Hello, I am trying to validate protein assignment with Protein Prophet using Libra protein ratios. I am trying to do this with two different methods of normalizing, against the sum of reagent profiles and against TIC. You can find the two condition files I have generated in an attachment. This should, in theory, give me different intensity values, however, I obtain identical quantitation files. How is this possible?
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condition_TMT10plex_TICNormalization.xml
Description: XML document
conditionTMT10plex_SumOfRegeantsNormalization.xml
Description: XML document
