This directory contains Python scripts demonstrating how to programmatically query the DigestedProteinDB database via its public REST API. DigestedProteinDB is a high-performance database of theoretically digested proteins, designed to support peptide identification in mass spectrometry (MS) experiments.

• Python 3.7+
• requests library

Install the dependency with:

pip install requests

A self-contained example script that demonstrates the three most common query patterns against the DigestedProteinDB REST API endpoint:

GET https://digestedproteindb.pbf.hr/search.php

The API returns JSON with the following structure:

{
    "totalResult": 431,
    "page": 1,
    "pageSize": 10,
    "duration": "00:00:00.024",
    "memory": "2012 MB",
    "result": [
        {
            "1247.5001": [
                {
                    "seq": "SSSTSSTDSTTST",
                    "acc": ["A0A822EEP4"]
                }
            ]
        }
    ]
}

• result — list of objects keyed by the peptide mass; each value is a list of peptides
• seq — peptide amino acid sequence (single-letter code)
• acc — list of UniProt accession numbers of proteins containing this peptide

python example_rest_api.py

Expected output (truncated):

=================================================================
Example 1: search by mass range (1247.50 – 1247.52)
=================================================================
Total results : 118
Page          : 1 / pageSize=5
Duration      : 00:00:00.001
Memory        : 2012 MB
-----------------------------------------------------------------
  Mass: 1247.5001     Sequence: SSSTSSTDSTTST        Acc: A0A822EEP4
  Mass: 1247.5002     Sequence: SWGDHNCHHR           Acc: M7BXC7
  ...

The helper functions can be imported and used directly in your own scripts or Jupyter notebooks:

from example_rest_api import search_by_mass, search_by_peptide

# Query a narrow mass window around a measured MS peak
results = search_by_mass(mass1=1500.70, mass2=1500.72, page_size=100)

# Or search by sequence with a custom tolerance
results = search_by_peptide("ALELFR", tolerance_da=0.01, page_size=50)

for item in results["result"]:
    for mass, peptides in item.items():
        for pep in peptides:
            print(pep["seq"], pep["acc"])

Full API documentation is available at:
https://digestedproteindb.pbf.hr/rest.php