Hello David, I am back with an additional question :) I have noticed that in my data set the vast majority of the mass shifts (outside the +/-0.02 Da window) are localized withing the fist 4 residues (from the n-term), except for position #2. This is for a localization probability > 0.75, but it does not change if I use > 0.9, except for # 3 and 4 that tend to be slightly less frequent that position #1. Have you noticed the same?
Thanks -Piero <https://lh3.googleusercontent.com/-pd1QudrhPDQ/W0MEr8yj6ZI/AAAAAAAAALQ/aPqqd0KQjBcjqI5-h7PAFnm5TrhL4dQXwCLcBGAs/s1600/loc.jpg> On Monday, June 11, 2018 at 8:57:53 PM UTC+2, David Shteynberg wrote: > > 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] > <javascript:>> 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] <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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