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What's driving false discovery rates?

Tabb DL. Tabb DL. J Proteome Res. 2008 Jan;7(1):45-6. doi: 10.1021/pr700728t. Epub 2007 Dec 15. J Proteome Res. 2008. PMID: 18081243 Free PMC article. Review.

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Integrating genomic, transcriptomic, and interactome data to improve Peptide and protein identification in shotgun proteomics.

Wang X, Zhang B. Wang X, et al. J Proteome Res. 2014 Jun 6;13(6):2715-23. doi: 10.1021/pr500194t. Epub 2014 May 12. J Proteome Res. 2014. PMID: 24792918 Free PMC article. Review.

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A cross-platform toolkit for mass spectrometry and proteomics.

Chambers MC, Maclean B, Burke R, Amodei D, Ruderman DL, Neumann S, Gatto L, Fischer B, Pratt B, Egertson J, Hoff K, Kessner D, Tasman N, Shulman N, Frewen B, Baker TA, Brusniak MY, Paulse C, Creasy D, Flashner L, Kani K, Moulding C, Seymour SL, Nuwaysir LM, Lefebvre B, Kuhlmann F, Roark J, Rainer P, Detlev S, Hemenway T, Huhmer A, Langridge J, Connolly B, Chadick T, Holly K, Eckels J, Deutsch EW, Moritz RL, Katz JE, Agus DB, MacCoss M, Tabb DL, Mallick P. Chambers MC, et al. Nat Biotechnol. 2012 Oct;30(10):918-20. doi: 10.1038/nbt.2377. Nat Biotechnol. 2012. PMID: 23051804 Free PMC article.

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Evaluating protein interactions through cross-linking mass spectrometry.

Tabb DL. Tabb DL. Nat Methods. 2012 Sep;9(9):879-81. doi: 10.1038/nmeth.2139. Nat Methods. 2012. PMID: 22936167 Free PMC article. No abstract available.

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QuaMeter: multivendor performance metrics for LC-MS/MS proteomics instrumentation.

Ma ZQ, Polzin KO, Dasari S, Chambers MC, Schilling B, Gibson BW, Tran BQ, Vega-Montoto L, Liebler DC, Tabb DL. Ma ZQ, et al. Anal Chem. 2012 Jul 17;84(14):5845-50. doi: 10.1021/ac300629p. Epub 2012 Jun 27. Anal Chem. 2012. PMID: 22697456 Free PMC article.

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The enterocyte microvillus is a vesicle-generating organelle.

McConnell RE, Higginbotham JN, Shifrin DA Jr, Tabb DL, Coffey RJ, Tyska MJ. McConnell RE, et al. J Cell Biol. 2009 Jun 29;185(7):1285-98. doi: 10.1083/jcb.200902147. J Cell Biol. 2009. PMID: 19564407 Free PMC article.

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Informatics of protein and posttranslational modification detection via shotgun proteomics.

Holman JD, Dasari S, Tabb DL. Holman JD, et al. Methods Mol Biol. 2013;1002:167-79. doi: 10.1007/978-1-62703-360-2_14. Methods Mol Biol. 2013. PMID: 23625403 Free PMC article.

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CanProVar: a human cancer proteome variation database.

Li J, Duncan DT, Zhang B. Li J, et al. Hum Mutat. 2010 Mar;31(3):219-28. doi: 10.1002/humu.21176. Hum Mutat. 2010. PMID: 20052754 Free PMC article.

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Identifying proteomic LC-MS/MS data sets with Bumbershoot and IDPicker.

Holman JD, Ma ZQ, Tabb DL. Holman JD, et al. Curr Protoc Bioinformatics. 2012 Mar;Chapter 13:Unit13.17. doi: 10.1002/0471250953.bi1317s37. Curr Protoc Bioinformatics. 2012. PMID: 22389012 Free PMC article.

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TagRecon: high-throughput mutation identification through sequence tagging.

Dasari S, Chambers MC, Slebos RJ, Zimmerman LJ, Ham AJ, Tabb DL. Dasari S, et al. J Proteome Res. 2010 Apr 5;9(4):1716-26. doi: 10.1021/pr900850m. J Proteome Res. 2010. PMID: 20131910 Free PMC article.

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