Fast and Accurate Protein False Discovery Rates on Large-Scale Proteomics Data Sets with Percolator 3.0

10.1038/nmeth1113

10.1016/1044-0305(94)80016-2

10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2

Craig, R., Beavis, R.C.: TANDEM: matching proteins with tandem mass spectra. Bioinformatics 20(9), 1466–1467 (2004)

10.1021/pr8001244

10.1021/pr501164r

10.1021/pr100594k

10.1074/mcp.T400006-MCP200

10.1021/pr9004794

Savitski, M.M., Wilhelm, M., Hahne, H., Kuster, B., Marcus Bantscheff, M.: A scalable approach for protein false discovery rate estimation in large proteomic data sets. Mol. Cell. Proteom. M114 (2015)

10.1038/nbt.1511

Fisher, R.A.: Statistical methods for research workers. Genesis Publishing Pvt Ltd. (1925)

10.1093/bioinformatics/btu717

10.1016/j.jprot.2012.12.007

10.1093/bioinformatics/btr089

10.1038/nature13302

10.1038/nature12223

10.1021/pr400705q

McDonald, W.H., Tabb, D.L., Sadygov, R.G., MacCoss, M.J., Venable, J., Graumann, J., Johnson, J.R., Cociorva, D., Yates, J.R.: MS1, MS2, and SQT — three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications. Rapid Commun. Mass Spectrom. 18(18), 2162–2168 (2004)

10.1093/bioinformatics/btn323

10.1021/ac0700833

10.1021/pr900816a

10.1021/pr500741y

The, M., Tasnim, A., Käll, L.: How to talk about protein-level false discovery rates in shotgun proteomics. Proteomics, forthcoming

10.1074/mcp.R500012-MCP200

10.4310/SII.2012.v5.n1.a2

10.1021/ac0341261

Oliver Serang, O., Käll, L.: Solution to statistical challenges in proteomics is more statistics, not less. J. Proteom. Res. 14(10), 4099–4103 (2015)