Hello Bo, 1. Libra can only report on one reference reporter per single run. You can use the tab-delimited export (quantitation.tsv) and calculate those in Excel or using another script/tool. 2. Libra does not calculate p-values; we will look into adding this when we re-work the Libra interface later this year. 3. The quantitation is done by going back to the MS2 spectra and extracting the peak intensities; thus, you need to have the (mz[x]ml) data available. Hope this helps, --Luis
On Sat, May 17, 2014 at 2:32 AM, Bo <[email protected]> wrote: > Hi All, > I want to use Libra for iTRAQ-8plex quantification. But I wonder: > 1. Whether Libra can support to select different reporter as the reference > at the same time, such as 115/114, 116/114, 116/115. I don't find the > function so far. > 2. Does Libra calculate p-value for each protein ration? I don't find the > p-value for protein ratio in the output file (interact.ipro.prot.xls). Many > iTRAQ quantification software can provide p-value for protein ratio, such > as isobar, IsobariQ and ProteinPilot. > 3. If I don't have mzXML or mzML file, can Libra do iTRAQ quantification? > Many thanks and best regards! > Bo > > -- > 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 http://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 http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
