OPTM-Analysis

This workflow aims to quantify oxidative stress induced post-translational modifications sites, peptides, and proteins occupancy from high-throughput proteomics raw files.

Test data can be found at: https://drive.google.com/drive/folders/1f_HVhH9rhb9l1ZOesmU8CGO_lod4tQsO?usp=sharing

dtaselect_read_step1.R

Run dtaselect_read_step1.R in the directory with the DTA files.
Type:

Rscript dtaselect_read_step1.R

dtaselect_merge_step2.R

Type:

Rscript dtaselect_merge_step2.R mass_shift site_mass_shift output_file

optm_calculation_step3.R

Upload the peptides to peptidematch, and download the result-file-from-PIR.txt.
https://research.bioinformatics.udel.edu/peptidematch/batchpeptidematch.jsp
To calculate O-PTM Occupancy
Type:

Rscript optm_calculation_step3.R input_file multiple_peptide_match_data