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] <javascript:>> > 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] <javascript:>. >> To post to this group, send email to [email protected] >> <javascript:>. >> 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.
