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 <azel...@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-discuss+unsubscr...@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-discuss+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/CAGJJY%3D-3E-%3D4OqMEjuio3wngty4anoHp-9n658HQHspH1%3D-cCg%40mail.gmail.com.
