ASAPRatio error (TPP4.6.0)

[Brian Hampton]

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)
.
.
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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

[David Shteynberg]

Hi Brian,

Have you tried removing the static option -S when running this command?

Thanks,

-David

Brian

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[Brian Hampton]

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