Determination of monoisotopic masses of chimera spectra from high-resolution mass spectrometric data by use of isotopic peak intensity ratio modeling

Rapid Communications in Mass Spectrometry

Volumn 26, Issue 16, 2012, Pages 1875-1886

  Niu, Ming ^a   Mao, Xinli ^a   Ying, Wantao ^a   Qin, Weijie ^a   Zhang, Yangjun ^a   Qian, Xiaohong ^a  

^a BEIJING INSTITUTE OF RADIATION MEDICINE   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ISOTOPES; MASS SPECTROMETERS; MASS SPECTROMETRY; MOLECULAR BIOLOGY;

COMPLEX MIXTURE; DETERMINATION ALGORITHM; HIGH RESOLUTION; LC-MS-MS; MASS SPECTROMETRIC DATA; MONOISOTOPIC MASS; OVERLAPPING CLUSTERS; PEAK INTENSITY RATIO; RATIO MODELS; SPECTRA'S;

PEPTIDES;

EID: 84863649683     PISSN: 09514198     EISSN: 10970231     Source Type: Journal    
DOI: 10.1002/rcm.6293     Document Type: Article

References (32)

1. A. J. Link, J Eng, D. M. Schieltz, E. Carmack, G. J. Mize, D. R. Morris, B. M. Garvik, J. R. Yates III,. Direct analysis of protein complexes using mass spectrometry. Nat. Biotechnol. 1999, 17, 676.
2. M. P. Washburn, D. Wolters, J. R. Yates III,. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 2001, 19, 242.
3. P. Roepstorff, J. Fohlman,. Proposal for a common nomenclature for sequence ions in mass spectra of peptides. Biomed. Mass Spectrom. 1984, 11, 601.
4. R. S. Johnson, S. A. Martin, K. Biemann, J. T. Stults, J. T. Watson,. Novel fragmentation process of peptides by collision-induced decomposition in a tandem mass spectrometer: differentiation of leucine and isoleucine. Anal. Chem. 1987, 59, 2621.
5. D. C. Stahl, K. M. Swiderek, M. T. Davis, T. D. Lee,. Data-controlled automation of liquid chromatography/tandem mass spectrometry analysis of peptide mixtures. J Am. Soc. Mass Spectrom. 1996, 7, 523.
6. W. Haas, B. K. Faherty, S. A. Gerber, J. E. Elias, S. A. Beausoleil, C. E. Bakalarski, X. Li, J. Villen, S. P. Gygi,. Optimization and use of peptide mass measurement accuracy in shotgun proteomics. Mol. Cell. Proteomics 2006, 5, 1326.
7. A. G. Marshall, C. L. Hendrickson, G. S. Jackson,. Fourier transform ion cyclotron resonance mass spectrometry: a primer. Mass Spectrom. Rev. 1998, 17, 1.
8. Q. Hu, R. J. Noll, H. Li, A. Makarov, M. Hardman, R. C. Graham,. The Orbitrap: a new mass spectrometer. J. Mass Spectrom. 2005, 40, 430.
9. S. Purvine, J.-T. Eppel, E. C. Yi, D. R. Goodlett,. Shotgun collision-induced dissociation of peptides using a time of flight mass analyzer. Proteomics 2002, 3, 847.
10. M. R. Hoopmann, G. L. Finney, M. J. MacCoss,. High-speed data reduction, feature detection, and MS/MS spectrum quality assessment of shotgun proteomics data sets using high-resolution mass spectrometry. Anal. Chem. 2007, 79, 5620.
11. B. E. Frewen, G. E. Merrihew, C. C. Wu, W. S. Noble, M. J. MacCoss,. Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries. Anal. Chem. 2006, 78, 5678.
12. N. Zhang, X. Li, M. Ye, S. Pan, B. Schwikowski, R. Aebersold,. ProbIDtree: an automated software program capable of identifying multiple peptides from a single collision-induced dissociation spectrum collected by a tandem mass spectrometer. Proteomics 2005, 5, 4096.
13. S. Houel, R. Abernathy, K. Renganathan, K. Meyer-Arendt, N. G. Ahn, W. M. Old,. Quantifying the impact of chimera MS/MS spectra on peptide identification in large-scale proteomics studies. J Proteome Res. 2010, 9, 4152.
14. A. Michalski, J. Cox, M. Mann,. More than 100 000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS. J. Proteome Res. 2011, 10, 1785.
15. D. M. Horn, R. A. Zubarev, F. W. McLafferty,. Automated reduction and interpretation of high resolution electrospray mass spectra of large molecules. J. Am. Soc. Mass Spectrom. 2000, 11, 320.
