1
|
Girod M, Arquier D, Helms A, Juetten K, Brodbelt JS, Lemoine J, MacAleese L. Characterization of Phosphorylated Peptides by Electron-Activated and Ultraviolet Dissociation Mass Spectrometry: A Comparative Study with Collision-Induced Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1040-1054. [PMID: 38626331 DOI: 10.1021/jasms.4c00048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2024]
Abstract
Mass-spectrometry-based methods have made significant progress in the characterization of post-translational modifications (PTMs) in peptides and proteins; however, room remains to improve fragmentation methods. Ideal MS/MS methods are expected to simultaneously provide extensive sequence information and localization of PTM sites and retain labile PTM groups. This collection of criteria is difficult to meet, and the various activation methods available today offer different capabilities. In order to examine the specific case of phosphorylation on peptides, we investigate electron transfer dissociation (ETD), electron-activated dissociation (EAD), and 193 nm ultraviolet photodissociation (UVPD) and compare all three methods with classical collision-induced dissociation (CID). EAD and UVPD show extensive backbone fragmentation, comparable in scope to that of CID. These methods provide diverse backbone fragmentation, producing a/x, b/y, and c/z ions with substantial sequence coverages. EAD displays a high retention efficiency of the phosphate modification, attributed to its electron-mediated fragmentation mechanisms, as observed in ETD. UVPD offers reasonable retention efficiency, also allowing localization of the PTM site. EAD experiments were also performed in an LC-MS/MS workflow by analyzing phosphopeptides spiked in human plasma, and spectra allow accurate identification of the modified sites and discrimination of isomers. Based on the overall performance, EAD and 193 nm UVPD offer alternative options to CID and ETD for phosphoproteomics.
Collapse
Affiliation(s)
- Marion Girod
- Universite Claude Bernard Lyon 1, CNRS, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Delphine Arquier
- Universite Claude Bernard Lyon 1, CNRS, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Amanda Helms
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Kyle Juetten
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jérôme Lemoine
- Universite Claude Bernard Lyon 1, CNRS, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Luke MacAleese
- Universite Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, UMR5306, F-69100 Villeurbanne, France
| |
Collapse
|
2
|
Joyce AW, Searle BC. Computational approaches to identify sites of phosphorylation. Proteomics 2024; 24:e2300088. [PMID: 37897210 DOI: 10.1002/pmic.202300088] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 10/07/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023]
Abstract
Due to their oftentimes ambiguous nature, phosphopeptide positional isomers can present challenges in bottom-up mass spectrometry-based workflows as search engine scores alone are often not enough to confidently distinguish them. Additional scoring algorithms can remedy this by providing confidence metrics in addition to these search results, reducing ambiguity. Here we describe challenges to interpreting phosphoproteomics data and review several different approaches to determine sites of phosphorylation for both data-dependent and data-independent acquisition-based workflows. Finally, we discuss open questions regarding neutral losses, gas-phase rearrangement, and false localization rate estimation experienced by both types of acquisition workflows and best practices for managing ambiguity in phosphosite determination.
Collapse
Affiliation(s)
- Alex W Joyce
- Department of Biomedical Informatics, The Ohio State University Medical Center, Columbus, Ohio, USA
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Brian C Searle
- Department of Biomedical Informatics, The Ohio State University Medical Center, Columbus, Ohio, USA
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| |
Collapse
|
3
|
Lau JKC, Hopkinson AC, Siu KWM. Phosphate Migration versus the Loss of Phosphoric Acid in Protonated Phosphopeptides: A Computational Study. J Phys Chem B 2024; 128:504-514. [PMID: 38190618 DOI: 10.1021/acs.jpcb.3c06767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Residue-specific phosphorylation is a protein post-translational modification that regulates cellular functions. Experimental determination of the exact sites of protein phosphorylation provides an understanding of the signaling and processes at work for a given cellular state. Any experimental artifact that involves migration of the phosphate group during measurement is a concern, as the outcome can lead to erroneous conclusions that may confound studies on cellular signal transduction. Herein, we examine computationally the mechanism by which a phosphate group migrates from one serine residue to another serine in monoprotonated pentapeptides [BA-pSer-Gly-Ser-BB + H]+ → [BA-Ser-Gly-pSer-BB + H]+ (where BA and BB are different combinations of the three basic amino acids, histidine, lysine, and arginine). In addition to moving the phosphate group, the overall mechanism involves transferring a proton from the N-terminal amino acid, BA, to the C-terminal amino acid, BB. This is not a synchronous process, and there is a key high-energy intermediate, structure C, that is zwitterionic with both the basic amino acids protonated and the phosphate group attached to both serine residues and carrying a negative charge. The barriers to moving the phosphate group are calculated to be in the range of 219-274 kJ mol-1 at the B3LYP/6-31G(d) level. These barriers are systematically slightly lower and in good agreement with single-point energy calculations at both M06-2X/6-311++G(d,p) and MP2/6-31++G(d,p) levels. The competitive reaction, loss of phosphoric acid from the protonated pentapeptides, has a barrier in the range of 176-202 kJ mol-1 at the B3LYP/6-31G(d) level. Extension of the theory to M06-2X/6-311++G(d,p)//B3LYP/6-31G(d) and MP2/6-31++G(d,p)// B3LYP/6-31G(d) gives higher values for the loss of phosphoric acid, falling in the range of 196-226 kJ mol-1; these are comparable to the barriers against phosphate migration at the same levels of theory. For larger peptides His-pSer-(Gly)n-Ser-His, where n has values from 2 to 5, the barriers against the loss of phosphoric acid are higher than those against the phosphate group migration. This difference is most pronounced and significant when n = 4 and 5 (the differences are approximately 80 kJ mol-1 under the single-point energy calculations at the M06-2X and MP2 levels). Energy differences using two more recent functionals, M08-HX and MN15, on His-pSer-(Gly)n-Ser-His, where n = 1 and 5, are in good agreement with the M06-2X and MP2 calculations. These results provide the mechanistic rationale for phosphate migration versus other competing reactions in the gas phase under tandem mass spectrometry conditions.
Collapse
Affiliation(s)
- Justin Kai-Chi Lau
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, ON N9B 3P4, Canada
| | - Alan C Hopkinson
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
| | - K W Michael Siu
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, ON N9B 3P4, Canada
| |
Collapse
|
4
|
Révész Á, Hevér H, Steckel A, Schlosser G, Szabó D, Vékey K, Drahos L. Collision energies: Optimization strategies for bottom-up proteomics. MASS SPECTROMETRY REVIEWS 2023; 42:1261-1299. [PMID: 34859467 DOI: 10.1002/mas.21763] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 11/17/2021] [Accepted: 11/17/2021] [Indexed: 06/07/2023]
Abstract
Mass-spectrometry coupled to liquid chromatography is an indispensable tool in the field of proteomics. In the last decades, more and more complex and diverse biochemical and biomedical questions have arisen. Problems to be solved involve protein identification, quantitative analysis, screening of low abundance modifications, handling matrix effect, and concentrations differing by orders of magnitude. This led the development of more tailored protocols and problem centered proteomics workflows, including advanced choice of experimental parameters. In the most widespread bottom-up approach, the choice of collision energy in tandem mass spectrometric experiments has outstanding role. This review presents the collision energy optimization strategies in the field of proteomics which can help fully exploit the potential of MS based proteomics techniques. A systematic collection of use case studies is then presented to serve as a starting point for related further scientific work. Finally, this article discusses the issue of comparing results from different studies or obtained on different instruments, and it gives some hints on methodology transfer between laboratories based on measurement of reference species.
Collapse
Affiliation(s)
- Ágnes Révész
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Helga Hevér
- Chemical Works of Gedeon Richter Plc, Budapest, Hungary
| | - Arnold Steckel
- Department of Analytical Chemistry, MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Institute of Chemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Gitta Schlosser
- Department of Analytical Chemistry, MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Institute of Chemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Dániel Szabó
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Károly Vékey
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - László Drahos
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| |
Collapse
|
5
|
A computational and experimental examination of the CID of phosphorylated serine-H +. Chem Phys Lett 2023. [DOI: 10.1016/j.cplett.2023.140442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
|
6
|
Identification, production and bioactivity of casein phosphopeptides – A review. Food Res Int 2022; 157:111360. [DOI: 10.1016/j.foodres.2022.111360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/28/2022] [Accepted: 05/10/2022] [Indexed: 01/23/2023]
|
7
|
Samarasimhareddy M, Mayer G, Hurevich M, Friedler A. Multiphosphorylated peptides: importance, synthetic strategies, and applications for studying biological mechanisms. Org Biomol Chem 2020; 18:3405-3422. [DOI: 10.1039/d0ob00499e] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Advances in the synthesis of multiphosphorylated peptides and peptide libraries: tools for studying the effects of phosphorylation patterns on protein function and regulation.
Collapse
Affiliation(s)
- Mamidi Samarasimhareddy
- The Institute of Chemistry
- Edmond J. Safra Campus
- Givat Ram
- The Hebrew University of Jerusalem
- Jerusalem
| | - Guy Mayer
- The Institute of Chemistry
- Edmond J. Safra Campus
- Givat Ram
- The Hebrew University of Jerusalem
- Jerusalem
| | - Mattan Hurevich
- The Institute of Chemistry
- Edmond J. Safra Campus
- Givat Ram
- The Hebrew University of Jerusalem
- Jerusalem
| | - Assaf Friedler
- The Institute of Chemistry
- Edmond J. Safra Campus
- Givat Ram
- The Hebrew University of Jerusalem
- Jerusalem
| |
Collapse
|
8
|
Bailey LS, Alves M, Galy N, Patrick AL, Polfer NC. Mechanistic insights into intramolecular phosphate group transfer during collision induced dissociation of phosphopeptides. JOURNAL OF MASS SPECTROMETRY : JMS 2019; 54:449-458. [PMID: 30860300 DOI: 10.1002/jms.4351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/22/2019] [Accepted: 03/04/2019] [Indexed: 05/28/2023]
Abstract
We report on the rearrangement chemistry of model phosphorylated peptides during collision-induced dissociation (CID), where intramolecular phosphate group transfers are observed from donor to acceptor residues. Such "scrambling" could result in inaccurate modification localization, potentially leading to misidentifications. Systematic studies presented herein provide mechanistic insights for the unusually high phosphate group rearrangements presented some time ago by Reid and coworkers (Proteomics 2013, 13 [6], 964-973). It is postulated here that a basic residue like histidine can play a key role in mediating the phosphate group transfer by deprotonating the serine acceptor site. The proposed mechanism is consistent with the observation that fast collisional activation by collision-cell CID and higher-energy collisional dissociation (HCD) can shut down rearrangement chemistry. Additionally, the rearrangement chemistry is highly dependent on the charge state of the peptide, mirroring previous studies that less rearrangement is observed under mobile proton conditions.
