Thank you On Thursday, August 14, 2014 3:03:05 PM UTC-7, Luis wrote: > > 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] <javascript:>> 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] <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. >> > >
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