|mProphet Modeling for MS1 XIC Analysis||aaron robinson||2018-09-17|
I was wondering if you can do mProphet modeling for MS1 XIC analysis of DDA data in Skyline.
Is this something that you guys have tried? I don't see why it wouldn't work and it would make MS1 quant a bit better/more accurate.
I've tried it by adding decoy peptides and training a model and it seems like it works ok...have you guys tried this at all/can you give me any feedback on if it is a reasonable way of filtering MS1 quant data...It seems like it would be the preferred way of analysis for MS1 data, especially since you can set a q-value filter for group comparison analysis.