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.
