Several recent articles have reviewed the basics of shotgun proteomics techniques and instrumentation (14, 15, 35), as well as identification and validation informatics of MS/MS data (42). A great resource for finding software tools for proteomics is the www.proteomecommons.org web site. Here we discuss the entire life span of MS/MS data, from raw mass spectrometer output, through analysis and validation of the data, and finally transfer to public proteomics data repositories, highlighting some successes and lessons learned that may well be relevant to other disciplines of biomedical informatics.