I am running PTMProphet (TPP v5.2.1-dev Flammagenitus, Build 202003100907-8034) on MSFragger (MSFragger version MSFragger-2.3) output and ending up with strange results in specific cases.
For example, for a specific PSM, 52782, MSFragger outputs: <spectrum_query start_scan="52782" uncalibrated_precursor_neutral_mass="2288.8486" assumed_charge="3" spectrum="QEP2_2018_0812_AZ_033_az736_AZ.52782.52782.3" end_scan="52782" index="41840" precursor_neutral_mass="2288.8384" retention_time_sec="6104.521"> <search_result> <search_hit peptide="RYKAAFTECCQAADK" massdiff="471.0195" calc_neutral_pep_mass="1817.8188" peptide_next_aa="A" num_missed_cleavages="2" num_tol_term="2" num_tot_proteins="5" tot_num_ions="56" hit_rank="1" num_matched_ions="23" protein="sp|P02768|ALBU_HUMAN Serum albumin OS=Homo sapiens GN=ALB PE=1 SV=2" peptide_prev_aa="K" is_rejected="0"> <modification_info> <mod_aminoacid_mass mass="160.0307" position="9"/> <mod_aminoacid_mass mass="160.0307" position="10"/> </modification_info> <search_score name="hyperscore" value="44.421"/> <search_score name="nextscore" value="12.357"/> <search_score name="expect" value="4.415e-15"/> </search_hit> </search_result> </spectrum_query> This would indicate that C9 is +57, C10 is +57 and there is an additional unlocalized mass diff of +471. After running TPP I end up with output like this in interact.ipro.pep.xml for that scan: <spectrum_query start_scan="52782" uncalibrated_precursor_neutral_mass="2288.8486" assumed_charge="3" spectrum="QEP2_2018_0812_AZ_033_az736_AZ.52782.52782.3" end_scan="52782" index="36796" precursor_neutral_mass="2288.8384" retention_time_sec="6104.521"> <search_result> <search_hit peptide="RYKAAFTECCQAADK" massdiff="471.0195" calc_neutral_pep_mass="1817.8188" peptide_next_aa="A" num_missed_cleavages="1" num_tol_term="2" num_tot_proteins="5" tot_num_ions="56" hit_rank="1" num_matched_ions="23" protein="sp|P02768|ALBU_HUMAN" peptide_prev_aa="K" is_rejected="0" protein_descr="Serum albumin OS=Homo sapiens GN=ALB PE=1 SV=2"> <modification_info modified_peptide="RYKAAF[618]TEC[160]C[160]QAADK"> <mod_aminoacid_mass position="6" mass="618.0879"/> <mod_aminoacid_mass position="9" mass="574.0287"/> <mod_aminoacid_mass position="10" mass="574.0287"/> </modification_info>....... So it seems to me that we now have a modification mass addition of +471 on residues 6 9 and 10 rather than a mass addition of +471 on residue 6 and then an addition of +57 on residues 9 and 10. In cases where there is just a mass diff (open modification) and no defined variable modifications output is as expected. This situation seems to occur when both defined variable modifications and open modifications are present. I have confirmed the same behavior in older versions of MSFragger and TPP. Any ideas would be much appreciated! Thanks, Alex -- 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/5a37d860-cd21-445a-a485-ed3684291f4d%40googlegroups.com.