Collapse
Affiliation(s)
- Laura S Bailey
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Mélanie Alves
- Département de chimie, UFR 926, Sorbonne Université, Paris, France
| | - Nicolas Galy
- Département de chimie, Université Paul Sabatier, Toulouse, France
| | - Amanda L Patrick
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Nicolas C Polfer
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| |
Collapse
|
9
|
Affiliation(s)
- Clement
M. Potel
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Simone Lemeer
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
| |
Collapse
|
10
|
|
11
|
Chen BJ, Lam TC, Liu LQ, To CH. Post-translational modifications and their applications in eye research (Review). Mol Med Rep 2017; 15:3923-3935. [PMID: 28487982 DOI: 10.3892/mmr.2017.6529] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 02/22/2017] [Indexed: 02/05/2023] Open
Abstract
Gene expression is the process by which genetic information is used for the synthesis of a functional gene product, and ultimately regulates cell function. The increase of biological complexity from genome to proteome is vast, and the post-translational modification (PTM) of proteins contribute to this complexity. The study of protein expression and PTMs has attracted attention in the post‑genomic era. Due to the limited capability of conventional biochemical techniques in the past, large‑scale PTM studies were technically challenging. The introduction of effective protein separation methods, specific PTM purification strategies and advanced mass spectrometers has enabled the global profiling of PTMs and the identification of a targeted PTM within the proteome. The present review provides an overview of current proteomic technologies being applied in eye research, with a particular focus on studies of PTMs in ocular tissues and ocular diseases.
Collapse
Affiliation(s)
- Bing-Jie Chen
- Department of Optometry and Visual Science, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Thomas Chuen Lam
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR, P.R. China
| | - Long-Qian Liu
- Department of Optometry and Visual Science, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Chi-Ho To
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR, P.R. China
| |
Collapse
|
12
|
Penkert M, Yates LM, Schümann M, Perlman D, Fiedler D, Krause E. Unambiguous Identification of Serine and Threonine Pyrophosphorylation Using Neutral-Loss-Triggered Electron-Transfer/Higher-Energy Collision Dissociation. Anal Chem 2017; 89:3672-3680. [DOI: 10.1021/acs.analchem.6b05095] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Martin Penkert
- Leibniz Institut für Molekulare Pharmakologie (FMP), Robert-Rössle Str. 10, 13125 Berlin, Germany
- Humboldt Universität zu Berlin, Department
of Chemistry, Brook-Taylor-Straße
2, 12489 Berlin, Germany
| | - Lisa M. Yates
- Princeton University, Department of Chemistry, Frick Chemistry Building, Washington
Road, Princeton, New Jersey 08544, United States
| | - Michael Schümann
- Leibniz Institut für Molekulare Pharmakologie (FMP), Robert-Rössle Str. 10, 13125 Berlin, Germany
| | - David Perlman
- Princeton University, Department of Molecular Biology, 119 Lewis Thomas Laboratory, Washington
Road, Princeton, New Jersey 08544, United States
| | - Dorothea Fiedler
- Leibniz Institut für Molekulare Pharmakologie (FMP), Robert-Rössle Str. 10, 13125 Berlin, Germany
- Humboldt Universität zu Berlin, Department
of Chemistry, Brook-Taylor-Straße
2, 12489 Berlin, Germany
| | - Eberhard Krause
- Leibniz Institut für Molekulare Pharmakologie (FMP), Robert-Rössle Str. 10, 13125 Berlin, Germany
| |
Collapse
|
13
|
Qian WJ, Park JE, Grant R, Lai CC, Kelley JA, Yaffe MB, Lee KS, Burke TR. Neighbor-directed histidine N (τ)-alkylation: A route to imidazolium-containing phosphopeptide macrocycles. Biopolymers 2016; 104:663-73. [PMID: 26152807 DOI: 10.1002/bip.22698] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 06/15/2015] [Accepted: 07/04/2015] [Indexed: 12/24/2022]
Abstract
Our recently discovered, selective, on-resin route to N(τ)-alkylated imidazolium-containing histidine residues affords new strategies for peptide mimetic design. In this, we demonstrate the use of this chemistry to prepare a series of macrocyclic phosphopeptides, in which imidazolium groups serve as ring-forming junctions. Interestingly, these cationic moieties subsequently serve to charge-mask the phosphoamino acid group that directed their formation. Neighbor-directed histidine N(τ)-alkylation opens the door to new families of phosphopeptidomimetics for use in a range of chemical biology contexts.
Collapse
Affiliation(s)
- Wen-Jian Qian
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD, 21702
| | - Jung-Eun Park
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892
| | - Robert Grant
- Department of Biology and Biological Engineering, Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139
| | - Christopher C Lai
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD, 21702
| | - James A Kelley
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD, 21702
| | - Michael B Yaffe
- Department of Biology and Biological Engineering, Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139
| | - Kyung S Lee
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892
| | - Terrence R Burke
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD, 21702
| |
Collapse
|
14
|
Wang B, Liu J, Cao J, Wang H, Guan X, Wei Z, Guo X. Investigation of c ions formed by N-terminally charged peptides upon collision-induced dissociation. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:989-997. [PMID: 27537939 DOI: 10.1002/jms.3841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 08/16/2016] [Indexed: 06/06/2023]
Abstract
Peptide fragments such as b and y sequence ions generated upon low-energy collision-induced dissociation have been routinely used for tandem mass spectrometry (MS/MS)-based peptide/protein identification. The underlying formation mechanisms have been studied extensively and described within the literature. As a result, the 'mobile proton model' and 'pathways in competition model' have been built to interpret a majority of peptide fragmentation behavior. However, unusual peptide fragments which involve unfamiliar fragmentation pathways or various rearrangement reactions occasionally appear in MS/MS spectra, resulting in confused MS/MS interpretations. In this work, a series of unfamiliar c ions are detected in MS/MS spectra of the model peptides having an N-terminal Arg or deuterohemin group upon low-energy collision-induced dissociation process. Both the protonated Arg and deuterohemin group play an important role in retention of a positive charge at the N-terminus that is remote from the cleavage sites. According to previous reports and our studies involving amino acid substitutions and hydrogen-deuterium exchange, we propose a McLafferty-type rearrangement via charge-remote fragmentation as the potential mechanism to explain the formation of c ions from precursor peptide ions or unconventional b ions. Density functional theory calculations are also employed in order to elucidate the proposed fragmentation mechanisms. Copyright © 2016 John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Bing Wang
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
| | - Jinrong Liu
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
| | - Jungang Cao
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
| | - Huixin Wang
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
| | - Xinshu Guan
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
| | - Zhonglin Wei
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
| | - Xinhua Guo
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, China.
| |
Collapse
|
15
|
Pilo AL, Peng Z, McLuckey SA. The dehydroalanine effect in the fragmentation of ions derived from polypeptides. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:857-866. [PMID: 27484024 PMCID: PMC5068825 DOI: 10.1002/jms.3831] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 07/27/2016] [Accepted: 07/28/2016] [Indexed: 05/11/2023]
Abstract
The fragmentation of peptides and proteins upon collision-induced dissociation (CID) is highly dependent on sequence and ion type (e.g. protonated, deprotonated, sodiated, odd electron, etc.). Some amino acids, for example aspartic acid and proline, have been found to enhance certain cleavages along the backbone. Here, we show that peptides and proteins containing dehydroalanine, a non-proteinogenic amino acid with an unsaturated side-chain, undergo enhanced cleavage of the N-Cα bond of the dehydroalanine residue to generate c- and z-ions. Because these fragment ion types are not commonly observed upon activation of positively charged even-electron species, they can be used to identify dehydroalanine residues and localize them within the peptide or protein chain. While dehydroalanine can be generated in solution, it can also be generated in the gas phase upon CID of various species. Oxidized S-alkyl cysteine residues generate dehydroalanine upon activation via highly efficient loss of the alkyl sulfenic acid. Asymmetric cleavage of disulfide bonds upon collisional activation of systems with limited proton mobility also generates dehydroalanine. Furthermore, we show that gas-phase ion/ion reactions can be used to facilitate the generation of dehydroalanine residues via, for example, oxidation of S-alkyl cysteine residues and conversion of multiply-protonated peptides to radical cations. In the latter case, loss of radical side-chains to generate dehydroalanine from some amino acids gives rise to the possibility for residue-specific backbone cleavage of polypeptide ions. Copyright © 2016 John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Alice L Pilo
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Zhou Peng
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA.
| |
Collapse
|
16
|
Kruse R, Højlund K. Mitochondrial phosphoproteomics of mammalian tissues. Mitochondrion 2016; 33:45-57. [PMID: 27521611 DOI: 10.1016/j.mito.2016.08.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Revised: 08/08/2016] [Accepted: 08/09/2016] [Indexed: 12/31/2022]
Abstract
Mitochondria are essential for several biological processes including energy metabolism and cell survival. Accordingly, impaired mitochondrial function is involved in a wide range of human pathologies including diabetes, cancer, cardiovascular, and neurodegenerative diseases. Within the past decade a growing body of evidence indicates that reversible phosphorylation plays an important role in the regulation of a variety of mitochondrial processes as well as tissue-specific mitochondrial functions in mammals. The rapidly increasing number of mitochondrial phosphorylation sites and phosphoproteins identified is largely ascribed to recent advances in phosphoproteomic technologies such as fractionation, phosphopeptide enrichment, and high-sensitivity mass spectrometry. However, the functional importance and the specific kinases and phosphatases involved have yet to be determined for the majority of these mitochondrial phosphorylation sites. This review summarizes the progress in establishing the mammalian mitochondrial phosphoproteome and the technical challenges encountered while characterizing it, with a particular focus on large-scale phosphoproteomic studies of mitochondria from human skeletal muscle.
