Hello, I perform searches with X!Tandem, allowing certain modifications (lysine methylation, for instance). The modification are set per-protein in a curated database.
However, Tandem2XML complains when creating pepXML files for further downstream processing: WARNING: Unknown modification 'K' (14.0156) for scan 57864. ... Is there a way to retain these modifications in the pepXML? I was startled to find that the scan (57864, for instance) for the methylated peptide is still written to the pepXML, but the modification is lost. Clearly, the precursor mh is now significantly off! In X!Tandem output: =============== <domain id="57864.1.1" start="46" end="59" expect="5.1e-06" mh="1617.787" delta="-0.081" hyperscore="37.9" nextscore="8.0" x_score="0.0" x_ions="0" y_score="10.7" y_ions="12" z_score="0.0" z_ions="0" a_score="0.0" a_ions="0" b_score="6.0" b_ions="3" c_score="0.0" c_ions="0" pre="GAAR" post="GITI" seq="AFDQIDNAPEEKAR" missed_cleavages="1"> <aa type="K" at="57" modified="14.01560" /> in pepXML: ========= <spectrum_query spectrum="17_search_cen.57864.57864.3" start_scan="57864" end_scan="57864" precursor_neutral_mass="1616.6988" assumed_charge="3" index="287" retention_time_sec="2221.43"> <search_result> <search_hit hit_rank="1" peptide="AFDQIDNAPEEKAR" peptide_prev_aa="R" peptide_next_aa="G" protein="sp|EFTU1_ECOLI" num_tot_proteins="1" num_matched_ions="15" tot_num_ions="52" calc_neutral_pep_mass="1616.7797" massdiff="-0.081" num_tol_term="2" num_missed_cleavages="1" is_rejected="0"> There is no <modification_info> for this spectrum_query in the pepXML. Thank you for your help! Vadim -- 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 post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
