The proteins are chopped into smaller fragments using an enzyme called trypsin... That's known as bottom up analysis. It is currently the most popular way to d

The proteins are chopped into smaller fragments using an enzyme called trypsin... That's known as bottom up analysis. It is currently the most popular way to do it, and IMHO it's crap. You can do intact whole protein analysis and that's much better. More higher end instruments will do both, starting with the intact protein, measuring its mass, and then breaking it down and measuring the mass of the peptides. The breaking down part is not deterministic but with the mass of the whole protein and the genetic sequence and a few runs you can figure out exactly what's what. None of that will tell you what the 3D shape of the protein is. That's a whole other ball of wax. --EDIT-- the initially deposited data had several problems, including incomplete files, proprietary software formats, and screenshots of data displays in software rather than actual data files Yep, there's companies that can help you with that: http://www.bioanalyte.com/ http://www.bioanalyte.com/