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 <[email protected] <javascript:>> > 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 [email protected] <javascript:>. >> 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 [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/4314cc4f-3944-4a51-bb34-dc43aae61848%40googlegroups.com.
