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. Author manuscript; available in PMC: 2010 Aug 1.
Published in final edited form as: J Proteome Res. 2009 Aug;8(8):3872–3881. doi: 10.1021/pr900360j

Table 1.

Experimental Data Sets Summary

data set namea replicates average no. of MS/MS scans database search tools precursor/fragment m/z tolerance databases used for searchb
Score Combination Evaluation Data Sets
Serum Orbi 5 6548 MyriMatch, Sequest, Mascot 0.1/0.5 ipi.HUMAN.v3.47
Plasma QSTAR 5 7058 MyriMatch, Sequest, Mascot 0.25/0.25 ipi.HUMAN.v3.47
DLD1 LTQ 4 12913 MyriMatch, Sequest, Mascot 1.25/0.5 ipi.HUMAN.v3.47
Peptide Segregation Evaluation Data Sets
DLD1 LTQ 4 12913 MyriMatch 1.25/0.5 ipi.HUMAN.v3.47
Serum Orbi 5 6548 MyriMatch 0.1/0.5 ipi.HUMAN.v3.47
Parsimony Performance Evaluation Data Sets
DLD1 LTQ 4 12913 MyriMatch 1.25/0.5 uniprot_sprot-rel56.2
Serum Orbi 5 6548 MyriMatch 0.1/0.5 uniprot_sprot-rel56.2
a

Data set names represent sample type and the mass spectrometer used in the analysis (see Materials and Methods for additional details).

b

All protein databases contained reversed sequence entries (decoys) for estimation of false discovery rates. Exhaustive database search configurations were made available in Supplemental File 2.