16. N. Jaitly, A. Mayampurath, K. Littlefield, J. N. Adkins, G. N. Anderson, R. D. Smith,. Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data. BMC Bioinformatics 2009, 10, 87.
17. A. M. Mayampurath, N. Jaitly, S. O. Purvine, M. E. Monroe, K. J. Auberry, J. N. Adkins, R. D. Smith,. DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra. Bioinformatics 2008, 24, 1021.
18. E. J. Hsieh, M. R. Hoopmann, B. MacLean, M. J. MacCoss,. Comparison of database search strategies for high precursor mass accuracy MS/MS data. J. Proteome Res. 2010, 9, 1138.
19. R. Luethy, D. E. Kessner, J. E. Katz, B. MacLean, R. Grothe, K. Kani, V. Faca, S. Pitteri, S. Hanash, D. B. Agus, P. Mallick,. Precursor-ion mass re-estimation improves peptide identification on hybrid instruments. J. Proteome Res. 2006, 7, 4031.
20. P. Mortensen, J. W. Gouw, J. V. Olsen, S. E. Ong, K. T. G. Rigbolt, J. Bunkenborg, J. Cox, L. J. Foster, A. J. R. Heck, B. Blagoev, J. S. Andersen, M. Mann,. MSQuant, an open source platform for mass spectrometry-based quantitative proteomics. J. Proteome Res. 2010, 9, 393.
21. M. W. Senko, S. C. Beu, F. W. Mclafferty,. Determination of monoisotopic masses and ion populations for large biomolecules from resolved isotopic distributions. J. Am. Soc. Mass Spectrom. 1995, 6, 229.
22. K. Park, J. Y. Yoon, S. Lee, E. Paek, H. Park, H. J. Jung, S. W. Lee,. Isotopic peak intensity ratio based algorithm for determination of isotopic clusters and monoisotopic masses of polypeptides from high-resolution mass spectrometric data. Anal. Chem. 2008, 80, 7294.
23. J. Zhang, E. Gonzalez, T. Hestilow, W. Haskins, Y. Huang,. Review of peak detection algorithms in liquid-chromatography-mass spectrometry. Curr. Genomics 2009, 10, 388.
24. J. Cox, N. Neuhauser, A. Michalski, R. A. Scheltema, J. V. Olsen, M. Mann,. Andromeda: a peptide search engine integrated into the MaxQuant environment. J Proteome Res. 2011, 10, 1794.
25. S. Cappadona, J. Muñoz, W. P. E. Spee, T. Y. Low, S. Mohammed, B. van Breukelen, A. J. Heck,. Deconvolution of overlapping isotopic clusters improves quantification of stable isotope-labeled peptides. J Proteomics 2011, 74, 2204.
26. J. Y. Yoon, K. Y. Lim, S. Lee, K. Park, E. Paek, U. B. Kang, J. Yeom, C. Lee,. Improved quantitative analysis of mass spectrometry using quadratic equations. J Proteome Res. 2010, 9, 2775.
27. J. Y. Yoon, J. Yeom, H. Lee, K. Kim, S. Na, K. Park, E. Paek, C. Lee,. High-throughput peptide quantification using mTRAQ reagent triplex. BMC Bioinformatics 2011, 12, S46.
28. Z. F. Yuan, C. Liu, H. P. Wang, R. X. Sun, Y. Fu, J. F. Zhang, L. H. Wang, H. Chi, Y. Li, L. Y. Xiu, W. P. Wang, S. M. He,. pParse: A method for accurate determination of monoisotopic peaks in high-resolution mass spectra. Proteomics 2012, 12, 226.
29. Q. Bao, Y. Tian, W. Li, Z. Xu, Z. Xuan, S. Hu, W. Dong, J. Yang, Y. Chen, Y. Xue, Y. Xu, X. Lai, L. Huang, X. Dong, Y. Ma, L. Ling, H. Tan, R. Chen, J. Wang, J. Yu, H. Yang,. A complete sequence of the T. tengcongensis genome. Genome Res. 2002, 12, 689.
30. J. Klimek, J. S. Eddes, L. Hohmann, J. Jackson, A. Peterson, S. Letarte, P. R. Gafken, J. E. Katz, P. Mallick, H. Lee, A. Schmidt, R. Ossola, J. K. Eng, R. Aebersold, D. B. Martin,. The standard protein mix database: a diverse data set to assist in the production of improved Peptide and protein identification software tools. J. Proteome Res. 2008, 7, 96.
31. L. H. Wang, D. Q. Li, Y. Fu, H. P. Wang, J. F. Zhang, Z. F. Yuan, R. X. Sun, R. Zeng, S. M. He, W. Gao,. pFind 2.0: a software package for peptide and protein identification via tandem mass spectrometry. Rapid Commun. Mass Spectrom. 2007, 21, 2985.
32. E. J. Hsieh, M. R. Hoopmann, B. MacLean, M. J. MacCoss,. Comparison of database search strategies for high precursor mass accuracy MS/MS data. J. Proteome Res. 2010, 9, 1138.