What search engine do you use?
We use Mascot (Matrix Science) for protein identification. Protein inference, grouping and FDR (false discovery rate) estimation is performed in Proteome Discoverer and Scaffold.
Perkins DN, Pappin DJ, Creasy DM, Cottrell JS "Probability-based protein identification by searching sequence databases using mass spectrometry data." Electrophoresis, 1999, 20(18) p. 3551-67.
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