornerstone in mass-spectrometry-based proteomics. As the study of post-translational modifications (PTMs) by means of shotgun proteomics progresses in depth and coverage, the ability to correctly identify PTM-bearing peptides is essential, increasing the demand for advanced data interpretation. Several PTMs are known to generate unique fragment ions during tandem mass spectrometry, the so-called diagnostic ions, which unequivocally identify a given mass spectrum as related to a specific PTM. Although such ions offer tremendous analytical advantages, algorithms to decipher MS/MS spectra for the presence of diagnostic ions in an unbiased manner are currently lacking. Here, we present a systematic spectral-pattern-based approach for the discovery of diagnostic ions and new fragmentation mechanisms in shotgun proteomics datasets. The developed software tool is designed to analyze large sets of high-resolution peptide fragmentation spectra independent of the fragmentation method, instrument type, or protease employed. To benchmark the software tool, we analyzed large higher-energy collisional activation dissociation datasets of samples containing phosphorylation, ubiquitylation, SUMOylation, formylation, and lysine acetylation. Using the developed software tool, we were able to identify known diagnostic ions by comparing histograms of modified and unmodified peptide spectra. Because the investigated tandem mass spectra data were acquired with high mass accuracy, unambiguous interpretation and determination of the chemical composition for the majority of detected fragment ions was feasible. Collectively we present a freely available software tool that allows for comprehensive and automatic analysis of analogous product ions in tandem mass spectra and systematic mapping of fragmentation mechanisms related to common amino acids.
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Affiliation(s)
- Christian D Kelstrup
- From the ‡Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health Sciences, DK-2200 Copenhagen, Denmark
| | - Christian Frese
- §Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
| | - Albert J R Heck
- §Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
| | - Jesper V Olsen
- From the ‡Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health Sciences, DK-2200 Copenhagen, Denmark
| | - Michael L Nielsen
- From the ‡Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health Sciences, DK-2200 Copenhagen, Denmark;
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13
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Fouquet T, Toniazzo V, Ruch D, Charles L. Use of doubly charged precursors to validate dissociation mechanisms of singly charged poly(dimethylsiloxane) oligomers. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1123-1129. [PMID: 23715871 DOI: 10.1007/s13361-013-0665-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 02/25/2013] [Accepted: 05/05/2013] [Indexed: 06/02/2023]
Abstract
Collision-induced dissociation of doubly charged poly(dimethylsiloxane) (PDMS) molecules was investigated to provide experimental evidence for fragmentation reactions proposed to occur upon activation of singly charged oligomers. This study focuses on two PDMS species holding trimethylsilyl or methoxy end-groups and cationized with ammonium. In both cases, introduction of the additional charge did not induce significant differences in dissociation behavior, and the use of doubly charged precursors enabled the occurrence of charge-separation reactions, allowing molecules always eliminated as neutrals upon activation of singly charged oligomers to be detected as cationized species. In the case of trimethylsilyl-terminated oligomers, random location of the adducted charge combined with rapid consecutive reactions proposed to occur from singly charged precursors could be validated based on MS/MS data of doubly charged oligomers. In the case of methoxy-terminated PDMS, favored interaction of the adducted ammonium with both end-groups, proposed to rationalize the dissociation behavior of singly charged molecules, was also supported by MS/MS data obtained for molecules adducted with two ammonium cations.
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Affiliation(s)
- Thierry Fouquet
- Aix-Marseille Université-CNRS, Institut de Chimie Radicalaire ICR, UMR 7273, 13397, Marseille, France
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14
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Chesnik M, Halligan B, Olivier M, Mirza SP. Sequential abundant ion fragmentation analysis (SAIFA): an alternative approach for phosphopeptide identification using an ion trap mass spectrometer. Anal Biochem 2011; 418:197-203. [PMID: 21855524 PMCID: PMC3188319 DOI: 10.1016/j.ab.2011.07.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Revised: 07/21/2011] [Accepted: 07/22/2011] [Indexed: 10/17/2022]
Abstract
Phosphorylation has been the most studied of all the posttranslational modifications of proteins. Mass spectrometry has emerged as a powerful tool for phosphomapping on proteins/peptides. Collision-induced dissociation (CID) of phosphopeptides leads to the loss of phosphoric or metaphosphoric acid as a neutral molecule, giving an intense neutral loss product ion in the mass spectrum. Dissociation of the neutral loss product ion identifies peptide sequence. This method of data-dependent constant neutral loss (DDNL) scanning analysis has been commonly used for mapping phosphopeptides. However, preferential losses of groups other than phosphate are frequently observed during CID of phosphopeptides. Ions that result from such losses are not identified during DDNL analysis due to predetermined scanning for phosphate loss. In this study, we describe an alternative approach for improved identification of phosphopeptides by sequential abundant ion fragmentation analysis (SAIFA). In this approach, there is no predetermined neutral loss molecule, thereby undergoing sequential fragmentation of abundant peak, irrespective of the moiety lost during CID. In addition to improved phosphomapping, the method increases the sequence coverage of the proteins identified, thereby increasing the confidence of protein identification. To the best of our knowledge, this is the first report to use SAIFA for phosphopeptide identification.
