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 <[email protected]> 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 <[email protected]> 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]. >>> 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 > <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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