Thats interesting. I went back to check my Xtandem parameters & this parameter is set to 'no' so it seems there is some other native logic within Xtandem that controls this behavior.
<note type="input" label="protein, quick acetyl">no</note> Regards Vidya On Fri, Jun 7, 2019 at 2:19 PM Jimmy Eng <[email protected]> wrote: > 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 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/CAJqD6EOK4YH25qE%3DQiZcr6mGnNSJ1%3DG9jFQM%3DQDdM2dzS44oUQ%40mail.gmail.com > <https://groups.google.com/d/msgid/spctools-discuss/CAJqD6EOK4YH25qE%3DQiZcr6mGnNSJ1%3DG9jFQM%3DQDdM2dzS44oUQ%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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