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Affiliation(s)
- Marla Chesnik
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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15
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Neta P, Stein SE. Charge states of y ions in the collision-induced dissociation of doubly charged tryptic peptide ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:898-905. [PMID: 21472524 DOI: 10.1007/s13361-011-0089-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Revised: 01/20/2011] [Accepted: 01/22/2011] [Indexed: 05/30/2023]
Abstract
Bonds that break in collision-induced dissociation (CID) are often weakened by a nearby proton, which can, in principle, be carried away by either of the product fragments. Since peptide backbone dissociation is commonly charge-directed, relative intensities of charge states of product y- and b-ions depend on the final location of that proton. This study examines y-ion charge distributions for dissociation of doubly charged peptide ions, using a large reference library of peptide ion fragmentation generated from ion-trap CID of peptide ions from tryptic digests. Trends in relative intensities of y(2+) and y(1+) ions are examined as a function of bond cleavage position, peptide length (n), residues on either side of the bond and effects of residues remote from the bond. It is found that y(n-2)/b(2) dissociation is the most sensitive to adjacent amino acids, that y(2+)/y(1+) steadily increase with increasing peptide length, that the N-terminal amino acid can have a major influence in all dissociations, and in some cases other residues remote from the bond cleavage exert significant effects. Good correlation is found between the values of y(2+)/y(1+) for the peptide and the proton affinities of the amino acids present at the dissociating peptide bond. A few deviations from this correlation are rationalized by specific effects of the amino acid residues. These correlations can be used to estimate trends in y(2+)/y(1+) ratios for peptide ions from amino acid proton affinities.
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Affiliation(s)
- Pedatsur Neta
- Chemical and Biochemical Reference Data Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
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16
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Harrison AG. Effect of the identity of Xaa on the fragmentation modes of doubly-protonated Ala-Ala-Xaa-Ala-Ala-Ala-Arg. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:906-911. [PMID: 21472525 DOI: 10.1007/s13361-011-0091-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Revised: 01/20/2011] [Accepted: 01/22/2011] [Indexed: 05/30/2023]
Abstract
The product ion mass spectra resulting from collisional activation of doubly-protonated tryptic-type peptides Ala-Ala-Xaa-Ala-Ala-Ala-Arg have been determined for Xaa = Ala(A), Ser(S), Val(V), Thr(T), Ile(I), Phe(F), Tyr(Y), Sar, Met(M), Trp(W), Pro(P), and Gln(Q). The major fragmentation reaction involves cleavage of the second amide bond (counting from the N-terminus) except for Xaa = Ser and Thr where elimination of H(2)O from the [M + 2H](+2) ion forms the base peak. In general, the extent of cleavage of the second amide bond shows little dependence on the identity of Xaa and little dependence on whether the bond cleavage involves symmetrical bond cleavage to form a y(5)/b(2) ion pair or asymmetrically to form y (5) (+2) and a neutral b(2) species. Notable exceptions to this generalization occur for Xaa equal to Pro or Sar. For Xaa = Pro only cleavage of the second amide bond is observed, consistent with a pronounced proline effect, i.e., cleavage N-terminal to Pro. When Xaa = Sar considerably enhanced cleavage of the second amide bond also is observed, suggesting that at least part of the proline effect relates to the tertiary nature of the amide nitrogen. In the competition between symmetric and asymmetric bond cleavage an attempt to establish a linear free energy correlation in relating ln(y(5)(+2)/y(5)) to PA(H-Xaa-OH) did not lead to a reasonable correlation although the trend of increasing y(5)(+2)/y(5) ratio with increasing proton affinity of H-Xaa-OH was clear. Proline showed a unique behavior in giving a much higher y(5)(+2)/y(5) ratio than any of the other residues studied.
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Affiliation(s)
- Alex G Harrison
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada.
