Hello, I have been using ASAPRatio from previous versions of the TPP successfully. However, now I cannot obtain appropriate data for the ratios with the version present in 4.7. ASAPRatio is not appropriately matching the corresponding heavy labeled peptide with its light partner. It is choosing a peptide partner with a mass delta that doesn't make sense.
I am labeling amines by reductive alkylation with acetone (D0 and D6). I use Tandem for the search and specify the mods as per the API instructions where I specify static mod of 42@[ and 42@K and potential mods of 6@[ and 6@K. In ASAPRatio setup, I specify the following (via Petunia not the command line): xinteract -Ninteract.pep.xml -p0 -l5 -Op -dDECOY -A-lnK-b-r0.5-mn48.0846K176.1795 Depending on the charge the mass delta between the light and heavy will be multiples of 6 for each labeled site, but I'm seeing multiples of 48 instead and so the h/l pairs are not correct. I am not certain if this is a problem with ASAPRatio, is it a newer version than what was in 4.6, or if it has something to do with the output of Tandem. If the former I can go and replace the new version of ASAPRatio with an older version and see if that fixes it. Any help much appreciated. Brian Brian Hampton Protein Analysis Lab Center for Vascular and Inflammatory Diseases University of Maryland School of Medicine 655 West Baltimore Street BRB 7-018 Baltimore MD 21201 V: 410-706-8207 -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
