Hello Piero, I have not looked at this, but I suspect it could be dataset related. Localizations at position 1 could indicate peptide extensions, and I am not sure why positions 3 and 4 are so populated. Have you tried looking at this while controlling for peptides of various lengths? If you can post your data in a share I could take a closer look.
Thanks, -David On Sun, Jul 8, 2018 at 11:51 PM, Piero Giansanti <[email protected]> wrote: > 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]> >> 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/grou >>>>>>>>> p/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. > 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.
