Dear all, My problem is: I have samples which are mix of light and heavy form after acetylation. I want to quantify proteins with ASAPRatio (Xpress works well). I searched those samples in MASCOT using N-acetyl only for light form. In XPress I just need to put a mass difference between light and heavy acetyl and it works. Here in ASAP i tried to put also a mass difference, but output is nonsense (I used static modifications, and in specified label mass I put mass difference between light and heavy form). As I tried to look for similar topics, I found out I should do also a search in mascot for heavy form and then use option "static modification" and in specified label mass I should paste both light and heavy acetyl? please let me know if I'm correct, or any other idea how to analyse it.
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