mProphet Modeling for MS1 XIC Analysis

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.


Aaron Robinson

aaron robinson responded:  2018-09-24

Can anyone comment on this?

Brendan MacLean responded:  2018-10-04

We have not done the work to prove the validity of doing this, but I have heard of it being done successfully. We make no guarantees.

It is probably worth a try to see how it works for you.