The modified peptides and sites identified from proteome database search using Proteome Discoverer can be summarized using PTM-Summarizer. This tool requires Peptide Spectrum Match (PSM) output file from PTM search with "ptmRS: Best Site Probabilities" column and the proteome database (FASTA format) used for the search.
How to run PTM-Summarizer:
PTM-Summarizer>python PTM_summarizer.py SARS_CoV2_Mulit-PTM_PSMs_PTMs.txt HumanRefSeq_GCF_000001405.39_GRCh38.p13_protein_refseq109_formated.fasta
The output of this tool consists of;
- List of modified site information for each modification in each protein (Infile_UniqueProteinSite.txt)
- Summary of the modification specific sites (Infile_summary.txt)
- Input file for Upset plot (ForUpset.txt)
- Modification and site specific test file (ex: Acetyl_K.txt, Crotonyl_K.txt etc)
For any enquiries please contact: [email protected] and [email protected] or [email protected]