Hello, This document may help you, especially the section on "Details about what Libra does" :
http://sourceforge.net/p/sashimi/code/HEAD/tree/trunk/trans_proteomic_pipeline/src/Quantitation/Libra/docs/libra_info.html?format=raw Cheers, --Luis On Thu, Aug 14, 2014 at 11:19 AM, SS <[email protected]> wrote: > Hi > > > I am wondering how the final ratio of reporter ions is calculated at a > protein level when there are multiple non-redundant unique peptides with > tags are identified. > > Thank you, > > SS > > > On Saturday, May 17, 2014 11:27:16 AM UTC-7, Luis wrote: > >> 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. > -- 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.