Collapse
Affiliation(s)
- Rikke Kruse
- Department of Endocrinology, Odense University Hospital, DK-5000, Odense, Denmark; The Section of Molecular Diabetes & Metabolism, Department of Clinical Research and Institute of Molecular Medicine, University of Southern Denmark, DK-5000 Odense, Denmark
| | - Kurt Højlund
- Department of Endocrinology, Odense University Hospital, DK-5000, Odense, Denmark; The Section of Molecular Diabetes & Metabolism, Department of Clinical Research and Institute of Molecular Medicine, University of Southern Denmark, DK-5000 Odense, Denmark.
| |
Collapse
|
17
|
Cotham VC, McGee WM, Brodbelt JS. Modulation of Phosphopeptide Fragmentation via Dual Spray Ion/Ion Reactions Using a Sulfonate-Incorporating Reagent. Anal Chem 2016; 88:8158-65. [PMID: 27467576 DOI: 10.1021/acs.analchem.6b01901] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The labile nature of phosphoryl groups has presented a long-standing challenge for the characterization of protein phosphorylation via conventional mass spectrometry-based bottom-up proteomics methods. Collision-induced dissociation (CID) causes preferential cleavage of the phospho-ester bond of peptides, particularly under conditions of low proton mobility, and results in the suppression of sequence-informative fragmentation that often prohibits phosphosite determination. In the present study, the fragmentation patterns of phosphopeptides are improved through ion/ion-mediated peptide derivatization with 4-formyl-1,3-benezenedisulfonic acid (FBDSA) anions using a dual spray reactor. This approach exploits the strong electrostatic interactions between the sulfonate moieties of FBDSA and basic sites to facilitate gas-phase bioconjugation and to reduce charge sequestration and increase the yield of phosphate-retaining sequence ions upon CID. Moreover, comparative CID fragmentation analysis between unmodified phosphopeptides and those modified online with FBDSA or in solution via carbamylation and 4-sulfophenyl isothiocyanate (SPITC) provided evidence for sulfonate interference with charge-directed mechanisms that result in preferential phosphate elimination. Our results indicate the prominence of charge-directed neighboring group participation reactions involved in phosphate neutral loss, and the implementation of ion/ion reactions in a dual spray reactor setup provides a means to disrupt the interactions by competing hydrogen-bonding interactions between sulfonate groups and the side chains of basic residues.
Collapse
Affiliation(s)
- Victoria C Cotham
- Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| | - William M McGee
- Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| |
Collapse
|
18
|
Identification, Quantification, and Site Localization of Protein Posttranslational Modifications via Mass Spectrometry-Based Proteomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 919:345-382. [PMID: 27975226 DOI: 10.1007/978-3-319-41448-5_17] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Posttranslational modifications (PTMs) are important biochemical processes for regulating various signaling pathways and determining specific cell fate. Mass spectrometry (MS)-based proteomics has been developed extensively in the past decade and is becoming the standard approach for systematic characterization of different PTMs on a global scale. In this chapter, we will explain the biological importance of various PTMs, summarize key innovations in PTMs enrichment strategies, high-performance liquid chromatography (HPLC)-based fractionation approaches, mass spectrometry detection methods, and lastly bioinformatic tools for PTMs related data analysis. With great effort in recent years by the proteomics community, highly efficient enriching methods and comprehensive resources have been developed. This chapter will specifically focus on five major types of PTMs; phosphorylation, glycosylation, ubiquitination/sumosylation, acetylation, and methylation.
Collapse
|
19
|
Brown R, Stuart SA, Houel S, Ahn NG, Old WM. Large-Scale Examination of Factors Influencing Phosphopeptide Neutral Loss during Collision Induced Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1128-42. [PMID: 25851653 PMCID: PMC4509682 DOI: 10.1007/s13361-015-1109-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 02/18/2015] [Accepted: 02/18/2015] [Indexed: 05/14/2023]
Abstract
Collision-induced dissociation (CID) remains the predominant mass spectrometry-based method for identifying phosphorylation sites in complex mixtures. Unfortunately, the gas-phase reactivity of phosphoester bonds results in MS/MS spectra dominated by phosphoric acid (H3PO4) neutral loss events, suppressing informative peptide backbone cleavages. To understand the major drivers of H3PO4 neutral loss, we performed robust nonparametric statistical analysis of local and distal sequence effects on the magnitude and variability of neutral loss, using a collection of over 35,000 unique phosphopeptide MS/MS spectra. In contrast to peptide amide dissociation pathways, which are strongly influenced by adjacent amino acid side chains, we find that neutral loss of H3PO4 is affected by both proximal and distal sites, most notably basic residues and the peptide N-terminal primary amine. Previous studies have suggested that protonated basic residues catalyze neutral loss through direct interactions with the phosphate. In contrast, we find that nearby basic groups decrease neutral loss regardless of mobility class, an effect only seen by stratifying spectra by charge-mobility. The most inhibitory bases are those immediately N-terminal to the phosphate, presumably because of steric hindrances in catalyzing neutral loss. Further evidence of steric effects is shown by the presence of proline, which can dramatically reduce the presence of neutral loss when between the phosphate and a possible charge donor. In mobile proton spectra, the N-terminus is the strongest predictor of high neutral loss, with proximity to the N-terminus essential for peptides to exhibit the highest levels of neutral loss.
Collapse
Affiliation(s)
- Robert Brown
- Department of Molecular Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309
| | - Scott A. Stuart
- Department of Molecular Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309
| | | | - Natalie G. Ahn
- Department of Molecular Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309
- Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309
| | - William M. Old
- Department of Molecular Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309
- Corresponding author: William M. Old, Department of Molecular Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309, Phone: 303-492-5519, Fax: 303-492-2439,
| |
Collapse
|
20
|
Bertran-Vicente J, Schümann M, Hackenberger CPR, Krause E. Gas-Phase Rearrangement in Lysine Phosphorylated Peptides During Electron-Transfer Dissociation Tandem Mass Spectrometry. Anal Chem 2015; 87:6990-4. [PMID: 26110354 DOI: 10.1021/acs.analchem.5b01389] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Tandem mass spectrometry (MS/MS) strategies coupled with collision-induced dissociation (CID) or radical-driven fragmentation techniques such as electron-capture dissociation (ECD) or electron-transfer dissociation (ETD) have been successfully used for comprehensive phosphoproteome analysis. However, the unambiguous characterization of the phosphorylation site remains a significant challenge due to phosphate-related neutral losses and gas-phase rearrangements, which have been observed during CID. In particular, for the analysis of labile N-phosphorylated peptides, ECD and ETD are emerging as a complementary method. In contrast to CID, the phosphorylation site of histidine, arginine, and lysine phosphorylated peptides can be characterized by ETD. Here, we present a study on the application of ETD for analysis of phospholysine (pLys) peptides. We show that, depending on the charge state of the precursor ion as well as the presence of basic amino acid side chains, phosphate transfer reactions during the ETD process can be observed leading to ambiguous fragment ion spectra. Basically, pLys is stable under ETD conditions allowing an unambiguous assignment of the site of phosphorylation, but some factors/parameters have to be considered to avoid gas-phase rearrangement which would lead to false positive results in phosphoproteomic studies.
Collapse
Affiliation(s)
- Jordi Bertran-Vicente
- †Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle Str. 10, 13125 Berlin, Germany.,§Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Michael Schümann
- †Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle Str. 10, 13125 Berlin, Germany
| | - Christian P R Hackenberger
- †Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle Str. 10, 13125 Berlin, Germany.,‡Department Chemie, Humboldt Universität zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
| | - Eberhard Krause
- †Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle Str. 10, 13125 Berlin, Germany
| |
Collapse
|
21
|
Svane S, Jørgensen TJD, McKenzie CJ, Kjeldsen F. Effect of Metals in Biomimetic Dimetal Complexes on Affinity and Gas-Phase Protection of Phosphate Esters. Anal Chem 2015; 87:7060-8. [DOI: 10.1021/acs.analchem.5b00257] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Simon Svane
- Department of Biochemistry
and Molecular Biology, and ‡Department of Physics, Chemistry
and Pharmacy, University of Southern Denmark, 5230, Odense M, Denmark
| | - Thomas J. D. Jørgensen
- Department of Biochemistry
and Molecular Biology, and ‡Department of Physics, Chemistry
and Pharmacy, University of Southern Denmark, 5230, Odense M, Denmark
| | - Christine J. McKenzie
- Department of Biochemistry
and Molecular Biology, and ‡Department of Physics, Chemistry
and Pharmacy, University of Southern Denmark, 5230, Odense M, Denmark
| | - Frank Kjeldsen
- Department of Biochemistry
and Molecular Biology, and ‡Department of Physics, Chemistry
and Pharmacy, University of Southern Denmark, 5230, Odense M, Denmark
| |
Collapse
|
22
|
Tveen-Jensen K, Gesellchen F, Wilson R, Spickett CM, Cooper JM, Pitt AR. Interfacing low-energy SAW nebulization with Liquid Chromatography-Mass Spectrometry for the analysis of biological samples. Sci Rep 2015; 5:9736. [PMID: 25978651 PMCID: PMC4432867 DOI: 10.1038/srep09736] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 03/10/2015] [Indexed: 01/29/2023] Open
Abstract
Soft ionization methods for the introduction of labile biomolecules into a mass spectrometer are of fundamental importance to biomolecular analysis. Previously, electrospray ionization (ESI) and matrix assisted laser desorption-ionization (MALDI) have been the main ionization methods used. Surface acoustic wave nebulization (SAWN) is a new technique that has been demonstrated to deposit less energy into ions upon ion formation and transfer for detection than other methods for sample introduction into a mass spectrometer (MS). Here we report the optimization and use of SAWN as a nebulization technique for the introduction of samples from a low flow of liquid, and the interfacing of SAWN with liquid chromatographic separation (LC) for the analysis of a protein digest. This demonstrates that SAWN can be a viable, low-energy alternative to ESI for the LC-MS analysis of proteomic samples.
