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Fernandez B, Armengaud J, Subra G, Enjalbal C. MALDI‐MS/MS of N‐Terminal TMPP‐Acyl Peptides: A Worthwhile Tool to Decipher Protein N‐Termini. European J Org Chem 2022. [DOI: 10.1002/ejoc.202101549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Bernard Fernandez
- IBMM Université de Montpellier, CNRS, ENSCM 34293 Montpellier France
- Université Paris-Saclay, CEA, INRAE Département Médicaments et Technologies pour la Santé (DMTS) SPI 30200 Bagnols-sur-Cèze France
- Present address: CIRAD, UMR ASTRE 34398 Montpellier France
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE Département Médicaments et Technologies pour la Santé (DMTS) SPI 30200 Bagnols-sur-Cèze France
| | - Gilles Subra
- IBMM Université de Montpellier, CNRS, ENSCM 34293 Montpellier France
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2
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Valli M, Russo HM, Pilon AC, Pinto MEF, Dias NB, Freire RT, Castro-Gamboa I, Bolzani VDS. Computational methods for NMR and MS for structure elucidation I: software for basic NMR. PHYSICAL SCIENCES REVIEWS 2019. [DOI: 10.1515/psr-2018-0108] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Abstract
Structure elucidation is an important and sometimes time-consuming step for natural products research. This step has evolved in the past few years to a faster and more automated process due to the development of several computational programs and analytical techniques. In this paper, the topics of NMR prediction and CASE programs are addressed. Furthermore, the elucidation of natural peptides is discussed.
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3
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Polasky DA, Lermyte F, Nshanian M, Sobott F, Andrews PC, Loo JA, Ruotolo BT. Fixed-Charge Trimethyl Pyrilium Modification for Enabling Enhanced Top-Down Mass Spectrometry Sequencing of Intact Protein Complexes. Anal Chem 2018; 90:2756-2764. [PMID: 29360341 PMCID: PMC6340295 DOI: 10.1021/acs.analchem.7b04806] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Mass spectrometry of intact proteins and protein complexes has the potential to provide a transformative level of information on biological systems, ranging from sequence and post-translational modification analysis to the structures of whole protein assemblies. This ambitious goal requires the efficient fragmentation of both intact proteins and the macromolecular, multicomponent machines they collaborate to create through noncovalent interactions. Improving technologies in an effort to achieve such fragmentation remains perhaps the greatest challenge facing current efforts to comprehensively analyze cellular protein composition and is essential to realizing the full potential of proteomics. In this work, we describe the use of a trimethyl pyrylium (TMP) fixed-charge covalent labeling strategy aimed at enhancing fragmentation for challenging intact proteins and intact protein complexes. Combining analysis of TMP-modified and unmodified protein complexes results in a greater diversity of regions within the protein that give rise to fragments, and results in an up to 2.5-fold increase in sequence coverage when compared to unmodified protein alone, for protein complexes up to 148 kDa. TMP modification offers a simple and powerful platform to expand the capabilities of existing mass spectrometric instrumentation for the complete characterization of intact protein assemblies.
