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.