Collapse
Affiliation(s)
- Karina Tveen-Jensen
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, UK. B4 7ET
| | - Frank Gesellchen
- Division of Biomedical Engineering, University of Glasgow, Oakfield Avenue, Glasgow, UK. G12 8LT
| | - Rab Wilson
- Division of Biomedical Engineering, University of Glasgow, Oakfield Avenue, Glasgow, UK. G12 8LT
| | - Corinne M Spickett
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, UK. B4 7ET
| | - Jonathan M Cooper
- Division of Biomedical Engineering, University of Glasgow, Oakfield Avenue, Glasgow, UK. G12 8LT
| | - Andrew R Pitt
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, UK. B4 7ET
| |
Collapse
|
23
|
Yakovlev I, Deming TJ. Controlled synthesis of phosphorylcholine derivatives of poly(serine) and poly(homoserine). J Am Chem Soc 2015; 137:4078-81. [PMID: 25790104 DOI: 10.1021/jacs.5b01543] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We report methods for the synthesis of polypeptides that are fully functionalized with desirable phosphorylcholine, PC, groups. Because of the inherent challenges in the direct incorporation of the PC group into α-amino acid N-carboxyanhydride (NCA) monomers, we developed a synthetic approach that combined functional NCA polymerization with efficient postpolymerization modification. While poly(L-phosphorylcholine serine) was found to be unstable upon synthesis, we successfully prepared poly(L-phosphorylcholine homoserine) with controlled chain lengths and found these to be water-soluble with disordered chain conformations.
Collapse
Affiliation(s)
- Ilya Yakovlev
- †Department of Chemistry and Biochemistry and ‡Department of Bioengineering, University of California, Los Angeles, California 90095, United States
| | - Timothy J Deming
- †Department of Chemistry and Biochemistry and ‡Department of Bioengineering, University of California, Los Angeles, California 90095, United States
| |
Collapse
|
24
|
Wang H, Wang B, Wei Z, Cao Y, Guan X, Guo X. Characteristic neutral loss of CH3CHO from Thr-containing sodium-associated peptides. JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:488-494. [PMID: 25800185 DOI: 10.1002/jms.3555] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 11/15/2014] [Accepted: 11/23/2014] [Indexed: 06/04/2023]
Abstract
A characteristic neutral loss of 44 Da is observed in the MS/MS spectra of Thr-containing sodiated peptides. A combination of tandem mass spectrometry and quantum chemical calculations calculated at the B3LYP/6-311G (d, p) level of ab initio theory is used to elucidate this fragmentation pathway. The high resolution mass spectrometry data indicate this neutral loss is acetaldehyde lost from the side chain of Thr rather than CO2. The intensity of this neutral loss can be enhanced when Thr residue is far from the C-terminus and when the C-terminus is esterified as well. The mechanism of the acetaldehyde loss is proposed to adopt a McLafferty-type rearrangement reaction, which involves a proton transfer from the hydroxyl of Thr side chain to its C-terminal neighboring carbonyl oxygen inducing the cleavage of the Ca-Cβ bond. This mechanism is further supported by examining the fragmentation of a [GT(tBu)G + Na](+) peptide derivative and by comparing the product ion spectra of [M + Na-44](+) of [GTGA + Na](+) with [M + Na](+) of [GGGA + Na](+). A similar neutral loss of HCHO can also be detected in Ser-containing peptides. Our computational results reveal that the most stable [GTG + Na](+) ion is present as a tridentate charge-solvated structure and the dissociation leading to the 44 loss is dynamically and energetically favorable.
Collapse
Affiliation(s)
- Huixin Wang
- College of Chemistry, Jilin University, Changchun, 130012, China
| | | | | | | | | | | |
Collapse
|
25
|
Bierhanzl VM, Čabala R, Ston M, Kubinec R, Szabó AH, Podolec P. Gas chromatography with mass spectrometry analysis of phosphoserine, phosphoethanolamine, phosphoglycerol, and phosphate. J Sep Sci 2014; 38:67-72. [DOI: 10.1002/jssc.201400657] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 09/12/2014] [Accepted: 10/19/2014] [Indexed: 11/10/2022]
Affiliation(s)
- Václav Matěj Bierhanzl
- Faculty of Science; Department of Analytical Chemistry; Charles University in Prague; Prague Czech Republic
| | - Radomír Čabala
- Faculty of Science; Department of Analytical Chemistry; Charles University in Prague; Prague Czech Republic
- Institute of Forensic Medicine and Toxicology; General University Hospital in Prague; Prague Czech Republic
| | - Martin Ston
- Faculty of Science; Department of Analytical Chemistry; Charles University in Prague; Prague Czech Republic
| | - Róbert Kubinec
- Faculty of Natural Sciences; Institute of Chemistry; Comenius University; Bratislava Slovakia
- Distillchem; s.r.o; Makov Slovakia
| | | | - Peter Podolec
- Faculty of Natural Sciences; Institute of Chemistry; Comenius University; Bratislava Slovakia
| |
Collapse
|
26
|
Wang B, Yu J, Wang H, Wei Z, Guo X, Xiao Z, Zeng Z, Kong W. Investigation of bn-44 peptide fragments using high resolution mass spectrometry and isotope labeling. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:2116-2124. [PMID: 25280401 DOI: 10.1007/s13361-014-0994-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 08/20/2014] [Accepted: 08/25/2014] [Indexed: 06/03/2023]
Abstract
An N-terminal deuterohemin-containing hexapeptide (DhHP-6) was designed as a short peptide cytochrome c (Cyt c) mimetic to study the effect of N-terminal charge on peptide fragmentation pathways. This peptide gave different dissociation patterns than normal tryptic peptides. Upon collision-induced dissociation (CID) with an ion trap mass spectrometer, the singly charged peptide ion containing no added proton generated abundant and characteristic bn-44 ions instead of bn-28 (an) ions. Studies by high resolution mass spectrometry (HRMS) and isotope labeling indicate that elimination of 44 Da fragments from b ions occurs via two different pathways: (1) loss of CH3CHO (44.0262) from a Thr side chain; (2) loss of CO2 (43.9898) from the oxazolone structure in the C-terminus. A series of analogues were designed and analyzed. The experimental results combined with Density Functional Theory (DFT) calculations on the proton affinity of the deuteroporphyrin demonstrate that the production of these novel bn-44 ions is related to the N-terminal charge via a charge-remote rather than radical-directed fragmentation pathway.
Collapse
Affiliation(s)
- Bing Wang
- College of Chemistry, Jilin University, Changchun, 130012, China
| | | | | | | | | | | | | | | |
Collapse
|
27
|
Bauer M, Ahrné E, Baron AP, Glatter T, Fava LL, Santamaria A, Nigg EA, Schmidt A. Evaluation of Data-Dependent and -Independent Mass Spectrometric Workflows for Sensitive Quantification of Proteins and Phosphorylation Sites. J Proteome Res 2014; 13:5973-88. [DOI: 10.1021/pr500860c] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Manuel Bauer
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Erik Ahrné
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Anna P. Baron
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Timo Glatter
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Luca L. Fava
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Anna Santamaria
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Erich A. Nigg
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Alexander Schmidt
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| |
Collapse
|
28
|
Qian WJ, Park JE, Lim D, Lai CC, Kelley JA, Park SY, Lee KW, Yaffe MB, Lee KS, Burke TR. Mono-anionic phosphopeptides produced by unexpected histidine alkylation exhibit high Plk1 polo-box domain-binding affinities and enhanced antiproliferative effects in HeLa cells. Biopolymers 2014; 102:444-55. [PMID: 25283071 PMCID: PMC4895914 DOI: 10.1002/bip.22569] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 09/12/2014] [Accepted: 09/27/2014] [Indexed: 11/07/2022]
Abstract
Binding of polo-like kinase 1 (Plk1) polo-box domains (PBDs) to phosphothreonine (pThr)/phosphoserine (pSer)-containing sequences is critical for the proper function of Plk1. Although high-affinity synthetic pThr-containing peptides provide starting points for developing PBD-directed inhibitors, to date the efficacy of such peptides in whole cell assays has been poor. This potentially reflects limited cell membrane permeability arising, in part, from the di-anionic nature of the phosphoryl group or its mimetics. In our current article we report the unanticipated on-resin N(τ)-alkylation of histidine residues already bearing a N(π)- alkyl group. This resulted in cationic imidazolium-containing pThr peptides, several of which exhibit single-digit nanomolar PBD-binding affinities in extracellular assays and improved antimitotic efficacies in intact cells. We enhanced the cellular efficacies of these peptides further by applying bio-reversible pivaloyloxymethyl (POM) phosphoryl protection. New structural insights presented in our current study, including the potential utility of intramolecular charge masking, may be useful for the further development of PBD-binding peptides and peptide mimetics.
