If you find something strange with MSFragger itself, or TPP tools as run through Philosopher, we would happy to help. At the moment Philosopher has an older version of PTMProphet, but we will move to the latest release likely soon. Best, Alexey Nesvizhskii
On Tuesday, May 22, 2018 at 12:43:33 PM UTC-4, David Shteynberg wrote: > > If you are able to build the TPP the code has been checked into the SVN > repository. You can find the code here: > > > https://sourceforge.net/p/sashimi/code/HEAD/tree/trunk/trans_proteomic_pipeline/ > > If not I can send you a precompiled executable. Which linux flavor are > you using? > > -David > > On Tue, May 22, 2018 at 5:40 AM, Piero Giansanti <[email protected] > <javascript:>> wrote: > >> 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 <[email protected]> >>> 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 <[email protected] >>>>> > 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 [email protected]. >>>>>> To post to this group, send email to [email protected]. >>>>>> 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 [email protected]. >>>> To post to this group, send email to [email protected]. >>>> 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 [email protected] <javascript:>. >> To post to this group, send email to [email protected] >> <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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