Hello Piero. The reason mass shift localizations are performed on all amino acids is to avoid any assumptions on the part of PTMProphet. The goal of PTMProphet in mass shift localization mode is to simply localize the mass shift without assuming anything else about the modification. This can help the user discover rare modifications. For instance, phosphorylation on D is listed as a rare modification in unimod.
Cheers, -David On Mon, Jun 11, 2018 at 9:40 AM, Piero Giansanti <[email protected]> wrote: > 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]> >> 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. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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