Statistical characterization of HCD fragmentation patterns of tryptic peptides on an LTQ Orbitrap Velos mass spectrometer

Journal of Proteomics

Volumn 109, Issue , 2014, Pages 26-37

  Shao, Chen ^a   Zhang, Yang ^b   Sun, Wei ^a  

^a INSTITUTE OF BASIC MEDICAL SCIENCES   (China)

^b CAPITAL MEDICAL UNIVERSITY   (China)

Author keywords

CID; Fragmentation pattern; HCD; Proteomics

Indexed keywords

PEPTIDE; ION; PROTEOME; TRYPSIN;

AMINO ACID SEQUENCE; ANALYTIC METHOD; ARTICLE; CELL LYSATE; CONTROLLED STUDY; HIGH ENERGY COLLISIONAL DISSOCIATION; HUMAN; MALE; MASS SPECTROMETER; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CLEAVAGE; PROTEOMICS; SEARCH ENGINE; TANDEM MASS SPECTROMETRY; ALGORITHM; CHEMICAL BOND; DATA BASE; MASS; MASS SPECTROMETRY; CHEMISTRY; DEVICES; INFORMATION PROCESSING; PROCEDURES;

ALGORITHMS; AUTOMATIC DATA PROCESSING; MASS SPECTROMETRY; PEPTIDES; PROTEOMICS; TRYPSIN;

EID: 84904096104     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2014.06.012     Document Type: Article

References (27)

