Seattle Proteome Center (SPC) - Proteomics Tools
NHLBI Proteomics Center at the Institute for Systems Biology

Pep3D

View LC-MS and LC-MS/MS results in a 2D mz vs. time plot. If identifications are available via an INTERACT interface with PeptideProphet results, sequencing attempts and identification quality are overlayed on the plot; each spot is then a hyperlink to the ms/ms spectrum and identification. The results can be used to evaluate data quality among its many applications.

Reference: Li X-J, Pedrioli PGA, Eng J, Martin D, Yi EC, Lee H, Aebersold R. (2004) "A tool to visualize and evaluate data obtained by liquid chromatography / electrospray ionization / mass spectrometry." Anal Chem 76:3856-60.

This software is part of the Trans-Proteomics Pipeline (TPP) software distribution. Please also see the Pep3D page and TPP documentation on the SPCTools wiki for addition information, including download instructions.