Hello David, Just tried with TPP 5.1.0 (linux), but same problem as you can see below. Is there a way to get hands on the version you have used? :)
<spectrum_query start_scan="3214" assumed_charge="2" spectrum="01928_GA1_P020123_S00_R01_R1.03214.03214.2" end_scan="3214" index="6" precursor_neutral_mass="1247.5479" retention_time_sec="1120.817"> <search_result> <search_hit peptide="GGMNGASPPTSQK" massdiff="0.9869" calc_neutral_pep_mass="1246.5610" peptide_next_aa="D" num_missed_cleavages="0" num_tol_term="2" num_tot_proteins="1" tot_num_ions="24" hit_rank="1" num_matched_ions="10" protein="sp|Q62234|MYOM1_MOUSE" peptide_prev_aa="R" is_rejected="0" protein_descr="Myomesin-1 OS=Mus musculus OX=10090 GN=Myom1 PE=1 SV=2"> <modification_info modified_peptide="G[58]GM[147]NGASPPTSQK"> <mod_aminoacid_mass position="1" mass="58.00836"/> <mod_aminoacid_mass position="3" mass="147.0354"/> </modification_info> <search_score name="hyperscore" value="21.034"/> <search_score name="nextscore" value="18.157"/> <search_score name="expect" value="1.601e-03"/> <analysis_result analysis="peptideprophet"> <peptideprophet_result probability="0.9995" all_ntt_prob="(0.9840,0.9981,0.9995)"> <search_score_summary> <parameter name="fval" value="5.8278"/> <parameter name="ntt" value="2"/> <parameter name="nmc" value="0"/> <parameter name="massd" value="0.987"/> </search_score_summary> </peptideprophet_result> </analysis_result> <analysis_result analysis="ptmprophet"> <ptmprophet_result prior="0.0769231" ptm="PTMProphet_ABCDEFGHIJKLMNOPQRSTUVXWYZ0.9869" ptm_peptide="G(0.000)G(0.000)M(0.000)N(0.000)G(0.000)A(0.000)S(0.000)P(0.000)P(0.000)T(0.000)S(0.000)Q(0.000)K(0.000)"> <mod_aminoacid_probability position="1" probability="0.000"/> <mod_aminoacid_probability position="2" probability="0.000"/> <mod_aminoacid_probability position="3" probability="0.000"/> <mod_aminoacid_probability position="4" probability="0.000"/> <mod_aminoacid_probability position="5" probability="0.000"/> <mod_aminoacid_probability position="6" probability="0.000"/> <mod_aminoacid_probability position="7" probability="0.000"/> <mod_aminoacid_probability position="8" probability="0.000"/> <mod_aminoacid_probability position="9" probability="0.000"/> <mod_aminoacid_probability position="10" probability="0.000"/> <mod_aminoacid_probability position="11" probability="0.000"/> <mod_aminoacid_probability position="12" probability="0.000"/> <mod_aminoacid_probability position="13" probability="0.000"/> </ptmprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> On Friday, May 18, 2018 at 6:58:36 PM UTC+2, David Shteynberg wrote: > > Hello Piero, > > It appears that the version of PTMProphet in Philosopher is a bit out of > date. The latest TPP version is 5.1.0, and PTMProphet has been updated > with bugfixes and new features in the meantime. I have run my latest > PTMProphet code (targeted for the 5.2.0 version of TPP) on your data. For > the PSMs matching this peptide I cannot replicate the issue you've > reported. Instead, PTMProphet seems to be positioning the mass > modification on the Asparagine in your peptide as you should see in the > following result file: > > > https://www.dropbox.com/s/z3xf379ulljr3rr/01928_GA1_P020123_S00_R01_R1.PTMPro.pep.xml?dl=0 > > Thanks for your interest in PTMProphet. > > Cheers! > > -David > > On Fri, May 18, 2018 at 8:40 AM, Piero Giansanti <p.gians...@gmail.com > <javascript:>> wrote: > >> Hello David, >> >> I am using PTMprophet via philosopher, and from the xml output it seems >> it is this version >> TPP v5.0.1 Post-Typhoon dev, Build 201706282113-exported (Linux-x86_64) >> >> Regarding the settings, I am using --massdiffmode --mztol 0.01. The mass >> tolerance is not exactly the one used for the database search (20 ppm), but >> it should be somehow close to it. >> >> Here https://ufile.io/wiqqb the mzML, pepXML and the output I generated. >> >> Thanks >> >> >> On Friday, May 18, 2018 at 4:21:27 PM UTC+2, David Shteynberg wrote: >>> >>> Hello Piero, >>> >>> Thank you for trying the software. This is indeed an unusual result. >>> Can you tell me which version of PTMProphet you are using and how you are >>> running the tool? Is it possible for you to post your pepXML file and data >>> file online for me to download and test this particular ID? >>> >>> Cheers, >>> -David >>> >>> On Fri, May 18, 2018 at 1:53 AM, Piero Giansanti <p.gians...@gmail.com> >>> wrote: >>> >>>> Hi, >>>> >>>> I am using PTMprophet to localize the set of modifications (i.e. mass >>>> shifts) identified by running an open search with MSfragger, but I have >>>> some doubt regarding the interpretation of the output. >>>> In particular, MSfragger identified this peptide >>>> *GG(ox)MNGASPPTSQK* >>>> with a mass shift of 0.9869 Da, which match to the following >>>> modification according to Unimod >>>> 0.9840:Deamidated (Deamidation), 0.9840:Asn->Asp (Asn->Asp >>>> substitution), 0.9840:Gln->Glu (Gln->Glu substitution). >>>> >>>> Of these 3 only the first 2 are possible (there is no Q in the >>>> sequence, so there cannot be any Gln->Glu substitution). >>>> >>>> Now, the output of PTMprophet is as follows: >>>> >>>> *G(0.000)G(0.000)M(0.000)N(0.000)G(0.000)A(0.000)S(0.000)P(0.000)P(0.000)T(0.000)S(0.000)Q(0.000)K(0.000)* >>>> >>>> Is a probability always 0 somehow an expected behavior? How do I >>>> interpret this? Am I right to say that the 0.9869 Da shift cannot be >>>> localized to any residues? >>>> My concerns comes from the fact that even if the mod cannot be >>>> localized, I would have expected to get a probability of (~0.008, i.e. >>>> 100/length of the peptides) for each residues... >>>> >>>> -- >>>> 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-discu...@googlegroups.com. >>>> To post to this group, send email to spctools...@googlegroups.com. >>>> Visit this group at https://groups.google.com/group/spctools-discuss. >>>> 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 spctools-discu...@googlegroups.com <javascript:>. >> To post to this group, send email to spctools...@googlegroups.com >> <javascript:>. >> Visit this group at https://groups.google.com/group/spctools-discuss. >> 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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