It is completely possible to prep a sample, run an instrument and process your data without ever knowing at all how any of it works. And that's fantastic -- until something goes wrong.
On the data processing side so many things are just assumed based on 15 or 20 years? of work developing this stuff. If you'd like an exceptionally clear walkthrough on two of the harder principles -- false discovery rate estimation (FDR) and how parsimony (what to do with peptide identifications that are not mappable directly to a single ID -- here are two great ones courtesy of Dr. Phil Wilmarth.
#1 -- Shotgun proteomics and FDR
#2 -- Parsimony (and maybe a better idea than parsimony?)
There are other great things at the GitHub as well. 100% recommended and added to the "Resources for NewBies section over there. --->
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