Holy cow. It has been nearly a month since my last entry. Apparently, I've been every bit as busy as I thought I had been....changing jobs, states, and buying a new house are all things that will cut into your free time.
Anyway, this amazing tool has been available for years now, but it only just now came to my attention. Peptide Atlas is an amazing set of tools, as well as a data repository for all of us out there who have interest in a specific protein or set of proteins and want to target them.
Say you are interested in a cool protein like STAT3 but you didn't see it in your discovery run. You can go to the Peptide Atlas and see what peptides from STAT3 are most commonly found in your normal proteomics experiment. You can then export the mass of those peptides and move them to your Include or Parent Mass lists, dramatically increasing the chances that you will find and be able to observe that protein. It takes the guess work out of your experiments, particularly what peptides or charge states you should be looking for. There are other tools that will help you build SRM methods but I havent' gotten to those yet. Data from the Peptide Atlas can also be directly imported into PinPoint if you are doing true label free and targeted quan.
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