Hi Brian, Perhaps a bug was introduced in 4.7.0? Did this work with the older version? If you could put together a small repro dataset to play with I can make sure to fix it in a future version.
Thanks! -David On Thu, Apr 10, 2014 at 10:06 AM, Brian Hampton <[email protected]>wrote: > 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. > -- 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.