Collapse
Affiliation(s)
- Wen-Jian Qian
- Chemical Biology Laboratory, Center for Cancer Research, National Institutes of Health, NCI at Frederick, Frederick, MD 21702, U. S. A
| | - Jung-Eun Park
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, U. S. A
| | - Dan Lim
- Department of Biology and Biological Engineering, Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, U. S. A
| | - Christopher C. Lai
- Chemical Biology Laboratory, Center for Cancer Research, National Institutes of Health, NCI at Frederick, Frederick, MD 21702, U. S. A
| | - James A. Kelley
- Chemical Biology Laboratory, Center for Cancer Research, National Institutes of Health, NCI at Frederick, Frederick, MD 21702, U. S. A
| | - Suk-Youl Park
- Advanced Institutes of Convergence Technology, Seoul National University, Suwon 443-270, Republic of Korea
| | - Ki-Won Lee
- Advanced Institutes of Convergence Technology, Seoul National University, Suwon 443-270, Republic of Korea
- World Class University Biomodulation Major and Department of Agricultural Biotechnology, Seoul National University, Seoul, 151-742, Republic of Korea
| | - Michael B. Yaffe
- Department of Biology and Biological Engineering, Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, U. S. A
| | - Kyung S. Lee
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, U. S. A
| | - Terrence R. Burke
- Chemical Biology Laboratory, Center for Cancer Research, National Institutes of Health, NCI at Frederick, Frederick, MD 21702, U. S. A
| |
Collapse
|
29
|
Oslund RC, Kee JM, Couvillon AD, Bhatia V, Perlman DH, Muir TW. A phosphohistidine proteomics strategy based on elucidation of a unique gas-phase phosphopeptide fragmentation mechanism. J Am Chem Soc 2014; 136:12899-911. [PMID: 25156620 PMCID: PMC4183637 DOI: 10.1021/ja507614f] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Indexed: 01/25/2023]
Abstract
Protein histidine phosphorylation is increasingly recognized as a critical posttranslational modification (PTM) in central metabolism and cell signaling. Still, the detection of phosphohistidine (pHis) in the proteome has remained difficult due to the scarcity of tools to enrich and identify this labile PTM. To address this, we report the first global proteomic analysis of pHis proteins, combining selective immunoenrichment of pHis peptides and a bioinformatic strategy based on mechanistic insight into pHis peptide gas-phase fragmentation during LC-MS/MS. We show that collision-induced dissociation (CID) of pHis peptides produces prominent characteristic neutral losses of 98, 80, and 116 Da. Using isotopic labeling studies, we also demonstrate that the 98 Da neutral loss occurs via gas-phase phosphoryl transfer from pHis to the peptide C-terminal α-carboxylate or to Glu/Asp side chain residues if present. To exploit this property, we developed a software tool that screens LC-MS/MS spectra for potential matches to pHis-containing peptides based on their neutral loss pattern. This tool was integrated into a proteomics workflow for the identification of endogenous pHis-containing proteins in cellular lysates. As an illustration of this strategy, we analyzed pHis peptides from glycerol-fed and mannitol-fed Escherichia coli cells. We identified known and a number of previously speculative pHis sites inferred by homology, predominantly in the phosphoenolpyruvate:sugar transferase system (PTS). Furthermore, we identified two new sites of histidine phosphorylation on aldehyde-alcohol dehydrogenase (AdhE) and pyruvate kinase (PykF) enzymes, previously not known to bear this modification. This study lays the groundwork for future pHis proteomics studies in bacteria and other organisms.
Collapse
Affiliation(s)
- Rob C. Oslund
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Jung-Min Kee
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | | | - Vivek
N. Bhatia
- Heartflow,
Inc., 1400 Seaport Boulevard,
Building B, Redwood City, California 94063, United States
| | - David H. Perlman
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department
of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
- Lewis-Sigler
Institute for Integrative Genomics and the Princeton Collaborative
Proteomics Mass Spectrometry Center, Princeton
University, Princeton, New Jersey 08544, United States
| | - Tom W. Muir
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| |
Collapse
|
30
|
Popov IA, Indeikina MI, Pekov SI, Starodubtseva NL, Kononikhin AS, Nikolaeva MI, Kukaev EN, Kostyukevich YI, Kozin SA, Makarov AA, Nikolaev EN. Estimation of phosphorylation level of amyloid-beta isolated from human blood plasma: Ultrahigh-resolution mass spectrometry. Mol Biol 2014. [DOI: 10.1134/s0026893314040098] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
31
|
Donohoe GC, Maleki H, Arndt JR, Khakinejad M, Yi J, McBride C, Nurkiewicz TR, Valentine SJ. A new ion mobility-linear ion trap instrument for complex mixture analysis. Anal Chem 2014; 86:8121-8. [PMID: 25068446 DOI: 10.1021/ac501527y] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A new instrument that couples a low-pressure drift tube with a linear ion trap mass spectrometer is demonstrated for complex mixture analysis. The combination of the low-pressure separation with the ion trapping capabilities provides several benefits for complex mixture analysis. These include high sensitivity, unique ion fragmentation capabilities, and high reproducibility. Even though the gas-phase separation and the mass measurement steps are each conducted in an ion filtering mode, detection limits for mobility-selected peptide ions are in the tens of attomole range. In addition to ion separation, the low-pressure drift tube can be used as an ion fragmentation cell yielding mobility-resolved fragment ions that can be subsequently analyzed by multistage tandem mass spectrometry (MS(n)) methods in the ion trap. Because of the ion trap configuration, these methods can be comprised of any number (limited by ion signal) of collision-induced dissociation (CID) and electron transfer dissociation (ETD) processes. The high reproducibility of the gas-phase separation allows for comparison of two-dimensional ion mobility spectrometry (IMS)-MS data sets in a pixel-by-pixel fashion without the need for data set alignment. These advantages are presented in model analyses representing mixtures encountered in proteomics and metabolomics experiments.
Collapse
Affiliation(s)
- Gregory C Donohoe
- C. Eugene Bennett Department of Chemistry, West Virginia University , Morgantown, West Virginia 26506, United States
| | | | | | | | | | | | | | | |
Collapse
|
32
|
Gonzalez-Sanchez MB, Lanucara F, Hardman GE, Eyers CE. Gas-phase intermolecular phosphate transfer within a phosphohistidine phosphopeptide dimer. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2014; 367:28-34. [PMID: 25844054 PMCID: PMC4375673 DOI: 10.1016/j.ijms.2014.04.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 04/14/2014] [Accepted: 04/22/2014] [Indexed: 05/26/2023]
Abstract
The hydrogen bonds and electrostatic interactions that form between the protonated side chain of a basic residue and the negatively charged phosphate of a phosphopeptide can play crucial roles in governing their dissociation pathways under low-energy collision-induced dissociation (CID). Understanding how phosphoramidate (i.e. phosphohistidine, phospholysine and phosphoarginine), rather than phosphomonoester-containing peptides behave during CID is paramount in investigation of these problematic species by tandem mass spectrometry. To this end, a synthetic peptide containing either phosphohistidine (pHis) or phospholysine (pLys) was analyzed by ESI-MS using a Paul-type ion trap (AmaZon, Bruker) and by traveling wave ion mobility-mass spectrometry (Synapt G2-Si, Waters). Analysis of the products of low-energy CID demonstrated formation of a doubly 'phosphorylated' product ion arising from intermolecular gas-phase phosphate transfer within a phosphopeptide dimer. The results are explained by the formation of a homodimeric phosphohistidine (pHis) peptide non-covalent complex (NCX), likely stabilized by the electrostatic interaction between the pHis phosphate group and the protonated C-terminal lysine residue of the peptide. To the best of our knowledge this is the first report of intermolecular gas-phase phosphate transfer from one phosphopeptide to another, leading to a doubly phosphorylated peptide product ion.
Collapse
Affiliation(s)
- Maria-Belen Gonzalez-Sanchez
- Michael Barber Centre for Mass Spectrometry, School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Francesco Lanucara
- Michael Barber Centre for Mass Spectrometry, School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - Gemma E. Hardman
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - Claire E. Eyers
- Michael Barber Centre for Mass Spectrometry, School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| |
Collapse
|
33
|
Lanucara F, Fornarini S, Eyers CE, Crestoni ME. Probing the exposure of the phosphate group in modified amino acids and peptides by ion-molecule reactions with triethoxyborane in Fourier transform ion cyclotron resonance mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:1107-1116. [PMID: 24711274 DOI: 10.1002/rcm.6884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Revised: 02/27/2014] [Accepted: 02/27/2014] [Indexed: 06/03/2023]
Abstract
RATIONALE Intramolecular hydrogen bonds between a phosphate group and charged residues play a crucial role in the chemistry of phosphorylated peptides, driving the species to specific conformations and affecting the exposure of the phosphate moiety. The nature and extent of these interactions can be investigated by measuring the reactivity of phosphate groups toward selected substrates in the gas phase. METHODS We used Fourier Transform Ion Cyclotron Resonance (FT-ICR) mass spectrometry (MS) to perform a systematic study on the gas-phase ionic reactivity of phosphorylated amino acids and peptides with triethoxyborane (TEB). Ions of interest were generated by electrospray ionization (ESI), isolated in the cell of the FT-ICR mass spectrometer, and allowed to react with a stationary pressure of TEB. The temporal evolution of the reaction was monitored and thermal rate constants were derived. The structure of the ionic products was confirmed by Collision-Induced Dissociation (CID) tandem mass spectrometry (MS/MS). RESULTS TEB was found to react with the phosphate of protonated phosphorylated amino acids and peptides by an addition-elimination pathway. The kinetic efficiency of the reaction showed a positive correlation with the charge state of the reagent ion, suggesting the existence of charge-state-dependent exposure of the phosphate groups towards the incoming neutral during the reaction. Isomeric phosphorylated peptides, only differing for the position of the modified serine residue, showed markedly different kinetic efficiencies. CONCLUSIONS The ability of a phosphorylated species to react with TEB depends on the ease of access to the phosphate moiety in the corresponding gaseous ion. Measuring the kinetic efficiency of such reactions can represent a valuable tool to explore the accessibility of phosphate groups in biomolecules.
