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ROC analysis of search results from the hierarchical MS2/MS3 searches in MassMatrix and two stage MS2/MS3 searches in MassMatrix, Mascot and X!Tandem for a tryptic of αCasein: (a) all the peptide matches for the LCQ data set, (b) all the peptide matches for the LTQ-FTICR data set, (c) phosphopeptide matches for the LCQ data set, and (d) phosphopeptide matches for the LTQ-FTICR data set.
