Hi, I am currently analyzing an iTRAQ experiment with 7 biological replicates. The analysis of the individual replicates works very nicely with the TPP, using the LIBRA quantitation. Two things,however, I was curious about. First of all, the Libra tsv file including all the quantitation data for each run does list one protein per quantitation result. In the proteinprophet results file, some of these proteins are part of protein groups, so why are not all proteins listed in the libra tsv file. Second, i was wondering whether there is a software tool already that allows for the analysis of multiple replicates when iTRAQ labels have been exchanged between replicates and does a statistical analysis based on all replicates.
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