The first step in any data processing workflow is getting the actual numbers out of your vendor's proprietary format. This is something most/all of us just take for granted. I did until this dumb paper messed up some perfectly established complacency on the topic back in December --
And this is where the cleverly named ThermoRAWFileParser comes to the rescue!
How you get the data out of your RAW files matters. Proof?!?!?
That's 3000 more peptides! For free? For just improving how you pull the data out of the RAW file and make it into mZxML!?!?
... make it into mzML!?!?
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