I believe this X!Tandem parameter affects the initiator methionine cleavage: https://www.thegpm.org/TANDEM/api/pqa.html And I'm not aware of any RefreshParser parameters that control this behavior; I am using an older version (5.0.0) of the TPP though.
On Fri, Jun 7, 2019 at 2:10 PM Vidya Venkatraman <[email protected]> wrote: > Thanks Jimmy for your prompt response. > > I do see that for isoform P06396-2, the preceding methionine is the first > residue of the sequence and I used both comet & tandem for the database > search. > > For Comet search, I did have the "clip_nterm_methionine > <http://comet-ms.sourceforge.net/parameters/parameters_201801/clip_nterm_methionine.php>" > parameter set to "1" so you explanation makes sense. > > But for Tandem search, I am not sure if Tandem has an equivalent > parameter. But i can see that the tandem peptideprophet pepxml also > identifies this peptide as unique to isoform P06396-2. > > <spectrum_query > spectrum="XL_150506_IDA_PDAY_F7_proteinpilot.09460.09460.2" > start_scan="9460" end_scan="9460" precursor_neutral_mass="1096.5930" > assumed_charge="2" index="28557" retention_time_sec="2248.41"> > <search_result> > <search_hit hit_rank="1" peptide="VVEHPEFLK" peptide_prev_aa="M" > peptide_next_aa="A" protein="sp|P06396-2|GELS_HUMAN" > protein_descr="Isoform 2 of Gelsolin OS=Homo sapiens OX=9606 GN=GSN" > num_tot_proteins="1" num_matched_ions="17" tot_num_ions="16" > calc_neutral_pep_mass="1096.5917" massdiff="0.001" num_tol_term="2" > num_missed_cleavages="0" is_rejected="0"> > > Do you know if there is a parameter similar to 'clip_nterm_methionine' in > tandem as well? and > Does RefreshParser have any parameters to control this behavior? > > Many Thanks > Vidya > > > > > > > > > On Wed, Jun 5, 2019 at 11:27 AM Jimmy Eng <[email protected]> wrote: > >> Without more info, here's my educated guess at an explanation: that >> peptide is not a fully tryptic peptide in the proteins you list as it is >> preceded by a methionine residue. For isoform P06396-2, the preceding >> methionine is the first residue of the sequence and I'm assuming you did a >> Comet search with the "clip_nterm_methionine >> <http://comet-ms.sourceforge.net/parameters/parameters_201801/clip_nterm_methionine.php>" >> parameter set to "1". With that start methionine removed, this allowed >> that peptide to be fully tryptic in that particular isoform hence only that >> isoform is listed as a matched protein. The enzyme context does matter >> with RefreshParser; it's simply not a peptide string match. >> >> On Wed, Jun 5, 2019 at 11:15 AM Vidya Venkatraman < >> [email protected]> wrote: >> >>> Hi Everyone, >>> >>> I am trying to run xinteract with the -D option so that RefreshParser >>> can use the fasta database to find all proteins corresponding to >>> identified peptides. >>> >>> This is the command I am using: >>> xinteract -OARPwd -dDECOY_ -PPM -nR >>> -D/scratch/venkatramanv/iphronesis/reference_files/Databases/UP_Human_Rev_Can+Iso_20190410_DECOY.fasta >>> -N/scratch/venkatramanv/iphronesis/platform_workspace/jobs/SJOB2122/peptideprophet/2122_PDAY_DDA_Isoforms.comet.interact.pep.xml >>> *.comet.pep.xml >>> >>> Despite using the -D database option, i noticed that some peptides in >>> the interact.pep.xml are matched uniquely to a specific isoform (even >>> though that peptide is not proteotypic or unique to any isoform). >>> >>> For example: >>> >>> <spectrum_query >>> spectrum="XL_150506_IDA_PDAY_F8_proteinpilot.08799.08799.2" >>> start_scan="8799" end_scan="8799" precursor_neutral_mass="1096.592165" >>> assumed_charge="2" index="20868" retention_time_sec="2254.3"> >>> <search_result> >>> <search_hit