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 On Mon, Apr 4, 2022 at 5:17 PM 'David Shteynberg' via spctools-discuss < [email protected]> wrote: > 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 > > On Wed, Mar 9, 2022 at 11:32 PM Farshad AbdollahNia < > [email protected]> wrote: > >> 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. >> >> https://www.dropbox.com/sh/exlp1c2czwqa56c/AACFtEmukZzP9GNEpAXl7SCsa?dl=0 >> >> 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 >> >> On Thu, Feb 24, 2022 at 2:32 PM David Shteynberg < >> [email protected]> wrote: >> >>> 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 >>> >>> On Sun, Jan 30, 2022 at 10:28 PM Farshad Abdollah-Nia < >>> [email protected]> wrote: >>> >>>> 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 >>>> <https://www.thegpm.org/tandem/api/pmrmf.html>. However, Tandem2XML >>>> simply uses hard-coded masses for the default special Tandem modifications, >>>> such as pyrolidone <https://www.thegpm.org/tandem/api/pqp.html>, 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 >>>> >>>> -- >>>> You received this message because you are subscribed to the Google >>>> Groups "spctools-discuss" group. >>>> To unsubscribe from this group and stop receiving emails from it, send >>>> an email to [email protected]. >>>> To view this discussion on the web visit >>>> https://groups.google.com/d/msgid/spctools-discuss/5b5b0fd4-6557-4ae2-b43c-db67d0019865n%40googlegroups.com >>>> <https://groups.google.com/d/msgid/spctools-discuss/5b5b0fd4-6557-4ae2-b43c-db67d0019865n%40googlegroups.com?utm_medium=email&utm_source=footer> >>>> . >>>> >>> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected]. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/spctools-discuss/CAFyEx3wEh%2BNaCokceQkcMpR57%2BMU9b39%2BpK0%3DNwsajW815ocEg%40mail.gmail.com >> <https://groups.google.com/d/msgid/spctools-discuss/CAFyEx3wEh%2BNaCokceQkcMpR57%2BMU9b39%2BpK0%3DNwsajW815ocEg%40mail.gmail.com?utm_medium=email&utm_source=footer> >> . >> > -- > You received this message because you are subscribed to a topic in the > Google Groups "spctools-discuss" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/spctools-discuss/QUfdwVGAhqk/unsubscribe > . > To unsubscribe from this group and all its topics, send an email to > [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/CAGJJY%3D8vM3fM8DMVwNWFHaScK-WH9DbFsmQjY992U%3D_QbFQ%2BDQ%40mail.gmail.com > <https://groups.google.com/d/msgid/spctools-discuss/CAGJJY%3D8vM3fM8DMVwNWFHaScK-WH9DbFsmQjY992U%3D_QbFQ%2BDQ%40mail.gmail.com?utm_medium=email&utm_source=footer> > . > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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