Collapse
Affiliation(s)
- Francesco Lanucara
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, M1 7DN, UK; Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | | | | | | |
Collapse
|
34
|
Lanucara F, Chiavarino B, Scuderi D, Maitre P, Fornarini S, Crestoni ME. Kinetic control in the CID-induced elimination of H3PO4 from phosphorylated serine probed using IRMPD spectroscopy. Chem Commun (Camb) 2014; 50:3845-8. [PMID: 24589658 DOI: 10.1039/c4cc00877d] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
InfraRed Multiple Photon Dissociation (IRMPD) spectroscopy was used to assay the structural features of the fragment ions resulting from the elimination of H3PO4 in the Collision-Induced Dissociation (CID) of protonated serine. The results are interpreted with the aid of density functional theory calculations. Experiment and theory point to an aziridine-ring structure, implying participation of the vicinal amino group in the formation of this species. This finding constitutes a benchmark for investigating the same process in the CID of phosphorylated peptides.
Collapse
Affiliation(s)
- Francesco Lanucara
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, M17DN Manchester, UK.
| | | | | | | | | | | |
Collapse
|
35
|
Lanucara F, Chi Hoo Lee D, Eyers CE. Unblocking the sink: improved CID-based analysis of phosphorylated peptides by enzymatic removal of the basic C-terminal residue. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:214-225. [PMID: 24297471 PMCID: PMC3899453 DOI: 10.1007/s13361-013-0770-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 10/08/2013] [Accepted: 10/08/2013] [Indexed: 06/02/2023]
Abstract
A one-step enzymatic reaction for improving the collision-induced dissociation (CID)-based tandem mass spectrometry (MS/MS) analysis of phosphorylated peptides in an ion trap is presented. Carboxypeptidase-B (CBP-B) was used to selectively remove C-terminal arginine or lysine residues from phosphorylated tryptic/Lys-C peptides prior to their MS/MS analysis by CID with a Paul-type ion trap. Removal of this basic C-terminal residue served to limit the extent of gas-phase neutral loss of phosphoric acid (H3PO4), favoring the formation of diagnostic b and y ions as determined by an increase in both the number and relative intensities of the sequence-specific product ions. Such differential fragmentation is particularly valuable when the H3PO4 elimination is so predominant that localizing the phosphorylation site on the peptide sequence is hindered. Improvement in the quality of tandem mass spectral data generated by CID upon CBP-B treatment resulted in greater confidence both in assignment of the phosphopeptide primary sequence and for pinpointing the site of phosphorylation. Higher Mascot ion scores were also generated, combined with lower expectation values and higher delta scores for improved confidence in site assignment; Ascore values also improved. These results are rationalized in accordance with the accepted mechanisms for the elimination of H3PO4 upon low energy CID and insights into the factors dictating the observed dissociation pathways are presented. We anticipate this approach will be of utility in the MS analysis of phosphorylated peptides, especially when alternative electron-driven fragmentation techniques are not available.
Collapse
Affiliation(s)
- Francesco Lanucara
- Manchester Institute of Biotechnology, Michael Barber Centre for Mass Spectrometry, School of Chemistry, University of Manchester, Manchester, M1 7DN UK
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB UK
| | - Dave Chi Hoo Lee
- Manchester Institute of Biotechnology, Michael Barber Centre for Mass Spectrometry, School of Chemistry, University of Manchester, Manchester, M1 7DN UK
| | - Claire E. Eyers
- Manchester Institute of Biotechnology, Michael Barber Centre for Mass Spectrometry, School of Chemistry, University of Manchester, Manchester, M1 7DN UK
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB UK
| |
Collapse
|
36
|
Wiese H, Kuhlmann K, Wiese S, Stoepel NS, Pawlas M, Meyer HE, Stephan C, Eisenacher M, Drepper F, Warscheid B. Comparison of alternative MS/MS and bioinformatics approaches for confident phosphorylation site localization. J Proteome Res 2014; 13:1128-37. [PMID: 24364495 DOI: 10.1021/pr400402s] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Over the past years, phosphoproteomics has advanced to a prime tool in signaling research. Since then, an enormous amount of information about in vivo protein phosphorylation events has been collected providing a treasure trove for gaining a better understanding of the molecular processes involved in cell signaling. Yet, we still face the problem of how to achieve correct modification site localization. Here we use alternative fragmentation and different bioinformatics approaches for the identification and confident localization of phosphorylation sites. Phosphopeptide-enriched fractions were analyzed by multistage activation, collision-induced dissociation and electron transfer dissociation (ETD), yielding complementary phosphopeptide identifications. We further found that MASCOT, OMSSA and Andromeda each identified a distinct set of phosphopeptides allowing the number of site assignments to be increased. The postsearch engine SLoMo provided confident phosphorylation site localization, whereas different versions of PTM-Score integrated in MaxQuant differed in performance. Based on high-resolution ETD and higher collisional dissociation (HCD) data sets from a large synthetic peptide and phosphopeptide reference library reported by Marx et al. [Nat. Biotechnol. 2013, 31 (6), 557-564], we show that an Andromeda/PTM-Score probability of 1 is required to provide an false localization rate (FLR) of 1% for HCD data, while 0.55 is sufficient for high-resolution ETD spectra. Additional analyses of HCD data demonstrated that for phosphotyrosine peptides and phosphopeptides containing two potential phosphorylation sites, PTM-Score probability cutoff values of <1 can be applied to ensure an FLR of 1%. Proper adjustment of localization probability cutoffs allowed us to significantly increase the number of confident sites with an FLR of <1%.Our findings underscore the need for the systematic assessment of FLRs for different score values to report confident modification site localization.
Collapse
Affiliation(s)
- Heike Wiese
- Faculty of Biology, Functional Proteomics, University of Freiburg , 79104 Freiburg, Germany
| | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Marchini FK, de Godoy LMF, Batista M, Kugeratski FG, Krieger MA. Towards the phosphoproteome of trypanosomatids. Subcell Biochem 2014; 74:351-378. [PMID: 24264253 DOI: 10.1007/978-94-007-7305-9_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The identification and localization of protein phosphorylation sites provide clues to what proteins or pathways might be activated in a given condition, helping to improve our understanding about signaling networks. Advances in strategies for enrichment of phosphorylated peptides/proteins, mass spectrometry (MS) instrumentation, and specific MS techniques for identification and quantification of post-translational modifications have allowed for large-scale mapping of phosphorylation sites, promoting the field of phosphoproteomics. The great promise of phosphoproteomics is to unravel the dynamics of signaling networks, a layer of the emerging field of systems biology. Until a few years ago only a small number of phosphorylation sites had been described. Following large-scale trends, recent phosphoproteomic studies have reported the mapping of thousands of phosphorylation sites in trypanosomatids. However, quantitative information about the regulation of such sites in different conditions is still lacking. In this chapter, we provide a historical overview of phosphoproteomic studies for trypanosomatids and discuss some challenges and perspectives in the field.
Collapse
|
38
|
Cui L, Yapici I, Borhan B, Reid GE. Quantification of competing H3PO4 versus HPO3 + H2O neutral losses from regioselective 18O-labeled phosphopeptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:141-148. [PMID: 24249041 DOI: 10.1007/s13361-013-0744-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 08/26/2013] [Accepted: 08/28/2013] [Indexed: 06/02/2023]
Abstract
Abundant neutral losses of 98 Da are often observed upon ion trap CID-MS/MS of protonated phosphopeptide ions. Two competing fragmentation pathways are involved in this process, namely, the direct loss of H3PO4 from the phosphorylated residue and the combined losses of HPO3 and H2O from the phosphorylation site and from an additional site within the peptide, respectively. These competing pathways produce product ions with different structures but the same m/z values, potentially limiting the utility of CID-MS(3) for phosphorylation site localization. To quantify the relative contributions of these pathways and to determine the conditions under which each pathway predominates, we have examined the ion trap CID-MS/MS fragmentation of a series of regioselective (18)O-phosphate ester labeled phosphopeptides prepared using novel solution-phase amino acid synthesis and solid-phase peptide synthesis methodologies. By comparing the intensity of the -100 Da (-H3PO3 (18)O) versus -98 Da (-[HPO3 + H2O]) neutral loss product ions formed upon MS/MS, quantification of the two pathways was achieved. Factors that affect the extent of formation of the competing neutral losses were investigated, with the combined loss pathway predominantly occurring under conditions of limited proton mobility, and with increased combined losses observed for phosphothreonine compared with phosphoserine-containing peptides. The combined loss pathway was found to be less dominant under ion activation conditions associated with HCD-MS/MS. Finally, the contribution of carboxylic acid functional groups and backbone amide bonds to the water loss in the combined loss fragmentation pathway was determined via methyl esterification and by examination of a phosphopeptide lacking side-chain hydroxyl groups.
