Hi, Libra gives you the results with the threshold applied only after you run protein prophet and the values are in a text file that is created in the folder you run the analysis. However those values are for each protein not the peptides. I use peptide level values so I apply the threshold myself after I export the data cheers gogce crynen On Mar 14, 1:17 pm, Davo <[email protected]> wrote: > In my LIBRA quantitation.tsv ouput, I see intensity values less than > the minimum threshold set in condition.xml (see below). Is my > condition file correct? When is this threshold applied? > > Since cutoff didn't seem to have been applied, I'd like to ensure that > the condition file is configured properly in case this indicates other > undetected issues with my setup. Thanks > -Dave > > Background info: Labeled 35ug peptides each with iTRAQ 8-plex reagents > (113, 114, 115, 116, 117, 118, 119). Acquired data using Agilent 6520 > QTOF in centroid only mode. Ran through XTandem. Ran Libra using cmd > line, set Peptide prophet probability 0.85 (<0.05 error), used > condition.xml (see below). > > <?xml version="1.0" encoding="UTF-8"?> > <SUMmOnCondition> > <fragmentMasses> > <reagent mz="113.1" /> > <reagent mz="114.1" /> > <reagent mz="115.1" /> > <reagent mz="116.1" /> > <reagent mz="117.1" /> > <reagent mz="118.1" /> > <reagent mz="119.1" /> > </fragmentMasses> > <isotopicContributions> > <contributingMz value="1"> > <affected mz="2" correction="0.0689" /> > <affected mz="3" correction="0.0022" /> > </contributingMz> > <contributingMz value="2"> > <affected mz="1" correction="0.0094" /> > <affected mz="3" correction="0.059" /> > <affected mz="4" correction="0.0016" /> > </contributingMz> > <contributingMz value="3"> > <affected mz="1" correction="0" /> > <affected mz="2" correction="0.0188" /> > <affected mz="4" correction="0.049" /> > <affected mz="5" correction="0.001" /> > </contributingMz> > <contributingMz value="4"> > <affected mz="2" correction="0" /> > <affected mz="3" correction="0.0282" /> > <affected mz="5" correction="0.039" /> > <affected mz="6" correction="0.0007" /> > </contributingMz> > <contributingMz value="5"> > <affected mz="3" correction="0.0006" /> > <affected mz="4" correction="0.0377" /> > <affected mz="6" correction="0.0299" /> > </contributingMz> > <contributingMz value="6"> > <affected mz="4" correction="0.0009" /> > <affected mz="5" correction="0.0471" /> > <affected mz="7" correction="0.0188" /> > </contributingMz> > <contributingMz value="7"> > <affected mz="5" correction="0.0014" /> > <affected mz="6" correction="0.0566" /> > </contributingMz> > </isotopicContributions> > <massTolerance value="0.2" /> > <centroiding type="0" iterations="1" /> > <normalization type="1" /> > <targetMs level="2" /> > <output type="1" /> > <quantitationFile name="quantitation.tsv" /> > <minimumThreshhold value="15" /> > </SUMmOnCondition>
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