Hi Adam, Yes, that is the column where the weight is found when displaying peptides. One last item: can you check if all of those spectra that correspond to those peptides contain TMT peaks?
If you are able to share your protXML file, I could have a closer look. Cheers, --Luis On Tue, Nov 14, 2017 at 3:06 PM, Adam R <[email protected]> wrote: > Hi Luis, > > Are you referring to the "%Coverage/Weight" column that is in the prot.xml > file when you say "peptide be matched to the protein via weight > 0.5" ? I > selected the protein in the prot.xml to bring up the view with all of the > peptides ID'd. All the peptides that I see in this window (11 of them) have > 1.00 right next to the yellow bar under this column "%Coverage/weight" Is > there another weight value written that I am missing? > > Best, > > Adam > > > On Friday, November 10, 2017 at 6:04:57 PM UTC-6, Luis wrote: >> >> Hi Adam, >> >> A further requirement is that the peptide be matched to the protein via a >> weight > 0.5 (i.e. used in the calculation of the protein probability as >> assigned by ProteinProphet). Let us know if this is not the case and we >> can delve into it further. >> >> Cheers, >> --Luis >> >> >> On Fri, Nov 10, 2017 at 2:05 PM, Adam R <[email protected]> wrote: >> >>> Hi Luis, >>> >>> Yes, about one quarter of them have prob <0.5 but for the other ones >>> with prob and iprob >0.5 I'm not sure why I'm not seeing this in the >>> quantitation.tsv... >>> >>> Best, >>> >>> Adam >>> >>> On Friday, November 10, 2017 at 3:48:16 PM UTC-6, Luis wrote: >>>> >>>> Hi Adam, >>>> >>>> Hard to tell exactly without looking at your file. One thing to note >>>> is that Libra will only use psm's with PeptideProphet probabilities > 0.5; >>>> it does not take into account iProphet probabilities (yet). Maybe this >>>> explains some of the ones that are missing? >>>> >>>> Cheers, >>>> --Luis >>>> >>>> On Fri, Nov 10, 2017 at 1:14 PM, Adam R <[email protected]> wrote: >>>> >>>>> Hi Luis, >>>>> >>>>> I just took a look at the quantitation.tsv file. Interestingly enough >>>>> for the protein I am looking at there is only one peptide listed in this >>>>> table, however, when looking at the ipro.pep.xml file for peptides of this >>>>> protein I have eleven of them, all with ipro > 0.99 and some with >>>>> intensities of 0 in the competitive inhibitor-treated channel...not sure >>>>> what to make of this. Other proteins are listed with peptides and have the >>>>> yes/no indicator for "kept?" and show intensities, in some cases zero... >>>>> Are there other parameters that are preventing these peptides from showing >>>>> up in the quantitation.tsv file? >>>>> >>>>> Best, >>>>> >>>>> Adam >>>>> >>>>> On Friday, November 10, 2017 at 2:58:08 PM UTC-6, Luis wrote: >>>>>> >>>>>> >>>>>> I forgot to add that once the protein quantitation is done, Libra >>>>>> will also produce a "quantitation.tsv" file that you can use downstream >>>>>> for >>>>>> re-evaluating protein ratios with any statistical(s) test you wish -- say >>>>>> in R, Excel, etc. The file structure is fairly straightforward: protein >>>>>> ratios and errors, followed by those of its peptides, including adjusted >>>>>> intensities and a kept flag (used/not used in quant). >>>>>> >>>>>> ---Luis >>>>>> >>>>>> >>>>>> On Fri, Nov 10, 2017 at 12:49 PM, Adam R <[email protected]> wrote: >>>>>> >>>>>>> Thanks Luis for the response! >>>>>>> >>>>>>> Adam >>>>>>> >>>>>>> On Friday, November 10, 2017 at 2:30:33 PM UTC-6, Luis wrote: >>>>>>>> >>>>>>>> Hi Adam, >>>>>>>> >>>>>>>> We have plans to add some of these features to Libra as well as >>>>>>>> others, but none are ready at the moment. >>>>>>>> >>>>>>>> One thing you could try is to select to normalize against the sum >>>>>>>> of the reagent profiles (instead of selecting a channel to quantify >>>>>>>> against) -- this should give you a value for all channels, even when >>>>>>>> some >>>>>>>> are missing. >>>>>>>> >>>>>>>> Cheers, >>>>>>>> --Luis >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Nov 10, 2017 at 11:44 AM, Adam R <[email protected]> wrote: >>>>>>>> >>>>>>>>> Is there a way to retain quantified peptides for the protein quant >>>>>>>>> with Libra? I understand that Libra discards peptides without all >>>>>>>>> channels...what about in instances where the you expect there to be >>>>>>>>> little >>>>>>>>> or no intensity? I have data from pulldowns where we don't expect to >>>>>>>>> see >>>>>>>>> much of the protein in the presence of a competitive inhibitor, so in >>>>>>>>> this >>>>>>>>> case it would be of use to retain such quants where the intensity is >>>>>>>>> zero >>>>>>>>> in the presence of inhibitor but several thousands in the pulldown >>>>>>>>> channel...Is there a way to toggle on/off the peptides that are used >>>>>>>>> for >>>>>>>>> the protein quant in Libra? I'm thinking along the lines like in >>>>>>>>> Xpress >>>>>>>>> where you can toggle whether or not a peptide is used for the protein >>>>>>>>> quant. Is there also a way to modify the number of standard >>>>>>>>> deviations that >>>>>>>>> are used to discard a peptide from being used in the protein quant? >>>>>>>>> >>>>>>>>> Best, >>>>>>>>> >>>>>>>>> Adam >>>>>>>>> >>>>>>>>> -- >>>>>>>>> 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. 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