Collapse
Affiliation(s)
- Li Cui
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA
| | | | | | | |
Collapse
|
39
|
Smith SA, Kalcic CL, Cui L, Reid GE. Femtosecond laser-induced ionization/dissociation tandem mass spectrometry (fsLID-MS/MS) of deprotonated phosphopeptide anions. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:2807-2817. [PMID: 24214867 DOI: 10.1002/rcm.6750] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Revised: 09/24/2013] [Accepted: 09/25/2013] [Indexed: 06/02/2023]
Abstract
RATIONALE Radical-directed dissociation techniques provide structural information which is complementary to that from conventional collision-induced dissociation (CID). The analysis of phosphopeptide anions is warranted due to their relatively acidic character. As femtosecond laser-induced ionization/dissociation tandem mass spectrometry (fsLID-MS/MS) is uniquely initiated by field ionization, an investigation is warranted to determine whether fsLID may provide novel analytical utility for phosphopeptide anions. METHODS Twenty-three synthetic deprotonated phosphopeptide anions were introduced into a three-dimensional quadrupole ion trap mass spectrometer via electrospray ionization. The ion trap was interfaced with a near-IR (802 nm) ultrashort-pulsed (35 fs FWHM) ultrahigh-powered (peak power ~10(14) W/cm(2)) laser system. Performance comparisons are made with other techniques applied to phosphopeptide anion analysis, including CID, electron detachment dissociation (EDD), negative electron transfer dissociation (NETD), activated electron photodetachment dissociation (activated-EPD), and ultraviolet photodissociation (UVPD). RESULTS FsLID-MS/MS of multiply deprotonated phosphopeptide anions provides sequence information via phosphorylation-intact a/x ions in addition to other sequence ions, satellite ions, and side-chain losses. Novel fragmentation processes include selective c-ion formation N-terminal to Ser/Thr and a phosphorylation-specific correlation between xn -98 ion abundances and phosphorylation at the n(th) residue. Sequencing-quality data required about 30 s of signal averaging. fsLID-MS/MS of singly deprotonated phosphopeptides did not yield product anions with stable trajectories, despite significant depletion of the precursor. CONCLUSIONS Multiply deprotonated phosphopeptide anions were sequenced via negative-mode fsLID-MS/MS, with phosphosite localization facilitated by a/x ion series in addition to diagnostic x(n)-98 ions. fsLID-MS/MS is qualitatively competitive with other techniques. Further efficiency enhancements (e.g., implementation on a linear trap or/and higher pulse frequencies) may permit sequence analyses on chromatographic timescales.
Collapse
Affiliation(s)
- Scott A Smith
- RTSF Mass Spectrometry & Metabolomics Core, Michigan State University, East Lansing, MI, 48824, USA
| | | | | | | |
Collapse
|
40
|
Cui L, Reid GE. Examining factors that influence erroneous phosphorylation site localization via competing fragmentation and rearrangement reactions during ion trap CID-MS/MS and -MS(3.). Proteomics 2013; 13:964-73. [PMID: 23335301 DOI: 10.1002/pmic.201200384] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 10/22/2013] [Accepted: 11/08/2012] [Indexed: 01/01/2023]
Abstract
Factors influencing the magnitude of competing fragmentation and intramolecular phosphate group rearrangement reactions during CID-MS/MS and CID-MS(3) of protonated phosphopeptide ions in ion trap mass spectrometers, and their effect on phosphorylation site localization using automated search algorithms, have been examined by systematically varying the peptide composition, the identity, number, and position of the phosphorylated "donor" and nonphosphorylated "acceptor" residues, and the proton mobility of the precursor ion charge states for a synthetic phosphopeptide library. CID-MS(3) of product ions formed via combined neutral losses of HPO3 and H2 O, rather than direct loss of H3 PO4 from phosphotyrosine containing peptides yielded incorrect phosphorylation site assignments, while correct phosphorylation site assignments for phosphothreonine and phosphoserine containing peptides were highly dependant on the relative abundance of these competing fragmentation pathways. Abundant phosphate group rearrangement product ions were observed from CID-MS/MS of multiply protonated phosphopeptide ions, with increased rearrangement under nonmobile or partially mobile protonation conditions, and as a function of the identity and number of the donor and acceptor residues. A clear inverse trend was observed between the amplitude of these rearrangement reactions and the confidence for phosphorylation site localization, and rearrangement played a contributing role in erroneous phosphorylation site assignment for several peptides.
Collapse
Affiliation(s)
- Li Cui
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | | |
Collapse
|
41
|
Zhang Y, Fonslow BR, Shan B, Baek MC, Yates JR. Protein analysis by shotgun/bottom-up proteomics. Chem Rev 2013; 113:2343-94. [PMID: 23438204 PMCID: PMC3751594 DOI: 10.1021/cr3003533] [Citation(s) in RCA: 970] [Impact Index Per Article: 88.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yaoyang Zhang
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bryan R. Fonslow
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bing Shan
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Moon-Chang Baek
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Molecular Medicine, Cell and Matrix Biology Research Institute, School of Medicine, Kyungpook National University, Daegu 700-422, Republic of Korea
| | - John R. Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| |
Collapse
|
42
|
Quan Q, Hao Q, Song T, Siu CK, Chu IK. Mechanistic investigation of phosphate ester bond cleavages of glycylphosphoserinyltryptophan radical cations under low-energy collision-induced dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:554-562. [PMID: 23516067 DOI: 10.1007/s13361-013-0597-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 02/18/2013] [Accepted: 02/21/2013] [Indexed: 06/01/2023]
Abstract
Under the conditions of low-energy collision-induced dissociation (CID), the canonical glycylphosphoserinyltryptophan radical cation having its radical located on the side chain of the tryptophan residue ([G(p)SW](•+)) fragments differently from its tautomer with the radical initially generated on the α-carbon atom of the glycine residue ([G(•)(p)SW](+)). The dissociation of [G(•)(p)SW](+) is dominated by the neutral loss of H3PO4 (98 Da), with backbone cleavage forming the [b2 - H](•+)/y1(+) pair as the minor products. In contrast, for [G(p)SW](•+), competitive cleavages along the peptide backbone, such as the formation of [G(p)SW - CO2](•+) and the [c2 + 2H](+)/[z(1) - H](•+) pair, significantly suppress the loss of neutral H3PO4. In this study, we used density functional theory (DFT) to examine the mechanisms for the tautomerizations of [G(•)(p)SW](+) and [G(p)SW](•+) and their dissociation pathways. Our results suggest that the dissociation reactions of these two peptide radical cations are more efficient than their tautomerizations, as supported by Rice-Ramsperger-Kassel-Marcus (RRKM) modeling. We also propose that the loss of H3PO4 from both of these two radical cationic tautomers is preferentially charge-driven, similar to the analogous dissociations of even-electron protonated peptides. The distonic radical cationic character of [G(•)(p)SW](+) results in its charge being more mobile, thereby favoring charge-driven loss of H3PO4; in contrast, radical-driven pathways are more competitive during the CID of [G(p)SW](•+).
Collapse
Affiliation(s)
- Quan Quan
- Department of Chemistry, University of Hong Kong, Hong Kong, China
| | | | | | | | | |
Collapse
|
43
|
Schmidt A, Ammerer G, Mechtler K. Studying the fragmentation behavior of peptides with arginine phosphorylation and its influence on phospho-site localization. Proteomics 2013; 13:945-54. [DOI: 10.1002/pmic.201200240] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Revised: 09/10/2012] [Accepted: 10/01/2012] [Indexed: 12/22/2022]
Affiliation(s)
- Andreas Schmidt
- Christian-Doppler-Laboratory for Proteome Analysis; Department of Biochemistry and Microbiology; Max F. Perutz Laboratories; University of Vienna; Vienna Austria
- Institute for Molecular Pathology (IMP); Vienna Austria
| | - Gustav Ammerer
- Christian-Doppler-Laboratory for Proteome Analysis; Department of Biochemistry and Microbiology; Max F. Perutz Laboratories; University of Vienna; Vienna Austria
| | - Karl Mechtler
- Institute for Molecular Pathology (IMP); Vienna Austria
- Institute for Molecular Biotechnology of the Austrian Academy of Sciences (IMBA); Vienna Austria
| |
Collapse
|
44
|
Kong RPW, Quan Q, Hao Q, Lai CK, Siu CK, Chu IK. Formation and dissociation of phosphorylated peptide radical cations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:2094-2101. [PMID: 22968907 PMCID: PMC3514703 DOI: 10.1007/s13361-012-0479-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 08/14/2012] [Accepted: 08/14/2012] [Indexed: 06/01/2023]
Abstract
In this study, we generated phosphoserine- and phosphothreonine-containing peptide radical cations through low-energy collision-induced dissociation (CID) of the ternary metal-ligand phosphorylated peptide complexes [Cu(II)(terpy)(p)M](·2+) and [Co(III)(salen)(p)M](·+) [(p)M: phosphorylated angiotensin III derivative; terpy: 2,2':6',2''-terpyridine; salen: N,N'-ethylenebis(salicylideneiminato)]. Subsequent CID of the phosphorylated peptide radical cations ((p)M(·+)) revealed fascinating gas-phase radical chemistry, yielding (1) charge-directed b- and y-type product ions, (2) radical-driven product ions through cleavages of peptide backbones and side chains, and (3) different degrees of formation of [M - H(3)PO(4)](·+) species through phosphate ester bond cleavage. The CID spectra of the (p)M(·+) species and their non-phosphorylated analogues featured fragment ions of similar sequence, suggesting that the phosphoryl group did not play a significant role in the fragmentation of the peptide backbone or side chain. The extent of neutral H(3)PO(4) loss was influenced by the peptide sequence and the initial sites of the charge and radical. A preliminary density functional theory study, at the B3LYP 6-311++G(d,p) level of theory, of the neutral loss of H(3)PO(4) from a prototypical model--N-acetylphosphorylserine methylamide--revealed several factors governing the elimination of neutral phosphoryl groups through charge- and radical-induced mechanisms.