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Affiliation(s)
- Daniel A. Polasky
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, MI 48109
| | - Frederik Lermyte
- ♯ Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Michael Nshanian
- ‡ Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095
| | - Frank Sobott
- ♯ Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
- ° The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
- + School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Phillip C. Andrews
- ‖ Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Dr., Ann Arbor MI, 48109
| | - Joseph A. Loo
- ‡ Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095
- § Department of Biological Chemistry, David Geffen School of Medicine, and UCLA/DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA 90095
| | - Brandon T. Ruotolo
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, MI 48109
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4
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Topolyan AP, Strizhevskaya DA, Slyundina MS, Belyaeva MA, Ivanova OM, Korshun VA, Ustinov AV, Mikhura IV, Formanovsky AA, Borisov RS. Tris(2,6-dimethoxyphenyl)methyl carbenium ion as a charge derivatization agent for the analysis of primary amines by MALDI mass spectrometry. JOURNAL OF ANALYTICAL CHEMISTRY 2017. [DOI: 10.1134/s106193481614015x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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5
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An M, Zou X, Wang Q, Zhao X, Wu J, Xu LM, Shen HY, Xiao X, He D, Ji J. High-confidence de novo peptide sequencing using positive charge derivatization and tandem MS spectra merging. Anal Chem 2013; 85:4530-7. [PMID: 23536960 DOI: 10.1021/ac4001699] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
De novo peptide sequencing holds great promise in discovering new protein sequences and modifications but has often been hindered by low success rate of mass spectra interpretation, mainly due to the diversity of fragment ion types and insufficient information for each ion series. Here, we describe a novel methodology that combines highly efficient on-tip charge derivatization and tandem MS spectra merging, which greatly boosts the performance of interpretation. TMPP-Ac-OSu (succinimidyloxycarbonylmethyl tris(2,4,6-trimethoxyphenyl)phosphonium bromide) was used to derivatize peptides at N-termini on tips to reduce mass spectra complexity. Then, a novel approach of spectra merging was adopted to combine the benefits of collision-induced dissociation (CID) and electron transfer dissociation (ETD) fragmentation. We applied this methodology to rat C6 glioma cells and the Cyprinus carpio and searched the resulting peptide sequences against the protein database. Then, we achieved thousands of high-confidence peptide sequences, a level that conventional de novo sequencing methods could not reach. Next, we identified dozens of novel peptide sequences by homology searching of sequences that were fully backbone covered but unmatched during the database search. Furthermore, we randomly chose 34 sequences discovered in rat C6 cells and verified them. Finally, we conclude that this novel methodology that combines on-tip positive charge derivatization and tandem MS spectra merging will greatly facilitate the discovery of novel proteins and the proteome analysis of nonmodel organisms.
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Affiliation(s)
- Mingrui An
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
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6
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Chemical and Biochemical Applications of MALDI TOF-MS Based on Analyzing the Small Organic Compounds. Top Curr Chem (Cham) 2012; 331:165-92. [DOI: 10.1007/128_2012_364] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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7
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Wang J, Zhang J, Arbogast B, Maier CS. Tandem mass spectrometric characterization of thiol peptides modified by the chemoselective cationic sulfhydryl reagent (4-iodobutyl)triphenylphosphonium--effects of a cationic thiol derivatization on peptide fragmentation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:1771-83. [PMID: 21952891 PMCID: PMC3187551 DOI: 10.1007/s13361-011-0192-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Revised: 05/18/2011] [Accepted: 06/08/2011] [Indexed: 05/24/2023]
Abstract
Fixed charge chemical modifications on peptides and proteins can impact fragmentation behaviors in tandem mass spectrometry (MS/MS). In this study, we employed a thiol-specific cationic alkylation reagent, (4-iodobutyl)triphenylphosphonium (IBTP), to selectively modify cysteine thiol groups in mitochondrial proteome samples. Tandem mass spectrometric characteristics of butyltriphenylphosphonium (BTP)-modified peptides were evaluated by comparison to their carbamidomethylated (CAM) analogues using a quadrupole time-of-flight (Q-TOF) instrument under low energy collision-induced dissociation (CID) conditions. Introduction of the fixed charge modification resulted in the observation of peptide and fragment (b(n) and y(n)) ions with higher charge states than those observed for CAM-modified analogues. The charged BTP moiety had a significant effect on the neighboring amide bond fragmentation products. A decrease in relative abundances of the product ions at the corresponding cleavage sites was observed compared with those from the CAM-modified derivatives. This effect was particularly noticeable when an Xxx-Pro bond was in the vicinity of a BTP group. We hypothesized that the presence of a phosphonium moiety will reduce the tendency for protonation of the proximal amide bonds in the peptide backbone. Indeed, calculations indicated that proton affinities of backbone amide bonds close to the modified cysteine residues were generally 20-50 kcal/mol lower for BTP-modified peptides than for the unmodified or CAM-modified analogues with the sequence motif -Ala-Cys-Ala(n)-Ala(2)-, -Ala-Cys-Ala(n)-Pro-Ala-, and -Ala-Pro-Ala(n)-Cys-Ala-, n=0-3.
