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/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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