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Table 2 Database searching parameters

From: Accelerating the scoring module of mass spectrometry-based peptide identification using GPUs

Exp. 1 Instrument QSTAR
Spectra 46195 DTA files
Database Yeast (13434 proteins, target + reversed)
Enzyme Trypsin (max missed cleavage sites = 2)
Tolerance Precursor: 0.2 Da; Fragment: 0.2 Da
Modifications Fixed: Carbamidomethylation (C)
Variable: Oxidation (M), Phosphorylation (S, T, Y)
Exp. 2 Instrument LTQ
Spectra 43493 DTA files
Database IPI.Human v3.49 ( 148034 protein, target + reversed)
Enzyme Trypsin (max missed cleavage sites = 2)
Tolerance Precursor: 3 Da; Fragment: 0.5 Da
Modifications Fixed: Carbamidomethylation (C)
Variable: Oxidation (M), Phosphorylation (S, T, Y)
Exp.3 Instrument QSTAR
Spectra 46195 DTA files
Database UniprotKB/Swiss-Prot (540171 proteins)
Enzyme Trypsin (max missed cleavage sites = 2)
Tolerance Precursor: 0.2 Da; Fragment: 0.2 Da
Modifications Fixed: Carbamidomethylation (C)
Variable: Oxidation (M), Phosphorylation (S, T, Y)