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Affiliation(s)
- Jing Wang
- Department of Chemistry, Oregon State University, Corvallis, OR 97331
| | - Jie Zhang
- Department of Chemistry, Oregon State University, Corvallis, OR 97331
| | | | - Claudia S. Maier
- Department of Chemistry, Oregon State University, Corvallis, OR 97331
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8
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Calligaris D, Villard C, Lafitte D. Advances in top-down proteomics for disease biomarker discovery. J Proteomics 2011; 74:920-34. [DOI: 10.1016/j.jprot.2011.03.030] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Revised: 03/01/2011] [Accepted: 03/29/2011] [Indexed: 11/16/2022]
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9
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Wang HY, Chu X, Zhao ZX, He XS, Guo YL. Analysis of low molecular weight compounds by MALDI-FTICR-MS. J Chromatogr B Analyt Technol Biomed Life Sci 2011; 879:1166-79. [DOI: 10.1016/j.jchromb.2011.03.037] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2010] [Revised: 03/11/2011] [Accepted: 03/18/2011] [Indexed: 10/18/2022]
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10
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Tran BQ, Hernandez C, Waridel P, Potts A, Barblan J, Lisacek F, Quadroni M. Addressing Trypsin Bias in Large Scale (Phospho)proteome Analysis by Size Exclusion Chromatography and Secondary Digestion of Large Post-Trypsin Peptides. J Proteome Res 2010; 10:800-11. [DOI: 10.1021/pr100951t] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bao Quoc Tran
- Center for Integrative Genomics, University of Lausanne, Batiment Genopode, 1015 Lausanne, Switzerland, and Swiss Institute of Bioinformatics, CMU-Rue Michel-Servet 1, 1211 Geneva 4 Geneva, Switzerland
| | - Celine Hernandez
- Center for Integrative Genomics, University of Lausanne, Batiment Genopode, 1015 Lausanne, Switzerland, and Swiss Institute of Bioinformatics, CMU-Rue Michel-Servet 1, 1211 Geneva 4 Geneva, Switzerland
| | - Patrice Waridel
- Center for Integrative Genomics, University of Lausanne, Batiment Genopode, 1015 Lausanne, Switzerland, and Swiss Institute of Bioinformatics, CMU-Rue Michel-Servet 1, 1211 Geneva 4 Geneva, Switzerland
| | - Alexandra Potts
- Center for Integrative Genomics, University of Lausanne, Batiment Genopode, 1015 Lausanne, Switzerland, and Swiss Institute of Bioinformatics, CMU-Rue Michel-Servet 1, 1211 Geneva 4 Geneva, Switzerland
| | - Jachen Barblan
- Center for Integrative Genomics, University of Lausanne, Batiment Genopode, 1015 Lausanne, Switzerland, and Swiss Institute of Bioinformatics, CMU-Rue Michel-Servet 1, 1211 Geneva 4 Geneva, Switzerland
| | - Frederique Lisacek
- Center for Integrative Genomics, University of Lausanne, Batiment Genopode, 1015 Lausanne, Switzerland, and Swiss Institute of Bioinformatics, CMU-Rue Michel-Servet 1, 1211 Geneva 4 Geneva, Switzerland
| | - Manfredo Quadroni
- Center for Integrative Genomics, University of Lausanne, Batiment Genopode, 1015 Lausanne, Switzerland, and Swiss Institute of Bioinformatics, CMU-Rue Michel-Servet 1, 1211 Geneva 4 Geneva, Switzerland
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11
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del Mar Contreras M, Gómez-Sala B, Martín-Álvarez PJ, Amigo L, Ramos M, Recio I. Monitoring the large-scale production of the antihypertensive peptides RYLGY and AYFYPEL by HPLC-MS. Anal Bioanal Chem 2010; 397:2825-32. [DOI: 10.1007/s00216-010-3647-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2009] [Revised: 03/02/2010] [Accepted: 03/08/2010] [Indexed: 11/28/2022]
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12
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Gallien S, Perrodou E, Carapito C, Deshayes C, Reyrat JM, Van Dorsselaer A, Poch O, Schaeffer C, Lecompte O. Ortho-proteogenomics: multiple proteomes investigation through orthology and a new MS-based protocol. Genome Res 2008; 19:128-35. [PMID: 18955433 DOI: 10.1101/gr.081901.108] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The progress in sequencing technologies irrigates biology with an ever-increasing number of genome sequences. In most cases, the gene repertoire is predicted in silico and conceptually translated into proteins. As recently highlighted, the predicted genes exhibit frequent errors, particularly in start codons, with a serious impact on subsequent biological studies. A new "ortho-proteogenomic" approach is presented here for the annotation refinement of multiple genomes at once. It combines comparative genomics with an original proteomic protocol that allows the characterization of both N-terminal and internal peptides in a single experiment. This strategy was applied to the Mycobacterium genus with Mycobacterium smegmatis as the reference, and identified 946 distinct proteins, including 443 characterized N termini. These experimental data allowed the correction of 19% of the characterized start codons, the identification of 29 proteins missed during the annotation process, and the curation, thanks to comparative genomics, of 4328 sequences of 16 other Mycobacterium proteomes.