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17
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Mayne SLN, Patterton HG. Bioinformatics tools for the structural elucidation of multi-subunit protein complexes by mass spectrometric analysis of protein-protein cross-links. Brief Bioinform 2011; 12:660-71. [PMID: 22101029 DOI: 10.1093/bib/bbq087] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Multi-subunit protein complexes are involved in many essential biochemical processes including signal transduction, protein synthesis, RNA synthesis, DNA replication and protein degradation. An accurate description of the relative structural arrangement of the constituent subunits in such complexes is crucial for an understanding of the molecular mechanism of the complex as a whole. Many complexes, however, lie in the mega-Dalton range, and are not amenable to X-ray crystallographic or nuclear magnetic resonance analysis. Techniques that are suited to structural studies of such large complexes, such as cryo-electron microscopy, do not provide the resolution required for a mechanistic insight. Mass spectrometry (MS) has increasingly been applied to identify the residues that are involved in chemical cross-links in compound protein assemblies, and have provided valuable insight into the molecular arrangement, orientation and contact surfaces of subunits within such large complexes. This approach is known as MS3D, and involves the MS analysis of cross-linked di-peptides following the enzymatic cleavage of a chemically cross-linked complex. A major challenge of this approach is the identification of the cross-linked di-peptides in a composite mixture of peptides, as well as the identification of the residues involved in the cross-link. These analyses require bioinformatics tools with capabilities beyond that of general, MS-based proteomic analysis software. Many MS3D software tools have appeared, often designed for very specific experimental methods. Here, we provide a review of all major MS3D bioinformatics programmes, reviewing their applicability to different workflows, specific experimental requirements and the computational approach taken by each.
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Affiliation(s)
- Shannon L N Mayne
- Department of Biotechnology, University of the Free State, Bloemfontein 9300, South Africa
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18
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Eyrich B, Sickmann A, Zahedi RP. Catch me if you can: mass spectrometry-based phosphoproteomics and quantification strategies. Proteomics 2011; 11:554-70. [PMID: 21226000 DOI: 10.1002/pmic.201000489] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2010] [Revised: 09/13/2010] [Accepted: 09/21/2010] [Indexed: 01/16/2023]
Abstract
Phosphorylation of proteins is one of the most prominent PTMs and for instance a key regulator of signal transduction. In order to improve our understanding of cellular phosphorylation events, considerable effort has been devoted to improving the analysis of phosphorylation by MS-based proteomics. Different enrichment strategies for phosphorylated peptides/proteins, such as immunoaffinity chromatography (IMAC) or titanium dioxide, have been established and constantly optimized for subsequent MS analysis. Concurrently, specific MS techniques were developed for more confident identification and phosphorylation site localization. In addition, more attention is paid to the LC-MS instrumentation to avoid premature loss of phosphorylated peptides within the analytical system. Despite major advances in all of these fields, the analysis of phosphopeptides still remains far from being routine in proteomics. However, to reveal cellular regulation by phosphorylation events, not only qualitative information about the phosphorylation status of proteins but also, in particular, quantitative information about distinct changes in phosphorylation patterns upon specific stimulation is mandatory. Thus, yielded insights are of outstanding importance for the emerging field of systems biology. In this review, we will give an insight into the historical development of phosphoproteome analysis and discuss its recent progress particularly regarding phosphopeptide quantification and assessment of phosphorylation stoichiometry.
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Affiliation(s)
- Beate Eyrich
- Leibniz-Institut für Analytische Wissenschaften-ISAS-eV, Dortmund, Germany
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19
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Gilmore JM, Washburn MP. Advances in shotgun proteomics and the analysis of membrane proteomes. J Proteomics 2010; 73:2078-91. [PMID: 20797458 DOI: 10.1016/j.jprot.2010.08.005] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Revised: 08/16/2010] [Accepted: 08/18/2010] [Indexed: 12/24/2022]
Abstract
The emergence of shotgun proteomics has facilitated the numerous biological discoveries made by proteomic studies. However, comprehensive proteomic analysis remains challenging and shotgun proteomics is a continually changing field. This review details the recent developments in shotgun proteomics and describes emerging technologies that will influence shotgun proteomics going forward. In addition, proteomic studies of integral membrane proteins remain challenging due to the hydrophobic nature in integral membrane proteins and their general low abundance levels. However, there have been many strategies developed for enriching, isolating and separating membrane proteins for proteomic analysis that have moved this field forward. In summary, while shotgun proteomics is a widely used and mature technology, the continued pace of improvements in mass spectrometry and proteomic technology and methods indicate that future studies will have an even greater impact on biological discovery.
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Affiliation(s)
- Joshua M Gilmore
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
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20
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Abstract
The current status of de novo sequencing of peptides by MS/MS is reviewed with focus on collision cell MS/MS spectra. The relation between peptide structure and observed fragment ion series is discussed and the exhaustive extraction of sequence information from CID spectra of protonated peptide ions is described. The partial redundancy of the extracted sequence information and a high mass accuracy are recognized as key parameters for dependable de novo sequencing by MS. In addition, the benefits of special techniques enhancing the generation of long uninterrupted fragment ion series for de novo peptide sequencing are highlighted. Among these are terminal (18)O labeling, MS(n) of sodiated peptide ions, N-terminal derivatization, the use of special proteases, and time-delayed fragmentation. The emerging electron transfer dissociation technique and the recent progress of MALDI techniques for intact protein sequencing are covered. Finally, the integration of bioinformatic tools into peptide de novo sequencing is demonstrated.
