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]> 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]. > 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.
