combine fractions, replicates and different parameters

[Asif Ahmed]

Hi, 

I have two treatment groups and want to identify (& quantify) the peptides.

1. Metabolic label with N15 sample (3 replicates)

2. Normal N14 sample (3 replicates).

I extracted & digested the protein using S-trap kit and fractionated each sample into 8 fractions using Pierce high Ph fractionation kit, resulting 48 samples (2 Treatment group X 3 replicates X 8 Fractions) in total. 

I matched all of the data using Comet and X!Tandem, using two different (N14 and N15) parameters - which produced separate .mzML files for each.

Now I am confused how to combine all fractions, replicates and parameters into single result file. 

I am thinking to go for N14 parameter first - 

merge all fractions and replicates of comet/tandem in peptide prophet, 

merge peptide-prophet results of Comet and Tandem in i-prophet afterwards.

Do the same for N15 parameter, and combine i-prophets of N15 and N14 in protein prophet.

I will run Xpress later on, for quantification.

Can you please advice me is it OK? or any other way to do?

ASIF