ucla-bd2k / optm-analysis

OPTM-Analysis

This workflow aims to extract and identify oxidative stress induced post-translational modifications sites, peptides, and proteins as well as quantify their occupancy from high-throughput proteomics raw files. In addition, the raw and processed files will be disseminated to the public available data repository “PRIDE Archive”.

Specifically, this workflow is divided into 4 major operation steps using Integrated Proteomics Pipeline, R programming, Protein Information Resource, and PRIDE Archive as listed below:

Step 1&2: To convert proprietary mass spectrometry result [.raw] file into [.ms1]/[.ms2] format and perform oxidative post-translational modification (O-PTM) identification using the Integrated Proteomics Pipeline (IP2).

Step 3: To quantify O-PTM occupancy from the search result of IP2 using R programming and Protein Information Resource (PIR). Example dataset can be downloaded from https://drive.google.com/drive/folders/1f_HVhH9rhb9l1ZOesmU8CGO_lod4tQsO?usp=sharing

Step 4: To submit the raw and result files to the proteomics data repository, PRIDE Archive, using ProteomeXchange Submission Tool.