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Affiliation(s)
- Joerg Seidler
- Molecular Structure Analysis, German Cancer Research Center, Heidelberg, Germany
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21
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Sherwood CA, Eastham A, Lee LW, Risler J, Vitek O, Martin DB. Correlation between y-type ions observed in ion trap and triple quadrupole mass spectrometers. J Proteome Res 2009; 8:4243-51. [PMID: 19603825 DOI: 10.1021/pr900298b] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Multiple reaction monitoring mass spectrometry (MRM-MS) is a technique for high-sensitivity targeted analysis. In proteomics, MRM-MS can be used to monitor and quantify a peptide based on the production of expected fragment peaks from the selected peptide precursor ion. The choice of which fragment ions to monitor in order to achieve maximum sensitivity in MRM-MS can potentially be guided by existing MS/MS spectra. However, because the majority of discovery experiments are performed on ion trap platforms, there is concern in the field regarding the generalizability of these spectra to MRM-MS on a triple quadrupole instrument. In light of this concern, many operators perform an optimization step to determine the most intense fragments for a target peptide on a triple quadrupole mass spectrometer. We have addressed this issue by targeting, on a triple quadrupole, the top six y-ion peaks from ion trap-derived consensus library spectra for 258 doubly charged peptides from three different sample sets and quantifying the observed elution curves. This analysis revealed a strong correlation between the y-ion peak rank order and relative intensity across platforms. This suggests that y-type ions obtained from ion trap-based library spectra are well-suited for generating MRM-MS assays for triple quadrupoles and that optimization is not required for each target peptide.
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22
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Abstract
Accurate modeling of peptide fragmentation is necessary for the development of robust scoring functions for peptide-spectrum matches, which are the cornerstone of MS/MS-based identification algorithms. Unfortunately, peptide fragmentation is a complex process that can involve several competing chemical pathways, which makes it difficult to develop generative probabilistic models that describe it accurately. However, the vast amounts of MS/MS data being generated now make it possible to use data-driven machine learning methods to develop discriminative ranking-based models that predict the intensity ranks of a peptide's fragment ions. We use simple sequence-based features that get combined by a boosting algorithm into models that make peak rank predictions with high accuracy. In an accompanying manuscript, we demonstrate how these prediction models are used to significantly improve the performance of peptide identification algorithms. The models can also be useful in the design of optimal multiple reaction monitoring (MRM) transitions, in cases where there is insufficient experimental data to guide the peak selection process. The prediction algorithm can also be run independently through PepNovo+, which is available for download from http://bix.ucsd.edu/Software/PepNovo.html.
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Affiliation(s)
- Ari M Frank
- Department of Computer Science and Engineering, University of California, San Diego (UCSD), 9500 Gilman Drive, La Jolla, California 92093-0404, USA.
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23
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Bythell BJ, Somogyi A, Paizs B. What is the structure of b(2) ions generated from doubly protonated tryptic peptides? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:618-624. [PMID: 19109036 DOI: 10.1016/j.jasms.2008.11.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2008] [Revised: 11/25/2008] [Accepted: 11/25/2008] [Indexed: 05/27/2023]
Abstract
A recent statistical study (Savitski, M. M.; Falth, M.; Eva Fung, Y. M.; Adams, C. M.; Zubarev, R. A. J. Am. Soc. for Mass Spectrom.doi: 10.1016/j.jasms.2008.08.003) of a large spectral database indicated that the product ion spectra of doubly protonated tryptic peptides fall into two distinct classes. The main factor distinguishing the two classes is the relative abundance of the y(N-2) fragment: for Class I spectra y(N-2) is the most abundant y fragment while for Class II other y ions dominate the corresponding spectra. To explain the dominance of y(N-2) for Class I spectra formation of a nontraditional b(2) ion with a diketopiperazine (6-membered cyclic peptide) rather than an oxazolone structure was proposed. Here we present evidence from tandem mass spectrometry, hydrogen/deuterium exchange, and density functional calculations that do not support this proposal. Namely, that CID of doubly protonated YIGSR, YGGFLR, and YIYGSFK produce Class I product ion spectra, yet the b(2) fragment is shown to have the traditional oxazolone structure.
