chinmayank22/ptm-site-validator

Validation of modified amino acid sites in peptide sequences by identifying immonium ions in the raw spectra (.mgf format)

PTM-Site-Validator

PTM site validator: Amino acid sites found to have post-translational modification (PTM) from Proteome Discoverer searches can be validated by identifying modification site specific immonium ion. Note: The tool requires raw files used for the search in .mgf format in the same folder where the PTM site validator is present.

For any enquiries please contact: [email protected] or [email protected]

How to use PTM-Site-Validator

Command line argument:

ptm_site_validator>python PTM_site_validator.py -i PSMs.txt -ft 0.02 -r Path_to_raw_data

positional arguments:
  -i          Path to the PSM file from PTM search in Proteome Discoverer.
  -ft         Immonium ion (m/z) search tolerance in Dalton. It is recommended to keep the same search
              tolerance used in the main search.
  -r          Path to the folder in which raw files are stored in .mgf format.

optional arguments:
  -h, --help  show this help message and exit