I have tried to download the EpiProfile software on the website for several times in order to identify and make quantification of histone modification during experiment, but failed every time. Hence, I want to make aquisition of the method for EpiProfile software download, so as to make analysis of histone modification on my own. Thank you very much!

Dear ZF Yuan,
As per title, in the histone_ratios.xls and histone_ratios_SILAC.xls peptides H4_03_24_35 and H4_68_78 are not present, in the sense that EpiProfile seems to 'skip' those peptides. I am using the 'EpiProfile2.0_pr_pic' version.
Thank you.
Best Regards,
A. Vai

Dear Dr. Yuan,

Thanks for making the tool! It is awesome!

I have a difficulty running EpiProfile2.0_PlasmodiumFalciparum. I have Xcalibur and Matlab + necessary packages installed. When I run EpiProfile, it shows "convert RAW to MS1 and MS2" all the time (tested for > 5 hours on a powerful PC), without stopping or giving any error messages. When I check the working folder, I see that it creates MS1 and MS2 folders, MS1 contains one MS1 file, while MS2 is empty. I run 3 samples, but it seems that it is stuck in on the first sample. Do you know what could be the reason for that?

Hello,

I am using EpiProfile 2.2 to analyze PTMs in histones. I am writing to request your assistance in adding the succinyl modification to the software. I have modified GetMods.m to include the necessary information for this modification, but I am unsure which other files need to be updated.

Your guidance on this matter would be greatly appreciated.

Best regards,
Rafael

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

LC-MS_Liver_rep3
MS1 scans: 7910
MS2 scans: 63280
MS1 tol: 10 ppm: 13, 14, 15, 16, 17, 18, 30 ppm: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,
Error using horzcat
Dimensions of arrays being concatenated are not consistent.

Error in get_nDAmode (line 60)
cur_ix = [0 cur_ix cycle_len];%#ok

Error in EpiProfile (line 53)
[nDAmodes,windows] = get_nDAmode(raw_path,raw_names,startmz);

Thanks