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Affiliation(s)
- Benjamin J Bythell
- Department of Molecular Biophysics, German Cancer Research Center (DKFZ), Heidelberg, Germany
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24
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Hohmann L, Sherwood C, Eastham A, Peterson A, Eng JK, Eddes JS, Shteynberg D, Martin DB. Proteomic analyses using Grifola frondosa metalloendoprotease Lys-N. J Proteome Res 2009; 8:1415-22. [PMID: 19195997 PMCID: PMC2798736 DOI: 10.1021/pr800774h] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proteomic analysis typically has been performed using proteins digested with trypsin because of the excellent fragmentation patterns they produce in collision induced dissociation (CID). For analyses in which high protein coverage is desirable, such as global monitoring of post-translational modifications, additional sequences can be seen using parallel digestion with a second enzyme. We have benchmarked a relatively obscure basidomycete-derived zinc metalloendopeptidase, Lys-N, that selectively cleaves the amide bond N-terminal of lysine residues. We have found that Lys-N digestion yields peptides with easily assigned CID spectra. Using a mixture of purified proteins as well as a complex yeast lysate, we have shown that Lys-N efficiently digests all proteins at the predicted sites of cleavage. Shotgun proteomics analyses of Lys-N digests of both the standard mixture and yeast lysate yielded peptide and protein identification numbers that were generally comparable to trypsin digestion, whereas the combination data from Lys-N and trypsin digestion substantially enhanced protein coverage. During CID fragmentation, the additional amino terminal basicity enhanced b-ion intensity which was reflected in long b-ion tags that were particularly pronounced during CID in a quadrupole. Finally, immonium ion peaks produced from Lys-N digested peptides originate from the carboxy terminus in contrast to tryptic peptides where immonium ions originate from the amino terminus.
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Affiliation(s)
- Laura Hohmann
- Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103
| | - Carly Sherwood
- Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103
| | - Ashley Eastham
- Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103
| | - Amelia Peterson
- University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706
| | - Jimmy K. Eng
- Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103
- UW Medicine at South Lake Union, 815 Mercer Street, Seattle, Washington 98109
| | - James S. Eddes
- Institute of Molecular Systems Biology, ETH Zurich and Faculty of Science, University of Zurich, Switzerland
| | - David Shteynberg
- Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103
| | - Daniel B. Martin
- Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103
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25
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Individual b2 ion fragmentation profiles combined with AspN digestion improve N-terminal peptide sequencing. Anal Bioanal Chem 2009; 393:1587-91. [DOI: 10.1007/s00216-009-2652-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Revised: 01/07/2009] [Accepted: 01/21/2009] [Indexed: 10/21/2022]
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26
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Deepalakshmi PD. Characterization of recombinant protein mutants by top-down sequencing using quadrupole time-of-flight mass spectrometry. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2009; 15:641-649. [PMID: 19679944 DOI: 10.1255/ejms.1012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Top-down sequencing using quadrupole time-of-flight mass spectrometry is used as a direct way of locating the mutated sites of recombinant proteins and posttranslational modification in a protein. Several mutants of barstar, expressed in E.coli, were confirmed by analyzing the fragmentation pattern of mutants. A contaminant protein, that appeared while purifying mutants of barstar, was identified as acyl carrier protein from E.coli with a posttranslational modification on serine residue, indicating that the protein was biologically active. A mutant of ribosomal protein S6 has been characterized with neutral loss of ammonia at the N-terminal region of the protein. The power of the "top-down" approach in characterizing the mutants of recombinant proteins has been demonstrated.
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27
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Cao X, Nesvizhskii AI. Improved sequence tag generation method for peptide identification in tandem mass spectrometry. J Proteome Res 2008; 7:4422-34. [PMID: 18785767 DOI: 10.1021/pr800400q] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The sequence tag-based peptide identification methods are a promising alternative to the traditional database search approach. However, a more comprehensive analysis, optimization, and comparison with established methods are necessary before these methods can gain widespread use in the proteomics community. Using the InsPecT open source code base ( Tanner et al., Anal. Chem. 2005, 77, 4626- 39 ), we present an improved sequence tag generation method that directly incorporates multicharged fragment ion peaks present in many tandem mass spectra of higher charge states. We also investigate the performance of sequence tagging under different settings using control data sets generated on five different types of mass spectrometers, as well as using a complex phosphopeptide-enriched sample. We also demonstrate that additional modeling of InsPecT search scores using a semiparametric approach incorporating the accuracy of the precursor ion mass measurement provides additional improvement in the ability to discriminate between correct and incorrect peptide identifications. The overall superior performance of the sequence tag-based peptide identification method is demonstrated by comparison with a commonly used SEQUEST/PeptideProphet approach.
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Affiliation(s)
- Xia Cao
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
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28
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Hohmann LJ, Eng JK, Gemmill A, Klimek J, Vitek O, Reid GE, Martin DB. Quantification of the compositional information provided by immonium ions on a quadrupole-time-of-flight mass spectrometer. Anal Chem 2008; 80:5596-606. [PMID: 18564857 PMCID: PMC2638499 DOI: 10.1021/ac8006076] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Immonium ions have been largely overlooked during the rapid expansion of mass spectrometry-based proteomics largely due to the dominance of ion trap instruments in the field. However, immonium ions are visible in hybrid quadrupole-time-of-flight (QTOF) mass spectrometers, which are now widely available. We have created the largest database to date of high-confidence sequence assignments to characterize the appearance of immonium ions in CID spectra using a QTOF instrument under "typical" operating conditions. With these data, we are able to demonstrate excellent correlation between immonium ion peak intensity and the likelihood of the appearance of the expected amino acid in the assigned sequence for phenylalanine, tyrosine, tryptophan, proline, histidine, valine, and the indistinguishable leucine and isoleucine residues. In addition, we have clearly demonstrated a positional effect whereby the proximity of the amino acid generating the immonium ion to the amino terminal of the peptide correlates with the strength of the immonium ion peak. This compositional information provided by the immonium ion peaks could substantially improve algorithms used for spectral assignment in mass spectrometry analysis using QTOF platforms.
