Protein Prospector is an on-line program developed by the UCSF Mass Spectrometry Facility. Tools for in silico digestion, fragmentation, as well as database search are available.
If you have not done mass spectrometry based proteomics, this tutorial will provide you a good understanding of how mass spec data is processed to generate protein identification report. It’s somewhat superficial and old, but still, it’s a good start.
ABRF is a society of core facility, besides annual meetings, the society host an active discussion forum. Sign up to the email list for the discussion group or surf the archive online, you’ll find lots of postings on technical tips, problems and solutions.
