That worked out, eventually :) I have an additional question though, which comes from the fact that the majority of the known mass shift in my data set has not been fully localized on a specific residue, even when spectra look OK-ish. My background is totally not bioinformatics/statistics, so this could be a silly question :) ...
Anyway, is there a reason why the localization of the mass shift is performed differently compared the the localization of a known modification? What I mean is that (as far as I understood), when one wants to perform localization on (phospho.STY)PEPTIDE, PTMprophet will simply return T4 as the phosphorylated residues (it will not even try to look at D6), but when trying on (+79.966Da)PEPTIDE, PTMprophet will not focus on just T and D, but rather 'look' at the entire sequence. Wouldn't this 'focusing' speed up the time need for the localization, and boost the localization rate? Thanks -Piero On Tuesday, May 22, 2018 at 6:43:33 PM UTC+2, 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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