I don't know if I've ever really gone into my obsessive love of this little node in Proteome Discoverer. BTW, Preview is by Protein Metrics, and its free and easy to install and it makes my life so much easier.
If you aren't familiar, you should check it out. Preview tells me about my sample. This is part of the front page read out from something I'm digging through today:
It took a look and said "you know what? this is a tryptic digest. and its a pretty good one. We miss about 10% of the Ks and Rs when we went through, but thats okay.
Then is says, "hey, looks like you used iodoacetamide, cause about 99% of your cysteines have a +57.00whatever on it"
Then is says: "man, you should really search for deamidation of N and Q, ou'll get an extra 900 peptides if you do. Oh, and oxidized Met will help as well. And it looks like you maybe over reduced/alkylated a little cause you've got some artifacts from those 2 processes around, but nothing too bad, just maybe use a little less heat next time or somethin'"
What a crazy useful tool! The sample I'm looking at seems just fine. Nothing to worry about there!
You can get Preview at the Protein Metrics page here.
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