I have been trying to run a search with peptide N-terminal modification. I tried both fixed as
<note label="residue, modification mass" type="input">42.065@N-Term,42.065@K</note> (or with 42.065@[ notation)
and potential
<note label="residue, potential modification mass" type="input">42.065@[</note>
and never had it show in the modifications view nor I identified peptides I know are there and I got identifications from standalone Xtandem.
Any ideas why it is not working?
Thanks guys,
Tomas |
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| brendanx responded: |
2007-09-04 09:54 |
Well, first, there was a bug in Tandem2XML (the X! Tandem output to pepXML converter) that was stripping some n-terminal modifications. That has been fixed, if you can grab the TPP, and build your own.
Second, the CPAS web site currently still ignores all terminal modifications in the pepXML. The seems to be increasing in importance for our users, but as yet none of our funders have agreed to fund the feature. I am hopeful that we can make it happen for our 2.4 release.
You will still want to pick up the Tandem2XML fix, if you want the rest of the TPP tools to work correctly.
Finally, wow, does X! Tandem actually accept "42.065@N-Term"? I have to admit the largest difficulty with correctly handling X! Tandem modifications in Tandem2XML has been the large variety of ways it allows modifications to be specified.
--Brendan |
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| tvaisar responded: |
2007-09-04 10:19 |
Hi Brendan,
yes it takes 42.065@N-Term. It was actually not easy to find how to specify the N-terminal modification. There are too many ways (about 3 different input lines where you can specify it - as fixed mod, potential mod, N-terminal mod, at protein, N-term mod where instead of +1.0078/H, you can specify whatever you want).
Second - I am not clear what you mean by CPAS web site ignores all terminal modifications in the pepXML. Does that mean that you cannot submit the search from within the CPAS and have N-terminal modification, or that after you do the search, and TPP, that the N-terminally modified hits are ignored, or lastly, that the CPAS just will not display them, but if you know that the modification is there (e.g. fixed mod) you can still use it?
Thanks,
Tomas |
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| brendanx responded: |
2007-09-04 10:28 |
The processing (once you have the Tandem2XML fix) should work just fine, and the peptide matches should get uploaded correctly. The CPAS user interface, however, will not show the modifications, and if you drill into the spectrum viewing page, it also will not be aware of the terminal modification, and will not correctly display the MS2 peak hits that caused the identification.
We'd like to fix this, and it seems like there may be enough interest to get it into our next release. |
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| brendanx responded: |
2007-09-04 15:59 |
I have attached a Windows Tandem2XML.exe that should work as a replacement for the one currently shipped with CPAS, and do a better job of handling terminal modifications.
--Brendan |
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Tandem2XML.exe