Tandem2XML all-15N issue

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Farshad Abdollah-Nia

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Jan 31, 2022, 1:28:52 AMJan 31
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Hello everyone,

I have been getting warnings of the following type from Tandem2XML when processing all-15N search results:

WARNING: Unknown modification 'C' (-18.0236) for scan 58137.
WARNING: Unknown modification 'Q' (-18.0236) for scan 66445.

The all-15N search uses modified residues as well as modified NH3 mass specification, as detailed here.  However, Tandem2XML simply uses hard-coded masses for the default special Tandem modifications, such as pyrolidone, etc:

// Special X! Tandem n-terminal AA variable modifications
  ModSpecData modSpec;
  modSpec.symbol = '^';
  modSpec.comment = "X! Tandem n-terminal AA variable modification";

  modSpec.aa = 'E';
  modSpec.mass = -18.0106;
  addModSpec(modSpec, true);
  modSpec.aa = 'Q';
  modSpec.mass = -17.0265;
  addModSpec(modSpec, true);
  if ((long) modsStatic['C'].mass == 57)
    {
      modSpec.aa = 'C';
      modSpec.mass = -17.0265;
      addModSpec(modSpec, true);
    }
  // deal with quick acetyl
  modSpec.aa = '[';
  modSpec.mass = 42.0106;
  addModSpec(modSpec, true);


I think these masses should be following the definitions provided by the user for specific isotopic labeling requirements (2H, 15N, ...) and not taken as fixed values.

Does this sound valid to the developers and would a fix be appropriate?

Thank you,
Farshad

David Shteynberg

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Feb 24, 2022, 5:32:09 PMFeb 24
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Dear Farshad,

Yes this looks like something that can be corrected.  The fix would use the user-specified mass modification and only when that is not available fall back to the hard-coded value.  I can make the change but would need your data so I can replicate the problem.  Are you able to compress your analysis directory and post it somewhere I can download it?

Thanks!
-David

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Farshad AbdollahNia

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Mar 10, 2022, 2:32:41 AMMar 10
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Hi David,

Thank you for your reply and volunteering to make the changes. Here is a link to a stand-alone example data set. Please make sure to change the paths in the input file p08_in.xml and the taxonomy file prokaryote.xml to point to your download location.


I agree with your proposed changes. Tandem2XML should look for user-specified residue masses in its input file (in this example p08_n15.xml, which is the output from X!Tandem) under the group labeled "residue mass parameters" (usually listed at the end of the file) and only if this group, or certain residue masses within it, are absent then fall back to the default values.

Thanks again for your help and please let me know if I can be of further assistance.

Farshad

David Shteynberg

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Apr 4, 2022, 8:17:02 PMApr 4
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Hi Farshad,

Thanks for providing your data and feedback so we can continue to improve our software.  In this particular case, the mass values used by Tandem2XML were based on N14  and were likely to result in problematic pepXML representations of N15 data.  I have added an option to Tandem2XML "N15" which will use the N15 masses as opposed to N14 masses, when specified by the user.   I have committed the code change to our repository.  This code will be available in the next official release of the TPP.

Cheers,
-David 

Farshad AbdollahNia

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Jun 8, 2022, 1:28:02 AMJun 8
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Hi David,

Thank you for updating the code and sorry for my late reply. This solves the problem for all 15N-labeling (I'll test with the new release). I hope in the future versions we can just read the "residue mass parameters" group from the input file to allow for more flexible user-defined labeling schemes, as is allowed by XTandem.

Thanks again,
Farshad

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