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Affiliation(s)
- Sébastien Gallien
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC-DSA, ULP, CNRS, UMR7178, 67 087 Strasbourg, France.
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13
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Li X, Cournoyer JJ, Lin C, O’Connor PB. The effect of fixed charge modifications on electron capture dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:1514-26. [PMID: 18657441 PMCID: PMC3116146 DOI: 10.1016/j.jasms.2008.06.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2007] [Revised: 05/20/2008] [Accepted: 06/20/2008] [Indexed: 05/11/2023]
Abstract
Electron capture dissociation (ECD) studies of two modified amyloid beta peptides (20-29 and 25-35) were performed to investigate the role of H* radicals in the ECD of peptide ions and the free-radical cascade (FRC) mechanism. 2,4,6-Trimethylpyridinium (TMP) was used as the fixed charge tag, which is postulated to both trap the originally formed radical upon electron capture and inhibit the H* generation. It was found that both the number and locations of the fixed charge groups influenced the backbone and side-chain cleavages of these peptides in ECD. In general, the frequency and extent of backbone cleavages decreased and those of side-chain cleavages increased with the addition of fixed charge tags. A singly labeled peptide with the tag group farther away from the protonated site experienced a smaller abundance decrease in backbone cleavage fragments than the one with the tag group closer to the protonated site. Despite the nonprotonated nature of all charge carriers in doubly labeled peptide ions, several c and z* ions were still observed in their ECD spectra. Thus, although H* transfer may be important for the NC(alpha) bond cleavage, there also exist other pathways, which would require a radical migration via H* abstraction through space or via an amide superbase mechanism. Finally, internal fragment ions were observed in the ECD of these linear peptides, indicating that the important role of the FRC in backbone cleavages is not limited to the ECD of cyclic peptides.
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Affiliation(s)
- Xiaojuan Li
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Jason J. Cournoyer
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Cheng Lin
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Peter B. O’Connor
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
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14
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Kuyama H, Shima K, Sonomura K, Yamaguchi M, Ando E, Nishimura O, Tsunasawa S. A simple and highly successful C-terminal sequence analysis of proteins by mass spectrometry. Proteomics 2008; 8:1539-50. [DOI: 10.1002/pmic.200701044] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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15
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Sierakowski J, Amunugama M, Roberts KD, Reid GE. Substituent effects on the gas-phase fragmentation reactions of sulfonium ion containing peptides. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2007; 21:1230-8. [PMID: 17330214 DOI: 10.1002/rcm.2959] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The multistage mass spectrometric (MS/MS and MS3) gas-phase fragmentation reactions of methionine side-chain sulfonium ion containing peptides formed by reaction with a series of para-substituted phenacyl bromide (XBr where X=CH2COC6H4R, and R=--COOH, --COOCH3, --H, --CH3 and --CH2CH3) alkylating reagents have been examined in a linear quadrupole ion trap mass spectrometer. MS/MS of the singly (M+) and multiply ([M++nH](n+1)+) charged precursor ions results in exclusive dissociation at the fixed charge containing side chain, independently of the amino acid composition and precursor ion charge state (i.e., proton mobility). However, loss of the methylphenacyl sulfide side-chain fragment as a neutral versus charged (protonated) species was observed to be highly dependent on the proton mobility of the precursor ion, and the identity of the phenacyl group para-substituent. Molecular orbital calculations were performed at the B3LYP/6-31+G** level of theory to calculate the theoretical proton affinities of the neutral side-chain fragments. The log of the ratio of neutral versus protonated side-chain fragment losses from the derivatized side chain were found to exhibit a linear dependence on the proton affinity of the side-chain fragmentation product, as well as the proton affinities of the peptide product ions. Finally, MS3 dissociation of the nominally identical neutral and protonated loss product ions formed by MS/MS of the [M++H]2+ and [M++2H]3+ precursor ions, respectively, from the peptide GAILM(X)GAILK revealed significant differences in the abundances of the resultant product ions. These results suggest that the protonated peptide product ions formed by gas-phase fragmentation of sulfonium ion containing precursors in an ion trap mass spectrometer do not necessarily undergo intramolecular proton 'scrambling' prior to their further dissociation, in contrast to that previously demonstrated for peptide ions introduced by external ionization sources.