hit_rank="1" peptide="VVEHPEFLK" peptide_prev_aa="M" >>> peptide_next_aa="A" protein="sp|P06396-2|GELS_HUMAN" num_tot_proteins="1" >>> num_matched_ions="11" tot_num_ions="16" calc_neutral_pep_mass="1096.591696" >>> massdiff="0.000470" num_tol_term="1" num_missed_cleavages="0" >>> num_matched_peptides="6184"> >>> <search_score name="xcorr" value="2.205"/> >>> <search_score name="deltacn" value="0.575"/> >>> <search_score name="deltacnstar" value="0.000"/> >>> <search_score name="spscore" value="350.4"/> >>> <search_score name="sprank" value="1"/> >>> <search_score name="expect" value="4.94E-03"/> >>> <analysis_result analysis="peptideprophet"> >>> <peptideprophet_result probability="1.0000" >>> all_ntt_prob="(0.0000,1.0000,1.0000)"> >>> <search_score_summary> >>> <parameter name="fval" value="5.5754"/> >>> <parameter name="ntt" value="1"/> >>> <parameter name="nmc" value="0"/> >>> <parameter name="massd" value="0.429"/> >>> <parameter name="isomassd" value="0"/> >>> <parameter name="RT" value="1372.21"/> >>> <parameter name="RT_score" value="0.02"/> >>> </search_score_summary> >>> </peptideprophet_result> >>> </analysis_result> >>> </search_hit> >>> </search_result> >>> </spectrum_query> >>> >>> See attached the sequence alignment of all isoforms of GELS_HUMAN, you >>> can see that this peptide matches the canonical form as well as all >>> isoforms hence the num_tot_proteins should be = "4" and protein should >>> be ="sp|P06396|GELS_HUMAN" with <alternative_protein protein=" >>> sp|P06396-2|GELS_HUMAN"/>, >>> <alternative_protein protein="sp|P06396-3|GELS_HUMAN"/> , >>> <alternative_protein protein="sp|P06396-4|GELS_HUMAN"/> >>> >>> I am happy to share all the comet.pep.xml & interact.pep.xml files along >>> with the fasta database via Box folder. >>> >>> Can someone please help me understand if this is expected behavior? if >>> so, how i can fix this? >>> >>> Regards >>> Vidya >>> >>> -- >>> 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 post to this group, send email to [email protected]. >>> Visit this group at https://groups.google.com/group/spctools-discuss. >>> To view this discussion on the web visit >>> https://groups.google.com/d/msgid/spctools-discuss/6b292366-55e1-4fe2-9994-ea9fff3d97a9%40googlegroups.com >>> <https://groups.google.com/d/msgid/spctools-discuss/6b292366-55e1-4fe2-9994-ea9fff3d97a9%40googlegroups.com?utm_medium=email&utm_source=footer> >>> . >>> For more options, visit https://groups.google.com/d/optout. >>> >> -- >> You received this message because you are subscribed to a topic in the >> Google Groups "spctools-discuss" group. >> To unsubscribe from this topic, visit >> https://groups.google.com/d/topic/spctools-discuss/Iq4P_h0DizM/unsubscribe >> . >> To unsubscribe from this group and all its topics, send an email to >> [email protected]. >> To post to this group, send email to [email protected]. >> Visit this group at https://groups.google.com/group/spctools-discuss. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/spctools-discuss/CAJqD6ENwEimtBu3twOwHUPzSQ_m0Q2bzNpqiYcghbpaoRqPUkA%40mail.gmail.com >> <https://groups.google.com/d/msgid/spctools-discuss/CAJqD6ENwEimtBu3twOwHUPzSQ_m0Q2bzNpqiYcghbpaoRqPUkA%40mail.gmail.com?utm_medium=email&utm_source=footer> >> . >> For more options, visit https://groups.google.com/d/optout. >> > -- > 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 post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/spctools-discuss. > To view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/CAD%3DmzOLMzpTvL7-L1zhASOU3_etz7WdqEczDrGO68RsRtNMHRA%40mail.gmail.com > <https://groups.google.com/d/msgid/spctools-discuss/CAD%3DmzOLMzpTvL7-L1zhASOU3_etz7WdqEczDrGO68RsRtNMHRA%40mail.gmail.com?utm_medium=email&utm_source=footer> > . > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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