I am running into a problem with ASAPRatio in TPP 4.6 that I didn't have with 4.5.2
Peptides are labeled on the N-terminus or K with either D0 or D6, and then combined for LC/MS. Raw file converted to mzXML with msconvert. I do separate searches with Tandem specifying static modification on [ and K. One search for the light the another search for heavy labeled peptides, same mzXML file two different tandem.xml files. I created a directory structure for the experiment with sub directories called light and heavy. I have not renamed the data file and hence, the tandem.xml files because the light and heavy searches reside in different directories. When I used ASAPRatio in TPP4.5.2 I would specify static modification quantification, each run is either all heavy or all light, tell it n and K were modified and run. ASAPRatio would correctly quantify the light and heavy peaks separated by 6 m/z for each modification. Now in TPP 4.6 if I select static modifications, it throws an error saying that you can't have variable modified n in static mode. This did not occur in 4.5.2. Without selecting the static modification,no matter how I configure it the ASAPRatio returns bogus results where it gets the quantitation for one labeled partner at the correct m/z but chooses a seemingly unrelated m/z to quantitate for the other labeled partner. Could it be that I need to rename the data files so they are different and redo the searches? Do they also have to be in the same directory? Or is ASAPRatio broken in 4.6? Thanks in advance for your help. Brian -- 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.
