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.