1. Xia Y., Liang X, McLuckey S.A. Ion trap versus low-energy beam-type collision-induced dissociation of protonated ubiquitin ions. Anal Chem 2006, 78(4):1218-1227.
2. Olsen J.V., Macek B., Lange O., Makarov A., Horning S., Mann M. Higher-energy C-trap dissociation for peptide modification analysis. Nat Methods 2007, 4(9):709-712.
3. Bantscheff M., Boesche M., Eberhard D., Matthieson T., Sweetman G., Kuster B. Robust and sensitive iTRAQ quantification on an LTQ Orbitrap mass spectrometer. Mol Cell Proteomics 2008, 7(9):1702-1713.
4. Pichler P., Kocher T., Holzmann J., Mohring T., Ammerer G., Mechtler K. Improved precision of iTRAQ and TMT quantification by an axial extraction field in an Orbitrap HCD cell. Anal Chem 2011, 83(4):1469-1474.
5. Nagaraj N., D'Souza R.C., Cox J., Olsen J.V., Mann M. Feasibility of large-scale phosphoproteomics with higher energy collisional dissociation fragmentation. J Proteome Res 2010, 9(12):6786-6794.
6. Nagaraj N., D'Souza R.C., Cox J., Olsen J.V., Mann M. Correction to Feasibility of Large-Scale Phosphoproteomics with Higher Energy Collisional Dissociation Fragmentation. J Proteome Res 2012, 11(6):3506-3508.
7. Jedrychowski M.P., Huttlin E.L., Haas W., Sowa M.E., Rad R., Gygi S.P. Evaluation of HCD- and CID-type fragmentation within their respective detection platforms for murine phosphoproteomics. Mol Cell Proteomics 2011, 10(12). M111 009910.
8. Frese C.K., Altelaar A.F., Hennrich M.L., Nolting D., Zeller M., Griep-Raming J., et al. Improved peptide identification by targeted fragmentation using CID. HCD and ETD on an LTQ-Orbitrap Velos. J Proteome Res 2011, 10(5):2377-2388.
9. Chi H., Sun R.X., Yang B., Song C.Q., Wang L.H., Liu C., et al. pNovo: de novo peptide sequencing and identification using HCD spectra. J Proteome Res 2010, 9(5):2713-2724.
10. Wysocki V.H., Tsaprailis G., Smith L.L., Breci L.A. Mobile and localized protons: a framework for understanding peptide dissociation. J Mass Spectrom 2000, 35(12):1399-1406.
11. Boyd R., Somogyi A. The mobile proton hypothesis in fragmentation of protonated peptides: a perspective. J Am Soc Mass Spectrom 2010, 21(8):1275-1278.
12. Kapp E.A., Schutz F., Reid G.E., Eddes J.S., Moritz R.L., O'Hair R.A., et al. Mining a tandem mass spectrometry database to determine the trends and global factors influencing peptide fragmentation. Anal Chem 2003, 75(22):6251-6264.
13. de Graaf E.L., Altelaar A.F., van Breukelen B., Mohammed S., Heck A.J. Improving SRM assay development: a global comparison between triple quadrupole, ion trap, and higher energy CID peptide fragmentation spectra. J Proteome Res 2011, 10(9):4334-4341.
14. Tabb D.L., Smith L.L., Breci L.A., Wysocki V.H., Lin D., Yates J.R. 3rd.Statistical characterization of ion trap tandem mass spectra from doubly charged tryptic peptides. Anal Chem 2003, 75(5):1155-1163.
15. Huang Y., Triscari J.M., Tseng G.C., Pasa-Tolic L., Lipton M.S., Smith R.D., et al. Statistical characterization of the charge state and residue dependence of low-energy CID peptide dissociation patterns. Anal Chem 2005, 77(18):5800-5813.
16. Zubarev R.A., Zubarev A.R., Savitski M.M. Electron capture/transfer versus collisionally activated/induced dissociations: solo or duet?. J Am Soc Mass Spectrom 2008, 19(6):753-761.
17. Savitski M.M., Kjeldsen F., Nielsen M.L., Zubarev R.A. Complementary sequence preferences of electron-capture dissociation and vibrational excitation in fragmentation of polypeptide polycations. Angew Chem Int Ed Engl 2006, 45(32):5301-5303.
18. Barton S.J., Richardson S., Perkins D.N., Bellahn I., Bryant T.N., Whittaker J.C. Using statistical models to identify factors that have a role in defining the abundance of ions produced by tandem MS. Anal Chem 2007, 79(15):5601-5607.
19. Michalski A., Neuhauser N., Cox J., Mann M. A systematic investigation into the nature of tryptic HCD spectra. J Proteome Res 2012, 11(11):5479-5491.
20. Wisniewski J.R., Zougman A., Nagaraj N., Mann M. Universal sample preparation method for proteome analysis. Nat Methods 2009, 6(5):359-362.
21. Kall L., Canterbury J.D., Weston J., Noble W.S. MacCoss MJ Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat Methods 2007, 41(1):923-925.
22. Schwartz J.C., Senko M.W., Syka J.E. A two-dimensional quadrupole ion trap mass spectrometer. J Am Soc Mass Spectrom 2002, 13(6):659-669.
23. Paizs B., Suhai S. Fragmentation pathways of protonated peptides. Mass Spectrom Rev 2005, 24(4):508-548.
24. Breci L.A., Tabb D.L., Yates J.R., Wysocki V.H. Cleavage N-terminal to proline: analysis of a database of peptide tandem mass spectra. Anal Chem 2003, 75(9):1963-1971.
25. Khatun J., Ramkissoon K., Giddings M.C. Fragmentation characteristics of collision-induced dissociation in MALDI TOF/TOF mass spectrometry. Anal Chem 2007, 79(8):3032-3040.
26. Farrugia J.M., Taverner T., O'Hair R.A.J. Side-chain involvement in the fragmentation reactions of the protonated methyl esters of histidine and its peptides. Int J Mass Spectrom 2001, 209(2-3):99-112.
27. Huang Y., Triscari J.M., Pasa-Tolic L., Anderson G.A., Lipton M.S., Smith R.D., et al. Dissociation behavior of doubly-charged tryptic peptides: correlation of gas-phase cleavage abundance with Ramachandran plots. J Am Chem Soc 2004, 126(10):3034-3035.