. Author manuscript; available in PMC: 2014 Feb 1.

Published in final edited form as: Curr Opin Biotechnol. 2012 Nov 8;24(1):10.1016/j.copbio.2012.10.013. doi: 10.1016/j.copbio.2012.10.013

Table 1.

Summary of software tools featured in this review

Software tool	Purpose
Andromeda	Database search
MS-GFDB	Database search
pFind	Database search
pNovo	De novo sequencing
PeptideProphet	PSM validation
Percolator	PSM validation
FDRAnalysis	Multiple search combination
iProphet	Multiple search combination
Pepitome	Spectral library searching
PeptideAtlas	Annotated spectrum repository
Fido	Protein inference
IDPicker 2.0	Protein inference
MAYU	Protein inference
ProteinProphet	Protein inference
MaxQuant	Analytical software suite
Trans-Proteomic Pipeline	Analytical software suite