Collapse
Affiliation(s)
- Ricky P. W. Kong
- Department of Chemistry, University of Hong Kong, Hong Kong, China
| | - Quan Quan
- Department of Chemistry, University of Hong Kong, Hong Kong, China
| | - Qiang Hao
- Department of Biology and Chemistry, City University of Hong Kong, Hong Kong, China
| | - Cheuk-Kuen Lai
- Department of Chemistry, University of Hong Kong, Hong Kong, China
| | - Chi-Kit Siu
- Department of Biology and Chemistry, City University of Hong Kong, Hong Kong, China
| | - Ivan K. Chu
- Department of Chemistry, University of Hong Kong, Hong Kong, China
| |
Collapse
|
45
|
Matheron L, Clavier S, Diebate O, Karoyan P, Bolbach G, Guianvarc'h D, Sachon E. Improving the selectivity of the phosphoric acid β-elimination on a biotinylated phosphopeptide. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1981-1990. [PMID: 22956181 DOI: 10.1007/s13361-012-0467-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 07/16/2012] [Accepted: 08/01/2012] [Indexed: 06/01/2023]
Abstract
This study aims at improving the MALDI-TOF detection of a phosphorylated peptide containing a cysteine residue by β-elimination of H(3)PO(4) hardly enriched by classical methods. The experimental conditions were optimized on this phosphopeptide (biot-pAdd) and its nonphosphorylated counterpart (biot-Add). The major side-reactions were H(2)S elimination on the cysteine residues and H(2)O elimination on the non phosphorylated serine residue of biot-Add. The former dilutes the MALDI-TOF signal for the desired species. The latter gives a product similar to what is obtained by H(3)PO(4) elimination and should prompt to caution when working with a mixture between phosphorylated and non phosphorylated peptides. Modifications on the solvent, the reaction temperature and time, the nature, and concentration of the base were made. Major improvement of the selectivity of the reaction was observed in 30 % ACN, at room temperature for 4 h. However, these optimizations are specific to these sequences and should be performed anew for different peptides. The selectivity of the reaction towards H(3)PO(4) elimination is improved, but the persistence of side-reactions renders a previous sample fractionation necessary. In these optimized conditions, the ionization enhancement is 3-fold and the detection limits for biot-pAdd are similar to biot-Add (100 fmol).
Collapse
Affiliation(s)
- Lucrèce Matheron
- Laboratoire des Biomolécules, Université P et M Curie, UMR 7203 UPMC-CNRS-ENS, Paris, France
| | | | | | | | | | | | | |
Collapse
|
46
|
Sun Z, Hamilton KL, Reardon KF. Phosphoproteomics and molecular cardiology: Techniques, applications and challenges. J Mol Cell Cardiol 2012; 53:354-68. [DOI: 10.1016/j.yjmcc.2012.06.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 05/26/2012] [Accepted: 06/03/2012] [Indexed: 12/16/2022]
|
47
|
Johnson H, White FM. Toward quantitative phosphotyrosine profiling in vivo. Semin Cell Dev Biol 2012; 23:854-62. [PMID: 22677333 DOI: 10.1016/j.semcdb.2012.05.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 05/29/2012] [Indexed: 11/25/2022]
Abstract
Tyrosine phosphorylation is a dynamic reversible post-translational modification that regulates many aspects of cell biology. To understand how this modification controls biological function, it is necessary to not only identify the specific sites of phosphorylation, but also to quantify how phosphorylation levels on these sites may be altered under specific physiological conditions. Due to its sensitivity and accuracy, mass spectrometry (MS) has widely been applied to the identification and characterization of phosphotyrosine signaling across biological systems. In this review we highlight the advances in both MS and phosphotyrosine enrichment methods that have been developed to enable the identification of low level tyrosine phosphorylation events. Computational and manual approaches to ensure confident identification of phosphopeptide sequence and determination of phosphorylation site localization are discussed along with methods that have been applied to the relative quantification of large numbers of phosphorylation sites. Finally, we provide an overview of the challenges ahead as we extend these technologies to the characterization of tyrosine phosphorylation signaling in vivo. With these latest developments in analytical and computational techniques, it is now possible to derive biological insight from quantitative MS-based analysis of signaling networks in vitro and in vivo. Application of these approaches to a wide variety of biological systems will define how signal transduction regulates cellular physiology in health and disease.
Collapse
Affiliation(s)
- Hannah Johnson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | | |
Collapse
|
48
|
Halgand F, Zabrouskov V, Bassilian S, Souda P, Loo JA, Faull KF, Wong DT, Whitelegge JP. Defining intact protein primary structures from saliva: a step toward the human proteome project. Anal Chem 2012; 84:4383-95. [PMID: 22509742 DOI: 10.1021/ac203337s] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Top-down mass spectrometry has been used to investigate structural diversity within some abundant salivary protein families. In this study, we report the identification of two isoforms of protein II-2 which differed in mass by less than 1 Da, the determination of a sequence for protein IB8a that was best satisfied by including a mutation and a covalent modification in the C-terminal part, and the assignment of a sequence of a previously unreported protein of mass 10433 Da. The final characterization of Peptide P-J was achieved, and the discovery of a truncated form of this peptide was reported. The first sequence assignment was done at low resolution using a hybrid quadrupole time-of-flight instrument to quickly identify and characterize proteins, and data acquisition was switched to Fourier-transform ion cyclotron resonance (FTICR) for proteins that required additional sequence coverage and certainty of assignment. High-resolution and high mass accuracy mass spectrometry on a FTICR-mass spectrometry (MS) instrument combined with electron-capture dissociation (ECD) provided the most informative data sets, with the more frequent presence of "unique" ions that unambiguously define the primary structure. A mixture of predictable and unusual post-translational modifications in the protein sequence precluded the use of shotgun-annotated databases at this stage, requiring manual iterations of sequence refinement in many cases. This led us to propose guidelines for an iterative processing workflow of MS and MSMS data sets that allow researchers to completely assign the identity and the structure of a protein.
Collapse
Affiliation(s)
- F Halgand
- NPI-Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90024, United States.
| | | | | | | | | | | | | | | |
Collapse
|
49
|
Lu Y, Zhou X, Stemmer PM, Reid GE. Sulfonium ion derivatization, isobaric stable isotope labeling and data dependent CID- and ETD-MS/MS for enhanced phosphopeptide quantitation, identification and phosphorylation site characterization. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:577-93. [PMID: 21952753 PMCID: PMC4228788 DOI: 10.1007/s13361-011-0190-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 06/03/2011] [Accepted: 06/03/2011] [Indexed: 05/12/2023]
Abstract
An amine specific peptide derivatization strategy involving the use of novel isobaric stable isotope encoded 'fixed charge' sulfonium ion reagents, coupled with an analysis strategy employing capillary HPLC, ESI-MS, and automated data dependent ion trap CID-MS/MS, -MS(3), and/or ETD-MS/MS, has been developed for the improved quantitative analysis of protein phosphorylation, and for identification and characterization of their site(s) of modification. Derivatization of 50 synthetic phosphopeptides with S,S'-dimethylthiobutanoylhydroxysuccinimide ester iodide (DMBNHS), followed by analysis using capillary HPLC-ESI-MS, yielded an average 2.5-fold increase in ionization efficiencies and a significant increase in the presence and/or abundance of higher charge state precursor ions compared to the non-derivatized phosphopeptides. Notably, 44% of the phosphopeptides (22 of 50) in their underivatized states yielded precursor ions whose maximum charge states corresponded to +2, while only 8% (4 of 50) remained at this maximum charge state following DMBNHS derivatization. Quantitative analysis was achieved by measuring the abundances of the diagnostic product ions corresponding to the neutral losses of 'light' (S(CH(3))(2)) and 'heavy' (S(CD(3))(2)) dimethylsulfide exclusively formed upon CID-MS/MS of isobaric stable isotope labeled forms of the DMBNHS derivatized phosphopeptides. Under these conditions, the phosphate group stayed intact. Access for a greater number of peptides to provide enhanced phosphopeptide sequence identification and phosphorylation site characterization was achieved via automated data-dependent CID-MS(3) or ETD-MS/MS analysis due to the formation of the higher charge state precursor ions. Importantly, improved sequence coverage was observed using ETD-MS/MS following introduction of the sulfonium ion fixed charge, but with no detrimental effects on ETD fragmentation efficiency.
Collapse
Affiliation(s)
- Yali Lu
- Department of Chemistry, Michigan State University, 229 Chemistry Building, Michigan State University, East Lansing, MI, 48824, USA
| | - Xiao Zhou
- Department of Chemistry, Michigan State University, 229 Chemistry Building, Michigan State University, East Lansing, MI, 48824, USA
| | - Paul M. Stemmer
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, USA
| | - Gavin E. Reid
- Department of Chemistry, Michigan State University, 229 Chemistry Building, Michigan State University, East Lansing, MI, 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| |
Collapse
|
50
|
Medzihradszky KF, Trinidad JC. Unusual fragmentation of Pro-Ser/Thr-containing peptides detected in collision-induced dissociation spectra. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:602-7. [PMID: 21952759 PMCID: PMC3384711 DOI: 10.1007/s13361-011-0216-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 07/14/2011] [Accepted: 07/14/2011] [Indexed: 05/12/2023]
Abstract
During collision-induced dissociation (CID)-, phosphoserine- and phosphothreonine-containing peptides frequently undergo neutral loss of phosphoric acid. Subsequent amide bond cleavage N-terminal to the site of phosphorylation results in a y ion with a mass 18 Da lower than the corresponding unmodified y fragment. We report here that when the phosphoserine or phosphothreonine is directly preceded by a proline, an unusual fragment with a mass 10 Da higher than the corresponding unmodified y ion is frequently observed. Accurate mass measurements are consistent with elimination of the phosphoric acid followed by fragmentation between the α carbon and the carbonyl group of the proline residue. We propose a cyclic oxazoline structure for this fragment. Our observation may be explained by the charge-directed S(N)2 neighboring group participation reaction proposed for the phosphoric acid elimination by Palumbo et al. [Palumbo, A. M., Tepe, J. J., Reid, G. E. Mechanistic Insights into the Multistage Gas-Phase Fragmentation Behavior of Phosphoserine- and Phosphothreonine-Containing Peptides. J. Protein Res. 7(2), 771-779 (2008)]. Considering such specific fragment ions for confirmation purposes after regular database searches may boost the confidence of peptide identifications as well as phosphorylation site assignments.
Collapse
Affiliation(s)
- Katalin F Medzihradszky
- Mass Spectrometry Facility, School of Pharmacy, University of California San Francisco, 600 16th Street Genentech Hall, Suite N472A, Box 2240, San Francisco, CA 94158-2517, USA.
| | | |
Collapse
|