MegaPX: fast and space-efficient peptide assignment method using IBF-based multi-indexing
preprint · bioRxiv · 2025
| Date | 2025-04-19 |
| Type | preprint |
| Venue | bioRxiv |
| Publisher | openRxiv |
| Contribution | post-processor |
| DOI | 10.1101/2025.04.14.648734 |
| Citations (OpenAlex) | 0 |
Peer-reviewed version: MegaPX: fast and space-efficient peptide assignment method using IBF-based multi-indexing (2026-05-03, Bioinformatics)
Abstract
MotivationA central problem for metaproteomic analysis is the often-unknown taxonomic composition of the analyzed microbiomes. Using a database search, the standard approach requires prior knowledge of which proteins and taxa to include in the protein reference database or to use tailored metagenome-derived databases, which are expensive and error-prone in their generation. A possible strategy to circumvent this database search issue is de novo sequencing, where peptide sequences are directly identified from mass spectra. However, these sequences must still be mapped back to potentially extensive databases. Here, alignment-based approaches enable robust and precise results, with the potential drawback of high memory usage and long run times. ResultsWe present MegaPX, a software for rapidly classifying de novo peptide sequences against large protein databases. MegaPX implemented as a C++-based tool, uses an alignment-free, k-mer-based approach as a taxonomic classification method with the possibility of generating mutated reference databases for error-tolerant searching. It uses various algorithms, including interleaved Bloom filters, to efficiently compute approximate membership queries, ensuring fast processing times while querying and indexing large databases in a multi-indexing fashion. We demonstrate the potential of MegaPX by analyzing different samples, including metaproteomics, against extensive reference databases, highlighting its use as a fast screening tool. Availability and implementationMegaPXs source code and all related documentation files are freely available in a GitHub repository (https://github.com/rki-mf2/MegaPX) under the MIT License. Supplementary informationAll supplementary tables and figures are included at the end of the preprint.
Methods and tools
- MegaPX: Alignment-free k-mer and interleaved Bloom filter tool that rapidly assigns de novo peptide sequences to taxa in very large protein databases, for metaproteomics.
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