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Protein Digestion

Protein Digestion

Protein digestion begins in the stomach, where the highly acidic environment can easily disrupt protein structure by exposing the peptide bonds of polypeptide chains. After polypeptide chains are broken into individual amino acids by a series of digestive enzymes, the amino acids are transported to the liver via the bloodstream to produce energy.

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Updated: Jun 28, 2026

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

Published on: August 19, 2025

DigestedProteinDB: A Compact and Scalable Key-Value Database for In Silico Peptide Digestion and Mass-Based Search.

Toni Cvrljak¹, Janko Diminic², Jurica Zucko²

¹Faculty of Mining, Geology and Petroleum Engineering, University of Zagreb, 10000 Zagreb, Croatia.

Journal of Proteome Research

|June 26, 2026

Summary

This summary is machine-generated.

DigestedProteinDB offers fast and compact storage for in silico-digested peptides, enabling efficient mass spectrometry analysis. This key-value database accelerates proteomics and biotyping by providing rapid access to large peptide collections.

Keywords:

RocksDB UniProt bioinformatics in silico digestion mass spectrometry peptide database peptide mass fingerprinting protein identification

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Published on: October 24, 2025

Area of Science:

Bioinformatics
Computational Biology
Mass Spectrometry

Background:

Efficient comparison of experimental peptide masses with theoretical values is crucial for proteomics, microbial biotyping, and MS imaging.
These analyses require fast and scalable access to large collections of in silico-digested peptides from evolving protein databases.

Purpose of the Study:

To present DigestedProteinDB, a compact and high-performance key-value database for peptides generated by enzymatic in silico digestion.
To optimize disk footprint and accelerate mass-range queries for large-scale peptide data.

Main Methods:

Implementation using RocksDB, a high-performance key-value store.
Incorporation of optimization layers: peptide mass discretization and multistage storage compression.
Benchmarking using 252 million UniProtKB protein sequences, generating 5.9 billion peptides.

Main Results:

DigestedProteinDB requires ~250 GB disk space and 16 GB system RAM for 5.9 billion peptides.
Database construction takes ~2 days.
End-to-end mass-range queries achieve a median latency of ~7 ms per query for 10,000 samples.

Conclusions:

DigestedProteinDB provides a compact and high-performance resource for mass spectrometry-based applications.
The database can be used as a standalone resource or integrated into bioinformatics pipelines.
Modular design allows rapid generation of new databases for various proteases, taxonomic subsets, or digestion parameters.