The "summary.txt" file gives a good overview of the data and the peptide sequence identification process. This file can be the base for your own descriptive record to link Raw file name with the actual experimental background.

The "proteinGroup.txt" file contains the protein identifications and quantities of the different proteins. 

This file is the major input to analyse the protein quantities on a statistical level using Perseus.

Comments: matthias.wilm@ucd.ie