Simplified validation of borderline hits of database searches

Proteomics

Volumn 8, Issue 20, 2008, Pages 4173-4177

  Thomas, Henrik ^a   Shevchenko, Andrej ^a  

^a MAX PLANCK INSTITUTE OF MOLECULAR CELL BIOLOGY AND GENETICS   (Germany)

Author keywords

De novo sequencing; Hit validation; MASCOT; MS BLAST; MS MS

Indexed keywords

ARTICLE; BIOINFORMATICS; DATA ANALYSIS SOFTWARE; DATA BASE; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SEQUENCE DATABASE; STATISTICAL ANALYSIS; VALIDATION PROCESS;

DATABASES, GENETIC; DATABASES, PROTEIN; MOLECULAR SEQUENCE DATA; PROTEOMICS; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE; TANDEM MASS SPECTROMETRY; VALIDATION STUDIES AS TOPIC;

EID: 55749111513     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.200800250     Document Type: Article

References (20)

1. Forner, F., Foster, L. J., Toppo, S., Mass spectrometry data analysis in the proteomics era. Curr. Bioinformatics 2007, 2, 63-93.
2. Choi, H., Ghosh, D., Nesvizhskii, A. I., Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling. J. Proteome Res. 2008, 7, 286-292.
3. Sadygov, R. G., Liu, H., Yates, J. R., Statistical models for protein validation using tandem mass spectral data and protein amino acid sequence databases. Anal. Chem. 2004, 76, 1664-1671.
4. Kall, L., Storey, J. D., MacCoss, M. J., Noble, W. S., Assigning significance to peptides identified by tandem mass spectrometry using decoy databases. J. Proteome Res. 2008, 7, 29-34.
5. Elias, J. E., Gygi, S. P., Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat. Methods 2007, 4, 207-214.
6. Taylor, J. A., Johnson, R. S., Implementation and uses of automated de novo peptide sequencing by tandem mass spectrometry. Anal. Chem. 2001, 73, 2594-2604.
7. An Thieu, V., Kirsch, D., Flad, T., Muller, C. et al., Direct protein identification from nonspecific peptide pools by high-accuracy MS data filtering. Angew. Chem. Int. Ed. Engl. 2006, 45, 3317-3319.
8. Savitski, M. M., Nielsen, M. L., Kjeldsen, F., Zubarev, R. A., Proteomics-grade de novo sequencing approach. J. Proteome Res. 2005, 4, 2348-2354.
9. Wielsch, N., Thomas, H., Surendranath, V., Waridel, P. et al., Rapid validation of protein identifications with the borderline statistical confidence via de novo sequencing and MS BLAST searches. J. Proteome Res. 2006, 5, 2448-2456.
10. Shevchenko, A., Sunyaev, S., Loboda, A., Shevchenko, A. et al., Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching. Anal. Chem. 2001, 73, 1917-1926.
11. Habermann, B., Oegema, J., Sunyaev, S., Shevchenko, A., The power and the limitations of cross-species protein identification by mass spectrometry-driven sequence similarity searches. Mol. Cell. Proteomics 2004, 3, 238-249.
12. Waridel, P., Frank, A., Thomas, H., Surendranath, V. et al., Sequence similarity-driven proteomics in organisms with unknown genomes by LC-MS/MS and automated de novo sequencing. Proteomics 2007, 7, 2318-2329.
13. Katz, A., Waridel, P., Shevchenko, A., Pick, U., Salt-induced changes in the plasma membrane proteome of the halotolerant alga Dunaliella salina as revealed by Blue-Native gel electrophoresis and nanoLC-MS/MS analysis. Mol. Cell. Proteomics 2007, 6, 1459-1472.
14. Gache, V., Waridel, P., Luche, S., Shevchenko, A. et al., Purification and mass spectrometry identification of microtubule-binding proteins from Xenopus egg extracts. Methods Mol. Med. 2007, 137, 29-43.
15. Yoo, H. Y., Kumagai, A., Shevchenko, A., Dunphy, W. G., Ataxia-telangiectasia mutated (ATM)-dependent activation of ATR occurs through phosphorylation of TopBP1 by ATM. J. Biol. Chem. 2007, 282, 17501-17506.
16. Charneau, S., Junqueira, M., Costa, C. M., Pires, D. L. et al., The saliva proteome of the blood-feeding insect Triatoma infestans is rich in platelet-aggregation inhibitors. Intl. J. Mass Spectrom. 2007, 268, 265-276.
17. Frank, A., Pevzner, P., PepNovo: de novo peptide sequencing via probabilistic network modeling. Anal. Chem. 2005, 77, 964-973.
18. Junqueira, M., Spirin, V., Balbuena, T. S., Waridel, P. et al., Separating the wheat from the chaff: unbiased filtering of background tandem mass spectra improves protein identification. J. Proteome Res. 2008, 7, 3382-3395.
19. Horn, D. M., Zubarev, R. A., McLafferty, F. W., Automated de novo sequencing of proteins by tandem high-resolution mass spectrometry. Proc. Natl. Acad. Sci. USA 2000, 97, 10313-10317.
20. Frank, A. M., Savitski, M. M., Nielsen, M. L., Zubarev, R. A. et al., De novo peptide sequencing and identification with precision mass spectrometry. J. Proteome Res. 2007, 6, 114-123.