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] <javascript:>> > 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] <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. 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.
