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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.
    Summary | Full Text (DOI)

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