Launching EpiProfile, quantifying different variants, and acylations

[Hassan Hijazi]

We are interested in quantifying histones and histone variants with their different modifications including ac, me, and different acylations from mice samples. We apply the label free quantification method.

For this, I have some questions:

1- From which specific folder shall I launch the Epiprofile.m file ? Does launching it from EpiProfile2.1_1Basic output results that meet our aim from using EpiProfile (i.e. does it account for all variants, for acylations beyond the acetylation?)

I modified the paras text file as follows:

[EpiProfile]
% the datapath of raw files
raw_path=C:\Users\hh268586\Downloads\raw

% 1: Human, 2: Mouse
norganism=2

% 1: histone_LFQ, 2: histone_SILAC, 3: histone_13CD3, 4: histone_15N, 5: histone_13C2, 6: histone_D3
nsource=1

% if histone_LFQ, 0: light only, 1: heavy R_no light, 2: heavy K and heavy R_no light
% if histone_SILAC, 0: heavy R, 1: heavy K and heavy R
% if histone_15N, 0: 14N light Mods, 1: 15N light Mods, 2: 14N heavy Mods, 3: 15N heavy Mods, 4: 0+1, 5: 0+3
nsubtype=0

2- I identified histones peptides containing H3K27ac and Epiprofile quantifies this PTM as zero, can you please highlight the problem in the parameter file, maybe?

Here is the output files

https://drive.google.com/drive/folders/1mmgWJwAfcHKQQUaWwPv_MPsMmq_3POar?usp=sharing