Postexperiment monoisotopic mass filtering and refinement (PE-MMR) of tandem mass spectrometric data increases accuracy of peptide identification in LC/MS/MS

Molecular and Cellular Proteomics

Volumn 7, Issue 6, 2008, Pages 1124-1134

  Shin, Byunghee ^a   Jung, Hee Jung ^b   Hyung, Seok Won ^b   Kim, Hokeun ^a   Lee, Dongkyu ^a   Lee, Cheolju ^a   Yu, Myeong Hee ^a   Lee, Sang Won ^b  

^a Korea Institute of Science and Technology   (South Korea)

^b Korea University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

GLYCOPEPTIDE; PEPTIDE; PEPTIDE DERIVATIVE; PROTEOME;

ACCURACY; ANALYTIC METHOD; ANALYTICAL ERROR; ARTICLE; CLUSTER ANALYSIS; CONTROLLED STUDY; CORRELATION ANALYSIS; DATA ANALYSIS; ELUTION; FEMALE; FILTRATION; HUMAN; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; NONHUMAN; POSTEXPERIMENT MONOISOTOPIC MASS FILTERING AND REFINEMENT; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN DETERMINATION; PROTEOMICS; TANDEM MASS SPECTROMETRY; YEAST;

AUTOMATION; BLOOD PROTEINS; CHROMATOGRAPHY, LIQUID; FEMALE; GLYCOPEPTIDES; GLYCOSYLATION; HUMANS; MODELS, STATISTICAL; PEPTIDE MAPPING; PEPTIDES; PROTEOMICS; REPRODUCIBILITY OF RESULTS; SACCHAROMYCES CEREVISIAE; SOFTWARE; TANDEM MASS SPECTROMETRY;

EID: 46749089668     PISSN: 15359476     EISSN: None     Source Type: Journal    
DOI: 10.1074/mcp.M700419-MCP200     Document Type: Article

References (17)

1. Elias, J. E., and Gygi, S. P. (2007) Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat. Methods 4, 207-214
2. Keller, A., Nesvizhskii, A. I., Kolker, E., and Aebersold, R. (2002) Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 74, 5383-5392
3. Venable, J. D., and Yates, J. R., III (2004) Impact of ion trap tandem mass spectra variability on the identification of peptides. Anal. Chem. 76, 2928-2937
4. Elias, J. E., Haas, W., Faherty, B. K., and Gygi, S. P. (2005) Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations. Nat Methods 2, 667-675
5. Wong, J. W. H., Sullivan, M. J., Cartwright, H. M., and Cagney, G. (2007) msmsEval: tandem mass spectral quality assignment for high-throughput proteomics. BMC Bioinformatics 8, 51
6. Sadygov, R. G., Eng, J., Durr, E., Saraf, A., McDonald, H., MacCoss, M. J., and Yates, J. R., III (2002) Code developments to improve the efficiency of automated MS/MS spectra interpretation. J. Proteome Res. 1, 211-215
7. Nesvizhskii, A. I., Roos, F. F., Grossmann, J., Vogelzang, M., Eddes, J. S., Gruissem, W., Baginsky, S., and Aebersold, R. (2006) Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides. Mol. Cell. Proteomics 5, 652-670
8. Olsen, J. V., Ong, S.-E., and Mann, M. (2004) Trypsin cleaves exclusively C-terminal to arginine and lysine residues. Mol. Cell. Proteomics 3, 608-614
9. Beausoleil, S. A., Villen, J., Gerber, S. A., Rush, J., and Gygi, S. P. (2006) A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nat. Biotechnol. 24, 1285-1299
10. Venable, J. D., Xu, T., Cociorva, D., and Yates, J. R., III (2006) Cross-correlation algorithm for calculation of peptide molecular weight from tandem mass spectra. Anal. Chem. 78, 1921-1929
11. Kim, M.-S., Choie, W.-S., Shin, Y. S., Yu, M.-H., and Lee, S.-W. (2004) Development of ultra-high pressure capillary reverse-phase liquid chromatography/tandem mass spectrometry for high-sensitive and high-throughput proteomics. Bull. Korean Chem. Soc. 25, 1833-1839
12. Zhang, H., Li, X., Martin, D. B., and Aebersold, R. (2003) Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry. Nat. Biotechnol. 21, 660-666
13. Min, H.-K., Hyung, S.-W., Shin, J.-W., Nam, H. S., Ahn, S. H., Jung, H. J., and Lee, S.-W. (2007) Ultrahigh-pressure dual on-line solid phase extraction/capillary reverse-phase liquid chromatography/tandem mass spectrometry (DO-SPE/cRPLC/MS/MS): A versatile separation platform for high-throughput and highly sensitive proteomic analyses. Electrophoresis 28, 1012-1021
14. Horn, D. M., Zubarev, R. A., and McLafferty, F. W. (2000) Automated reduction and interpretation of high resolution electrospray mass spectra of large molecules. J. Am. Soc. Mass Spectrom. 11, 320-332
15. Zimmer, J. S. D., Monroe, M. E., Qian, W.-J., and Smith, R. D. (2006) Advances in proteomics data analysis and display using an accurate mass and time tag approach. Mass Spectrom. Rev. 25, 450-482
16. Olsen, J. V., de Godoy, L. M. F., Li, G., Macek, B., Mortensen, P., Pesch, R., Makarov, A., Lange, O., Horning, S., and Mann, M. (2005) Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trap. Mol. Cell. Proteomics 4, 2010-2021
17. Na, S. J., and Paek, E. (2006) Quality assessment of tandem mass spectra based on cumulative intensity normalization. J. Proteome Res. 5, 3241-3248