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29
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Huidobro A, Pruim P, Schoenmakers P, Barbas C. Ultra rapid liquid chromatography as second dimension in a comprehensive two-dimensional method for the screening of pharmaceutical samples in stability and stress studies. J Chromatogr A 2008; 1190:182-90. [DOI: 10.1016/j.chroma.2008.02.114] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2007] [Revised: 02/25/2008] [Accepted: 02/29/2008] [Indexed: 11/26/2022]
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30
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Jansson M, Wårell K, Levander F, James P. Membrane Protein Identification: N-Terminal Labeling of Nontryptic Membrane Protein Peptides Facilitates Database Searching. J Proteome Res 2007; 7:659-65. [DOI: 10.1021/pr070545t] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Maria Jansson
- Department of Protein Technology, BMC D13, Lund University, Lund SE-221 84, Sweden
| | - Kristofer Wårell
- Department of Protein Technology, BMC D13, Lund University, Lund SE-221 84, Sweden
| | - Fredrik Levander
- Department of Protein Technology, BMC D13, Lund University, Lund SE-221 84, Sweden
| | - Peter James
- Department of Protein Technology, BMC D13, Lund University, Lund SE-221 84, Sweden
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31
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Ulintz PJ, Bodenmiller B, Andrews PC, Aebersold R, Nesvizhskii AI. Investigating MS2/MS3 matching statistics: a model for coupling consecutive stage mass spectrometry data for increased peptide identification confidence. Mol Cell Proteomics 2007; 7:71-87. [PMID: 17872894 DOI: 10.1074/mcp.m700128-mcp200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Improvements in ion trap instrumentation have made n-dimensional mass spectrometry more practical. The overall goal of the study was to describe a model for making use of MS(2) and MS(3) information in mass spectrometry experiments. We present a statistical model for adjusting peptide identification probabilities based on the combined information obtained by coupling peptide assignments of consecutive MS(2) and MS(3) spectra. Using two data sets, a mixture of known proteins and a complex phosphopeptide-enriched sample, we demonstrate an increase in discriminating power of the adjusted probabilities compared with models using MS(2) or MS(3) data only. This work also addresses the overall value of generating MS(3) data as compared with an MS(2)-only approach with a focus on the analysis of phosphopeptide data.
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Affiliation(s)
- Peter J Ulintz
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48103, USA
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32
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Lehmann WD, Krüger R, Salek M, Hung CW, Wolschin F, Weckwerth W. Neutral loss-based phosphopeptide recognition: a collection of caveats. J Proteome Res 2007; 6:2866-73. [PMID: 17569551 DOI: 10.1021/pr060573w] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The standard strategy for analysis by tandem mass spectrometry of protein phosphorylation at serine or threonine utilizes the neutral loss of H3PO4 (= 97.977/z) from proteolytic peptide molecular ions as marker fragmentation. Manual control of automatically performed neutral loss-based phosphopeptide identifications is strongly recommended, since these data may contain false-positive results. These are connected to the experimental neutral loss m/z error, to competing peptide fragmentation pathways, to limitations in data interpretation software, and to the general growth of protein sequence databases. The fragmentation-related limitations of the neutral loss approach cover (i) the occurrence of abundant 'close-to-98/z' neutral loss fragmentations, (ii) the erroneous assignment of a neutral loss other than loss of H3PO4 due to charge state mix-up, and (iii) the accidental occurrence of any fragment ion in the m/z windows of interest in combination with a charge-state mix-up. The 'close-to-98/z' losses comprise loss of proline (97.053/z), valine (99.068/z), threonine (101.048/z), or cysteine (103.009/z) preferably from peptides with N-terminal sequences PP, VP, TP, or CP, and loss of 105.025/z from alkylated methionine. Confusion with other neutral losses may occur, when their m/z window coincides with a 98/z window as result of a charge state mix-up. Neutral loss of sulfenic acid from oxidized methionine originating from a doubly charged precursor (63.998/2 = 31.999) may thus mimic the loss of phosphoric acid from a triply charged phosphopeptide (97.977/3 = 32.659). As a consequence of the large complexity of proteomes, peptide sequence ions may occur in one of the mass windows of H3PO4 loss around 97.977/z. Practical examples for false-positive annotations of phosphopeptides are given for the first two groups of error. The majority of these can be readily recognized using the guidelines presented in this study.
