Hello Filip, Xpress works using delta mass. Asap ratio on the other hand takes the mass of the modified form as input. If the dataset is high mass accuracy you also need to specify the monoisotopic masses of ALL your modifications even the ones not used for the label, unless you are doing the whole analysis with monoisotopic mass. In case of high mass accuracy data you probably also want to specify tigher mass tolerances for both quantitation tools. Hope this helps you get started with asapratio.
-David On 6/13/09, Filip <[email protected]> wrote: > > 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. > > best regards, > > Filip > > > > > -- Sent from my mobile device --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
