proteomic data improves peptide and protein
identification rates and error estimates. Mol
Cell Proteomics 10:M111.007690
12. Keller A, Nesvizhskii AI, Kolker E, 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
13. MacLean B, Tomazela DM, Shulman N,
Chambers M, Finney GL, Frewen B, Kern R,
Tabb DL, Liebler DC, MacCoss MJ (2010)
Skyline: an open source document editor for
creating and analyzing targeted proteomics
experiments. Bioinformatics 26:966–968
14. R Development Core Team. (2008) R: a language and environment for statistical computing. R Foundation for Statistical Computing
15. Shannon P, Markiel A, Ozier O, Baliga NS,
Wang
JT,
Ramage
D,
Amin
N,
Schwikowski B, Ideker T (2003) Cytoscape: a
software environment for integrated models of
biomolecular interaction networks. Genome
Res 13:2498–2504
16. Bindea
G,
Mlecnik
B,
Hackl
H,
Charoentong P, Tosolini M, Kirilovsky A, Fridman WH, Page `s F, Trajanoski Z, Galon J
(2009) ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and
pathway annotation networks. Bioinformatics
25:1091–1093
308
Jesse G. Meyer