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Affiliation(s)
- Wolf D Lehmann
- Central Spectroscopy, German Cancer Research Center, Heidelberg, Germany.
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Falkner JA, Kachman M, Veine DM, Walker A, Strahler JR, Andrews PC. Validated MALDI-TOF/TOF mass spectra for protein standards. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:850-5. [PMID: 17329120 DOI: 10.1016/j.jasms.2007.01.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2006] [Revised: 01/14/2007] [Accepted: 01/16/2007] [Indexed: 05/14/2023]
Abstract
A current focus of proteomics research is the establishment of acceptable confidence measures in the assignment of protein identifications in an unknown sample. Development of new algorithmic approaches would greatly benefit from a standard reference set of spectra for known proteins for the purpose of testing and training. Here we describe an openly available library of mass spectra generated on an ABI 4700 MALDI TOF/TOF from 246 known, individually purified and trypsin-digested protein samples. The initial full release of the Aurum Dataset includes gel images, peak lists, spectra, search result files, decoy database analysis files, FASTA file of protein sequences, manual curation, and summary pages describing protein coverage and peptides matched by MS/MS followed by decoy database analysis using Mascot, Sequest, and X!Tandem. The data are publicly available for use at ProteomeCommons.org.
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Affiliation(s)
- Jayson A Falkner
- National Resource for Proteomics and Pathway, Michigan Proteome Consortium, Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
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Zhang Z. Prediction of low-energy collision-induced dissociation spectra of peptides with three or more charges. Anal Chem 2007; 77:6364-73. [PMID: 16194101 DOI: 10.1021/ac050857k] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A kinetic model, based on the "mobile proton" model of peptide fragmentation, has been reported previously for quantitative prediction of low-energy collision-induced dissociation (CID) spectra of singly or doubly charged peptides. For peptides with three or more charges, however, the simulation process is complex and time-consuming. This paper describes a simplified model for quantitative prediction of CID spectra of peptide ions with three or more charges. Improvements on other aspects of the model were also made to accommodate large peptides. The performance of the simplified model was evaluated by generating predictions for many known highly charged peptides that were not included in the training data set. It was shown that the model is able to predict peptide CID spectra with reasonable accuracy in fragment ion intensities for highly charged peptide ions up to 5000 u in mass.
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Affiliation(s)
- Zhongqi Zhang
- Analytical Sciences, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, USA.
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Mouls L, Aubagnac JL, Martinez J, Enjalbal C. Low energy peptide fragmentations in an ESI-Q-Tof type mass spectrometer. J Proteome Res 2007; 6:1378-91. [PMID: 17311442 DOI: 10.1021/pr060574o] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Efficient peptide sequencing relies on both high quality MS/MS data acquisition and exhaustive knowledge of gas-phase dissociation mechanisms. We report our contribution to the elaboration of more comprehensive fragmentation models required for efficient automated MS/MS spectra interpretation. Following a statistical approach, various peptides (296 sequences of variable compositions and lengths) were prepared and subjected to low-energy collision-induced dissociations (CID) in an electrospray hybrid instrument (ESI-Q-q-Tof type mass spectrometer) that has retained relatively limited attention so far. Besides, our studies were focused on low molecular weight singly charged peptides that often failed to be identified by sequencing algorithms. Only half of the studied compounds showed charge directed dissociations in accordance with the mobile proton model producing fragment ions directly related to the primary sequence. For the peptides that did not exhibit the expected fragment ion series, alternative dissociation behaviors issued from complex rearrangements were evidenced.
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Affiliation(s)
- Laetitia Mouls
- Laboratoire des Amino acides, Peptides et Protéines, LAPP-UMR 5810, CNRS, Universités Montpellier I and II, Place E. Bataillon, 34095 Montpellier Cédex 05, France
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Ferguson PL, Pan J, Wilson DJ, Dempsey B, Lajoie G, Shilton B, Konermann L. Hydrogen/Deuterium Scrambling during Quadrupole Time-of-Flight MS/MS Analysis of a Zinc-Binding Protein Domain. Anal Chem 2006; 79:153-60. [PMID: 17194133 DOI: 10.1021/ac061261f] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
It remains an open question as to whether experiments involving collision-induced dissociation (CID) can provide a viable approach for monitoring spatially resolved deuteration levels in electrosprayed polypeptide ions. A number of laboratories reported the successful application of CID following solution-phase H/D exchange (HDX), whereas others found that H/D scrambling precluded site-specific measurements. The aim of the current work is to help clarify the general feasibility of HDX-CID methods, using a 22-residue zinc-bound protein domain (Zn-ZBD) as model system. Metal binding in Zn-ZBD should confer structural rigidity, and the presence of several basic residues should sequester mobile charge carriers in the gas phase. Both of these factors were expected to suppress the extent of scrambling. HDX was carried out by employing rapid on-line mixing, thereby mimicking conditions typically encountered in kinetic pulse-labeling studies. Quadrupole time-of-flight MS/MS of pulse-labeled Zn-ZBD provides high sequence coverage. However, the measured fragment deuteration levels do not correlate with the known H-bonding pattern of Zn-ZBD, suggesting the occurrence of extensive scrambling. Instead of showing a uniform distribution, the fragment ions reveal a distinct nonrandom pattern of deuteration levels. In the absence of prior information, these data could erroneously be ascribed to the presence of protected sites. However, the observed patterns clearly originate from other factors; possibly they are caused by modulations of the amide CID efficiency by kinetic isotope effects. It is concluded that scrambling does not represent the only conceptual problem in HDX-CID studies and that control experiments on uniformly labeled samples are essential for ruling out interpretation artifacts.
