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/CAGJJY%3D-K9_wy5oOc%3DmF2E8sffwfQ8djKVNBpv7Rt5H0VOLROyw%40mail.gmail.com.
