I appreciate that this is a pretty naive question, so apologies in advance.
I do a lot of high-throughput DNA sequencing, and I've made a few findings (particularly involving uORFs) that would make getting an idea of different protein levels in different cell types very useful indeed.
What with the few big recent human proteome papers, I was hoping that I'd be able to dip into this data and just look for panels of peptides from my proteins of interest and get a rough handle on how frequently they might be occurring (I was naively imagining there were just large tables of all the peptides that come off a mass spec that I could write a custom script to grep for sliding windows of the proteins I'm interested in).
It turns out that this really isn't how things work in proteomics!
What I'm asking is, given say the kind of files produced by those papers (such as this) how might I go about looking for specific peptides of interest (as opposed to just browsing the lists of what proteins they've looked at.
I don't even know what file type I should be looking at, any help anyone could provide me to point me in the right direction would be very warmly received.