Hi David. Thanks for your response. The problem was solved after I closely looked at the tandem.params file I created after upgrading from 4.5.2 to 4.6. I made a silly copy paste error. In the static modifications section I had two decimal points in one of the modification mass specifications. I am not certain how Tandem treated this, but ASAPRatio treated it as multiple modifications to a single residue, in this case it was [.
This was the erroneous modifications line: <note type="input" label="residue, modification mass">57.021464@C ,48.085.047@[,48.085@K</note> This is the correct modifications line: <note type="input" label="residue, modification mass">57.021464@C,48.085@ [,48.085@K</note> The Tandem API suggests that it will use the last instance of a modification to the same residue e.g. 48@K,28@K then it will use 28@K and ignore the 48@K. However, in my case the mistake of 48.085.047@[ was apparently treated as multiple modifications to [. Useless anyway because ASAPRatio could not do anything with that. All the output I got was wrong no matter how I specified the modification masses for ASAPRatio. And setting the -S static flag would cause ASAPRation to fail. Brian On Tue, Aug 28, 2012 at 7:29 PM, David Shteynberg < [email protected]> wrote: > Hi Brian, > > Have you tried removing the static option -S when running this command? > > Thanks, > -David > > On Tue, Aug 28, 2012 at 2:50 PM, Brian Hampton <[email protected]>wrote: > >> Hello, >> >> I am trying the newest TPP installed on Win7 using the installer. I have >> two small data sets of differentially labelled peptides searched separately >> with Tandem where one search specifies all light and the second all heavy >> labelled modifications. When running ASAPRatio, I select static >> modifications and tell it N-terminus & K are modified. It is pulling the >> correct mods from the tandem result file. But I get "error: cannot have >> variablel modified n in static mode." >> >> This worked well with TPP 4.5.2, but now it isn't working. Is the new >> version of Tandem using different defaults for mods? I am not specifying >> any in the tandem.params file. I get the following error: (relevant part >> of pipeline output below) >> . >> . >> . >> >> running: "C:/Inetpub/tpp-bin/ASAPRatioPeptideParser >> "TEST-HL-interact.pep.xml" -lnK -b -F -C -Z -r0.5 -S" >> K 170.142 176.18 >> n 43.0548 49.0928 >> error: cannot have variable modified n in static mode >> >> command "C:/Inetpub/tpp-bin/ASAPRatioPeptideParser >> "TEST-HL-interact.pep.xml" -lnK -b -F -C -Z -r0.5 -S" failed: Operation not >> permitted >> >> command "C:/Inetpub/tpp-bin/ASAPRatioPeptideParser >> "TEST-HL-interact.pep.xml" -lnK -b -F -C -Z -r0.5 -S" exited with non-zero >> exit code: 1 >> QUIT - the job is incomplete >> >> command "c:\Inetpub\tpp-bin\xinteract -NTEST-HL-interact.pep.xml -p0.05 -l6 >> -Op -I4 -I5 -A-lnK-b-F-C-Z-r0.5-S >> 120827_S-Aorta_GuanidineExtract-RABA-QC01.tandem.pep.xml >> c:/Inetpub/wwwroot/ISB/data/projects/S_Aorta/120827_Guanidine/light/120827_S-Aorta_GuanidineExtract-RABA-QC01.tandem.pep.xml" >> failed: Operation not permitted >> >> >> >> Thanks in advance for any help. >> >> Brian >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To view this discussion on the web visit >> https://groups.google.com/d/msg/spctools-discuss/-/Z0vbkWp9-l4J. >> 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. >> > > -- > 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. > -- 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.
