There are a lot of proteomics data analysis pipelines out there, but MetaMorpheus should be at the top of your list, especially if you're using Orbitraps.
You can get 1.0 here (you will likely need a Windows .Net update that takes like 2 minutes).
Version 1.0 just launched and it is an even more comprehensive package than before. I just searched my data against a spectral library (.msp format)!
I don't know how secret my collaborator's stuff is above, so I blanked it out just in case. We're all in last phase grant panic here and when people do have time to talk you get sleepy sentence fragments.
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