Good day. Can anyone tell me or point to any site on how to correctly analyze the fragmentation evidence (MS/MS spectrum) in ProteinPilot? I just started using the software yesterday.
From the protein sequence coverage, I can tell the % confidence of the peptides I have. If there are green colored peptides, I usually have no problem with the spectrum.
But sometimes, only yellow colored peptides are shown. In this case, if there are at most 3 y-peaks on the spectrum, I mark the protein as false positive, and if there are at least 4 y-peaks, I mark the protein as true positive. I do not consider the b-peaks in my analysis.
Is this correct? Please advise. Thank you in advance.
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