Digested Protein DB REST API

Endpoint

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

Retrieves peptide/protein ptmSearchResults filtered by a specific mass range or peptide query.
Returns ptmSearchResults in JSON format.

Query Parameters

Name	Type	Required	Description
`mass1`	float	Yes (or peptide)	Lower bound of the mass range (inclusive). If `peptide` parameter is used, `mass1` and `mass2` will be calculated from its mass.
`mass2`	float	Yes (or peptide)	Upper bound of the mass range (inclusive).
`peptide`	string	No	Peptide sequence. If provided, calculates `mass1` and `mass2` for the sequence.
`page`	integer	No	Page number for pagination. Default is `1`.
`pageSize`	integer	No	Number of ptmSearchResults per page. Default is `10`. Maximum allowed is `1000`.

Request Example

GET https://digestedproteindb.pbf.hr/search.php?mass1=1247.5&mass2=1247.7&page=1&pageSize=10

Response

Content-Type: application/json

Response structure:

{
    "totalResult": 431,
    "memory": "2008 MB",
    "duration": "00:00:54.966",
    "page": 1,
    "pageSize": 10,
    "result": [
        {
            "1247.6087": [
                {
                    "seq": "SYTFHFKYR",
                    "acc": [
                        "A0A0C9U8Z7",
                        "A0A0C9UZS6",
                        "A0A0C9UMQ1"
                    ]
                },
                {
                    "seq": "AIGFDGWHAFK",
                    "acc": [
                        "A0A8J3B0H4",
                        "A4G425",
                        "A0A4R6G671"
                    ]
                }
                // ... more peptide objects for this mass
            ]
        }
        // ... more mass keys and peptide arrays
    ]
}

Top-level fields:

totalResult – Total number of matching entries.
memory – Memory usage for the request.
duration – Query execution time.
page – Current page number.
pageSize – Number of ptmSearchResults per page.
result – Array of objects, each key is the peptide mass (as a string/number), value is an array of peptide objects:
- seq – Peptide sequence
- acc – List of protein accession numbers for this peptide

Error Responses

400 Bad Request – Returned if required parameters are missing or invalid.
{"error": "Peptide is required"}
500 Internal Server Error – Returned if the server encounters an error.
{"error": "Error details"}

Example cURL Request

curl "https://digestedproteindb.pbf.hr/search.php?mass1=1247.5&mass2=1247.7&page=1&pageSize=10"

Usage Notes

Use either mass1/mass2 for direct mass range filtering or peptide for sequence-based mass search.
Each entry in result is an object with the mass as the key, mapping to an array of peptide/protein hitPeptides.
The endpoint is optimized for read-only, high-performance querying.
Maximum pageSize is 1000.

Implementation Note (Java server method)

private void handleBySearch(HttpServerExchange http) {
    if (http.isInIoThread()) {
        http.dispatch(this::handleBySearch);
        return;
    }
    Map<String, String> params = createParam(http);

    try {
        String peptide = params.getOrDefault("peptide", "");
        if (peptide.isEmpty()) {
            sendJsonResponse(http, StatusCodes.BAD_REQUEST,
                    "{\"error\": \"Peptide is required\"}");
            return;
        }
        double mass1 = BioUtil.calculateMassWidthH2O(peptide);
        double mass2 = mass1;
        int page = Integer.parseInt(params.getOrDefault("page", "1"));
        int pageSize = Integer.parseInt(params.getOrDefault("pageSize", "1000"));

        searchByMass(http, mass1, mass2, page, pageSize);
    } catch (Exception e) {
        sendJsonResponse(http, StatusCodes.INTERNAL_SERVER_ERROR,
                "{\"error\": \"" + e.getMessage() + "\"}");
    }
}

For peptide queries, mass is computed server-side and search is performed for that precise mass.

Digested Protein DB REST API Documentation

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