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Affiliation(s)
- James Sierakowski
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
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16
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Amunugama M, Roberts KD, Reid GE. Mechanisms for the selective gas-phase fragmentation reactions of methionine side chain fixed charge sulfonium ion containing peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2006; 17:1631-42. [PMID: 16935522 DOI: 10.1016/j.jasms.2006.07.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2006] [Revised: 07/14/2006] [Accepted: 07/14/2006] [Indexed: 05/11/2023]
Abstract
To enable the development of improved tandem mass spectrometry based methods for selective proteome analysis, the mechanisms, product ion structures, and other factors influencing the gas-phase fragmentation reactions of methionine side-chain derivatized "fixed-charge" phenacylsulfonium ion containing peptide ions have been examined. Dissociation of these peptide ions results in the exclusive characteristic loss of the derivatized side chain, thereby enabling their selective identification. The resultant product ion(s) are then subjected to further dissociation to obtain sequence information for subsequent protein identification. Molecular orbital calculations (at the B3LYP/6-31 + G (d,p) level of theory) performed on a simple peptide model, together with experimental evidence obtained by multistage dissociation of a regioselectively deuterated methionine derivatized sulfonium ion containing tryptic peptide, indicate that fragmentation of the fixed charge containing peptide ions occurs via SN2 reactions involving the N- and C-terminal amide bonds adjacent to the methionine side chain, resulting in the formation of stable cyclic five- and six-membered iminohydrofuran and oxazine product ions, respectively. These studies further indicate that the rings formed via these neighboring group reactions are stable to further dissociation by MS3. As a consequence, the formation of b- or y-type sequence ions are "skipped" at the site of cyclization. Despite this, complete sequence information is still obtained because of the presence of both cyclic products.
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Affiliation(s)
- Mahasilu Amunugama
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
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17
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Olson MT, Epstein JA, Yergey AL. De novo peptide sequencing using exhaustive enumeration of peptide composition. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2006; 17:1041-1049. [PMID: 16735127 DOI: 10.1016/j.jasms.2006.03.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2005] [Revised: 03/09/2006] [Accepted: 03/13/2006] [Indexed: 05/09/2023]
Abstract
We introduce the use of a peptide composition lookup table indexed by residual mass and number of amino acids for de novo sequencing of polypeptides. Polypeptides of 1600 Daltons (Da) or more can be sequenced effectively through exhaustive compositional analysis of MS/MS spectra obtained by unimolecular decomposition (without CID) in a MALDI TOF/TOF despite a fragment mass accuracy of 50 mDa. Peaks are referenced against the lookup table to obtain a complete profile of amino acid combinations, and combinations are assembled into series of increasing length. Concatenating the differences between successive entries in compositional series yields peptide sequences that can be scored and ranked according to signal intensity. While the current work involves measurements acquired on MALDI TOF-TOF, such general treatment of the data anticipates extension to other types of mass analyzers.
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Affiliation(s)
- Matthew T Olson
- Laboratory of Cellular and Molecular Biophysics, NICHD, NIH, Bethesda, Maryland, USA
| | | | - Alfred L Yergey
- Laboratory of Cellular and Molecular Biophysics, NICHD, NIH, Bethesda, Maryland, USA.
