PepC: Proteomics software for identifying differentially expressed proteins based on spectral counting

Bioinformatics

Volumn 26, Issue 12, 2010, Pages 1574-1575

  Heinecke, N L ^a   Pratt, B S ^a   Vaisar, T ^a   Becker, L ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PETUNIA;

PROTEIN; PROTEOME;

ARTICLE; CHEMISTRY; COMPUTER INTERFACE; COMPUTER PROGRAM; MASS SPECTROMETRY; METHODOLOGY; PROTEIN DATABASE; PROTEOMICS;

DATABASES, PROTEIN; MASS SPECTROMETRY; PROTEINS; PROTEOME; PROTEOMICS; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 77954205753     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq171     Document Type: Article

References (16)

1. Aebersold, R. and Mann, M. (2003) Mass spectrometry-based proteomics. Nature, 422, 198-207.
2. Becker, L. et al. (2010)Amacrophage sterol-responsive network linked to atherogenesis. Cell Metab., 11, 125-135.
3. Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate-a practical and powerful approach to multiple testing. J.R. Stat. Soc. B., 57, 289-300.
4. Bondarenko, P.V. et al. (2002) Identification and relative quantitation of protein mixtures by enzymatic digestion followed by capillary reversed-phase liquid chromatography-tandem mass spectrometry. Anal. Chem., 74, 4741-4749.
5. Choi, H. et al. (2008) Significance analysis of spectral count data in label-free shotgun proteomics. Mol. Cell. Proteomics, 7, 2373-2385.
6. Cui, X. and Churchill, G.A. (2003) Statistical tests for differential expression in cDNA microarray experiments. Genome Biol., 4, 210.
7. Fu, X. et al. (2008) Spectral index for assessment of differential protein expression in shotgun proteomics. J. Proteome Res., 7, 845-854.
8. Liu, H. et al. (2004) A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem., 76, 4193-4201.
9. Mason, D.E. and Liebler, D.C. (2003) Quantitative analysis of modified proteins by LC-MS/MS of peptides labeled with phenyl isocyanate. J. Proteome Res., 2, 265-272.
10. Old, W.M. et al. (2005) Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol. Cell. Proteomics, 4, 1487-1502.
11. Pavelka, N. et al. (2008) Statistical similarities between transcriptomics and quantitative shotgun proteomics data. Mol. Cell. Proteomics, 7, 631-644.
12. Sadygov, R.G. et al. (2004) Large-scale database searching using tandem mass spectra: looking up the answer in the back of the book. Nat. Methods, 1, 195-202.
13. Sokal, R.R. and Rohlf, F.J. (1994). Biometry: the Principles and Practice of Statistics in Biological Research, 3rd edn. Freeman, New York.
14. Wiener, M.C. et al. (2004) Differential mass spectrometry: a label-free LC-MS method for finding significant differences in complex peptide and protein mixtures. Anal. Chem., 76, 6085-6096.
15. Zhang, B. et al. (2006) Detecting differential and correlated protein expression in label-free shotgun proteomics. J. Proteome Res., 5, 2909-2918.
16. Zhu, W. et al. (2010) Mass spectrometry-based label-free quantitative proteomics. J. Biomed. Biotechnol., 2010, 840518.