Getting the software
This software is included in the current TPP distribution.
In a nutshell
View LC-MS and LC-MS/MS results in a 2D mz vs. time plot.
If identifications are available via an INTERACT or pepXML Viewer 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.
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. download PDF
The link to the supplemental information referenced in the manuscript is incorrect. Here's the correct link to the supplemental information.