Hi David, Your v5.2.1-dev Flammagenitus, Build 202003241419-80410 has fixed this problem. Thank you! Alex
On Wednesday, March 18, 2020 at 12:00:34 PM UTC-7, David Shteynberg wrote: > > Thanks Alex. I suspect it is a possible bug in PTMProphet. Can you see > what step of your analysis created these additional mods on C? I would > help me narrow down the places to look. > > Cheers, > David > > On Wed, Mar 18, 2020 at 11:56 AM Alex Zelter <aze...@uw.edu <javascript:>> > wrote: > >> Hi David, >> Thanks for the fast response! >> >> My list of commands are as follows (after running MSFragger): >> >> tpp/bin/InteractParser interact.pep.xml FraggerOutput.pepXML >> tpp/bin/DatabaseParser interact.pep.xml >> tpp/bin/RefreshParser interact.pep.xml >> /path/to/database/fastaFile.fasta >> tpp/bin/PeptideProphetParser interact.pep.xml ACCMASS DECOYPROBS >> DECOY=random NONPARAM MASSWIDTH=520 MINPROB=0 >> tpp/bin/InterProphetParser interact.pep.xml interact.ipro.pep.xml >> tpp/bin/PTMProphetParser MASSDIFFMODE interact.pep.xml >> tpp/bin/PTMProphetParser MASSDIFFMODE interact.ipro.pep.xml >> >> I'm happy to share the full set of files with you if that helps. >> >> Thanks! >> Alex >> >> On Wednesday, March 18, 2020 at 11:42:22 AM UTC-7, David Shteynberg wrote: >>> >>> Hi Alex, >>> >>> This seems like a bug that should be fixed. Are you running PTMProphet >>> at any point in your analysis pipeline? >>> >>> Thanks, >>> -David >>> >>> On Wed, Mar 18, 2020 at 11:38 AM Alex Zelter <aze...@uw.edu> wrote: >>> >>>> 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 spctools...@googlegroups.com. >>>> To view this discussion on the web visit >>>> https://groups.google.com/d/msgid/spctools-discuss/5a37d860-cd21-445a-a485-ed3684291f4d%40googlegroups.com >>>> >>>> <https://groups.google.com/d/msgid/spctools-discuss/5a37d860-cd21-445a-a485-ed3684291f4d%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 spctools...@googlegroups.com <javascript:>. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/spctools-discuss/4314cc4f-3944-4a51-bb34-dc43aae61848%40googlegroups.com >> >> <https://groups.google.com/d/msgid/spctools-discuss/4314cc4f-3944-4a51-bb34-dc43aae61848%40googlegroups.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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