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] <javascript:>> > 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/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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