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Affiliation(s)
- Peter L Ferguson
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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Schöneich C, Sharov VS. Mass spectrometry of protein modifications by reactive oxygen and nitrogen species. Free Radic Biol Med 2006; 41:1507-20. [PMID: 17045919 DOI: 10.1016/j.freeradbiomed.2006.08.013] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2006] [Revised: 08/04/2006] [Accepted: 08/11/2006] [Indexed: 10/24/2022]
Abstract
The modification of proteins by reactive oxygen and nitrogen species plays an important role in various biologic processes involving protein activation and inactivation, protein translocation and turnover during signal transduction, stress response, proliferation, and apoptosis. Recent advances in protein and peptide separation and mass spectrometry provide increasingly sophisticated tools for the quantitative analysis of such protein modifications, which are absolutely necessary for their correlation with biologic phenomena. The present review focuses specifically on the qualitative and quantitative mass spectrometric analysis of the most common protein modifications caused by reactive oxygen and nitrogen species in vivo and in vitro and details a case study on a membrane protein the sarco/endoplasmic reticulum Ca-ATPase (SERCA).
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Affiliation(s)
- Christian Schöneich
- Department of Pharmaceutical Chemistry, University of Kansas, 2095 Constant Avenue, Lawrence, KS 66047, USA.
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Budnik BA, Lee RS, Steen JAJ. Global methods for protein glycosylation analysis by mass spectrometry. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:1870-80. [PMID: 17118724 DOI: 10.1016/j.bbapap.2006.10.005] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2006] [Revised: 10/01/2006] [Accepted: 10/10/2006] [Indexed: 12/14/2022]
Abstract
Mass spectrometry has been an analytical tool of choice for glycosylation analysis of individual proteins. Over the last 5 years several previously and newly developed mass spectrometry methods have been extended to global glycoprotein studies. In this review we discuss the importance of these global studies and the advances that have been made in enrichment analyses and fragmentation methods. We also briefly describe relevant sample preparation methods that have been used for the analysis of a single glycoprotein that could be extrapolated to global studies. Finally this review covers aspects of improvements and advances on the instrument front which are important to future global glycoproteomic studies.
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Affiliation(s)
- Bogdan A Budnik
- Department of Pathology, Children's Hospital Boston and Harvard Medical School, Boston, MA 02115, USA
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Hoffman MD, Sniatynski MJ, Rogalski JC, Le Blanc JCY, Kast J. Multiple neutral loss monitoring (MNM): a multiplexed method for post-translational modification screening. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2006; 17:307-17. [PMID: 16443369 DOI: 10.1016/j.jasms.2005.11.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2005] [Revised: 11/03/2005] [Accepted: 11/07/2005] [Indexed: 05/06/2023]
Abstract
Post-translational modifications of proteins are involved in determining the activity of proteins and are essential for proper protein function. Current mass spectrometric strategies require one to specify a particular type of modification, in some cases also a particular charge state of a protein or peptide that is to be studied before the actual analysis. Due to these requirements, most of the modifications on proteins are not considered in such an experiment and, thus, a series of similar analyses need to be performed to ensure a more extensive characterization. A novel scan strategy has been developed, multiple neutral loss monitoring (MNM), allowing for the comprehensive screening of post-translational modifications (PTM) on proteins that fragment as neutral losses in a mass spectrometer. MNM method parameters were determined by performing product ion scans on a number of modified peptides over a range of collision energies, providing neutral loss energy profiles and optimal collision energies (OCE) for each modification, supplying valuable information pertaining to the fragmentation of these modifications and the necessary parameters that would be required to obtain the best analysis. As the optimal collision energy was highly dependent on the type of modification and the charge state of the peptide, the MNM scan was operated with a collision energy gradient. Autocorrelation analyses identified the type of modification, and convolution mapping analyses identified the associated peptide. The MNM scan with the new collision energy parameters was successfully applied to a mixture of four modified peptides in a BSA digest. The implementation of this technique will allow for comprehensive screening of all modifications that fragment as neutral losses.
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Affiliation(s)
- Michael D Hoffman
- The Biomedical Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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