False discovery rate estimation for cross-linked peptides identified by mass spectrometry

Nature Methods

Volumn 9, Issue 9, 2012, Pages 901-903

  Walzthoeni, Thomas ^a,b   Claassen, Manfred ^c   Leitner, Alexander ^a   Herzog, Franz ^a   Bohn, Stefan ^d   Förster, Friedrich ^d   Beck, Martin ^e   Aebersold, Ruedi ^a,b  

^a ETH ZURICH   (Switzerland)

^b UNIVERSITY OF ZURICH   (Switzerland)

^c Stanford University   (United States)

^d MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

^e EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN;

ARTICLE; COMPLEX FORMATION; COMPUTER ANALYSIS; COMPUTER PROGRAM; ESCHERICHIA COLI; FALSE POSITIVE RESULT; MASS SPECTROMETRY; MATHEMATICAL MODEL; NONHUMAN; PRIORITY JOURNAL; PROTEIN CROSS LINKING;

ALGORITHMS; AUTOMATION; CROSS-LINKING REAGENTS; DATA INTERPRETATION, STATISTICAL; DATABASES, PROTEIN; FALSE POSITIVE REACTIONS; MASS SPECTROMETRY; MODELS, MOLECULAR; PEPTIDES; PROTEIN CONFORMATION; PROTEOMICS; SOFTWARE;

EID: 84866118432     PISSN: 15487091     EISSN: 15487105     Source Type: Journal    
DOI: 10.1038/nmeth.2103     Document Type: Article

References (18)

1. Young, M.M. et al. Proc. Natl. Acad. Sci. USA 97, 5802-5806 (2000).
2. Rappsilber, J. et al. Anal. Chem. 72, 267-275 (2000).
3. Leitner, A. et al. Mol. Cell. Proteomics 9, 1634-1649 (2010).
4. Rappsilber, J. J. Struct. Biol. 173, 530-540 (2011).
5. Sinz, A. Mass Spectrom. Rev. 25, 663-682 (2006).
6. Back, J.W. et al. J. Mol. Biol. 331, 303-313 (2003).
7. Mayne, S.L. & Patterton, H.G. Brief. Bioinform. 12, 660-671 (2011).
8. Lasker, K. et al. Proc. Natl. Acad. Sci. USA 109, 1380-1387 (2012).
9. Chen, Z.A. et al. EMBO J. 29, 717-726 (2010).
10. Bohn, S. et al. Proc. Natl. Acad. Sci. USA 107, 20992-20997 (2010).
11. Jennebach, S. et al. Nucleic Acids Res. doi:10.1093/nar/gks220 (6 March 2012).
12. Rinner, O. et al. Nat. Methods 5, 315-318 (2008).
13. Elias, J.E. & Gygi, S.P. Nat. Methods 4, 207-214 (2007).
14. Leitner, A. et al. Mol. Cell Proteomics 11, M111.014126 (2012).
15. Petrotchenko, E.V. & Borchers, C.H. Mass Spectrom. Rev. 29, 862-876 (2010).
16. Pettersen, E.F. et al. J. Comput. Chem. 25, 1605-1612 (2004).
17. Pieper, U. et al. Nucleic Acids Res. 30, 255-259 (2002).
18. Efron, B. & Tibshirani, R. Genet. Epidemiol. 23, 70-86 (2002).