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18
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Marekov LN, Steinert PM. Charge derivatization by 4-sulfophenyl isothiocyanate enhances peptide sequencing by post-source decay matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2003; 38:373-377. [PMID: 12717748 DOI: 10.1002/jms.448] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
High-sensitivity, rapid identification of proteins in proteomic studies normally uses a combination of one- or two-dimensional electrophoresis together with mass spectrometry. The simplicity and sensitivity of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) have increased its application in recent years. The most common method of 'peptide fingerprinting' often may not provide robust identification. Normally additional sequence information by post-source decay (PSD) MALDI-TOFMS provides additional constraints for database searches to achieve highly confident results. Here we describe a derivatization procedure to facilitate the acquisition of such sequence information. Peptide digests from a skin-expressed protein were modified with 4-sulfophenyl isothiocyanate. The resulting peptides carry a fixed negative charge at the N-terminal end and the resulting PSD spectrum is dominated by C-terminal y-type ions. The sequence information in most cases can be obtained manually or with simple programming tools. Methods of optimizing the procedure and increasing the sensitivity are discussed.
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Affiliation(s)
- Lyuben N Marekov
- Laboratory of Skin Biology, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
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Abstract
This review focuses on biological and biomedical mass spectrometry, and covers a selection of publications in this area included in the MEDLINE database for the period 1987-2001. Over the last 15 years, biological and biomedical mass spectrometry has progressed out of all recognition. The development of soft ionization methods, such as electrospray ionization and matrix-assisted laser desorption ionization, has mainly contributed to the remarkable progress, because they can easily produce gas-phase ions of large, polar, and thermally labile biomolecules, such as proteins, peptides, nucleic acids and others. The innovations of ionization methods have led to remarkable progress in mass spectrometric technology and in biochemistry, biotechnology and molecular biology research. In addition, mass spectrometry is one of the powerful and effective technologies for drug discovery and development. It is applicable to studies on structural determination, drug metabolism, including pharmacokinetics and toxicokinetics, and de novo drug discovery by applying post-genomic approarches. In the present review, the innovative soft ionization methods are first discussed along with their features. Also, the characteristics of the mass spectrometers which are active in the biological and biomedical research fields are also described. In addition, examples of the applications of biological and biomedical mass spectrometry are provided.
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Affiliation(s)
- Nariyasu Mano
- Graduate School of Pharmaceutical Sciences, Tohoku University, Aobayama, Sendai 980-8578, Japan.
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Adamczyk M, Gebler JC, Wu J, Yu Z. Complete sequencing of anti-vancomycin fab fragment by liquid chromatography-electrospray ion trap mass spectrometry with a combination of database searching and manual interpretation of the MS/MS spectra. J Immunol Methods 2002; 260:235-49. [PMID: 11792392 DOI: 10.1016/s0022-1759(01)00552-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sequencing of anti-vancomycin monoclonal antibody (mAb) Fab region (48,000 Da) was carried out using liquid chromatography-electrospray ionization ion trap mass spectrometry (LC/ESI-MS). Comprehensive strategies were employed to ensure complete sequence coverage. The sequence information was obtained from the spectra of collision-induced dissociation (CID) (MS/MS) of the protonated proteolytic peptides resulting from multiple enzymatic digestions of reduced/S-carboxymethylated (RCM) light chain and Fd fragment. Database searching of the spectra against the published immunoglobulin G (IgG) sequences allowed the identification of all the peptides in constant domains as well as partial sequences in variable domains. The rest of the sequences were deduced by manual interpretation of the peptide tandem mass spectrometry (MS/MS) spectra. The analysis showed that the N-terminus of the heavy chain was modified by the conversion of a glutamine residue to pyroglutamic acid.
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Affiliation(s)
- Maciej Adamczyk
- Department of Organic Chemistry (9NM), Abbott Diagnostics Division, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, IL 60064-6016, USA.
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Naaby-Hansen S, Waterfield MD, Cramer R. Proteomics--post-genomic cartography to understand gene function. Trends Pharmacol Sci 2001; 22:376-84. [PMID: 11431033 DOI: 10.1016/s0165-6147(00)01663-1] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The completion of the genomic sequences of numerous organisms from human and mouse to Caenorhabditis elegans and many microorganisms, and the definition of their genes provides a database to interpret cellular protein-expression patterns and relate them to protein function. Proteomics technologies that are dependent on mass spectrometry and involve two-dimensional gel electrophoresis are providing the main window into the world of differential protein-expression analysis. In this article, the limitations and expectations of this research field are examined and the future of the analytical needs of proteomics is explored.
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Affiliation(s)
- S Naaby-Hansen
- Ludwig Institute for Cancer Research and Dept of Biochemistry and Molecular Biology, Royal Free and University College London Medical School, 91 Riding House Street, London, UK W1W 7BS
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Affiliation(s)
- J Godovac-Zimmermann
- Center for Molecular Medicine, Department of Medicine, University College London, 5 University Street, London WC1E 6JJ, United Kingdom.
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Adamczyk M, Gebler JC, Wu J. Sequencing of anti-thyroxine monoclonal antibody fab fragment by ion trap mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2000; 14:999-1007. [PMID: 10844738 DOI: 10.1002/(sici)1097-0231(20000615)14:11<999::aid-rcm978>3.0.co;2-p] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A comprehensive mass spectrometric strategy is described for the sequencing of anti-thyroxine monoclonal antibody Fab region (48 000 Da). After reduction and S-carboxymethylation of the Fab, the modified light chain and Fd fragment were separated and subjected to multiple proteolytic digestions. The resulting digests were characterized by on-line microbore liquid chromatography/electrospray ionization ion trap mass spectrometry. Database search against published immunoglobulins (IgGs) allowed identification of all the peptides in constant domains. The homologous framework residues in the IgGs were utilized as 'sequence maps' for the sequence determination of variable domains. S-Carboxymethylation with an isotopic-enriched moiety greatly facilitated the recognition and data elucidation of cysteinyl peptides through the unique isotopic distribution patterns specific to the modified peptides. Methylation of peptide mixtures provided additional information for the interpretation of MS/MS spectra, allowing easy differentiation of Asp/Asn and Gln/Glu pairs. This study clearly demonstrates the power of mass spectrometry for the sequencing of antibodies without knowing the corresponding DNA sequences.
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Affiliation(s)
- M Adamczyk
- Department of Chemistry (9NM), Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, IL 60064-6016, USA.
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Bauer MD, Sun Y, Keough T, Lacey MP. Sequencing of sulfonic acid derivatized peptides by electrospray mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2000; 14:924-929. [PMID: 10825258 DOI: 10.1002/(sici)1097-0231(20000530)14:10<924::aid-rcm967>3.0.co;2-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We report the application of nanoelectrospray ionization tandem mass spectrometry (nES-MS/MS) and capillary LC/microelectrospray MS/MS (cLC/&mgr;ES-MS/MS) for sequencing sulfonic acid derivatized tryptic peptides. These derivatives were specifically prepared to facilitate low-energy charge-site-initiated fragmentation of C-terminal arginine-containing peptides, and to enhance the selective detection of a single series of y-type fragment ions. Both singly and doubly protonated peptides were analyzed by MS/MS and the results were compared with those from their derivatized counterparts. Model peptides and peptides from tryptic digests of gel-isolated proteins were analyzed. Derivatized singly protonated peptides fragment in the same way by nES-MS/MS as they do by post-source decay matrix-assisted laser desorption/ionization mass spectrometry (PSD-MALDI-MS). They produce fragment ion spectra dominated by y-ions, and the simplified spectra are readily interpreted de novo. Doubly protonated peptides fragment in much the same way as their non-derivatized doubly protonated counterparts. The fragmentation of doubly protonated derivatives is especially useful for sequencing peptides that possess a proline residue near the N-terminus of the molecule. The singly protonated forms of these proline-containing derivatives often show enhanced fragmentation on the N-terminal side of the proline and considerably reduced fragmentation on the C-terminal side. In addition, sulfonic acid derivatization increases the in-source fragmentation of arginine-containing peptides. This could be useful for sequence verification and sequence tagging for use in single stage mass spectrometry. Copyright 2000 John Wiley & Sons, Ltd.
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Affiliation(s)
- MD Bauer
- The Procter and Gamble Company, Miami Valley Laboratories, P.O. Box 538707, Cincinnati, OH 45253-8707, USA
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