Tanja Holstein

MegaPX is a fast and space-efficient tool for classifying de novo peptide sequences against large protein databases using k-mer-based methods and Bloom filters.

The paper introduces Peptonizer2000, a tool that improves taxonomic identification in metaproteomics by combining peptide scores and taxon links with statistical models, showing higher specificity and confidence.

This study benchmarks eight de novo peptide sequencing models on proteomics datasets to evaluate their performance and identify limitations in resolving sequence ambiguity.

MS2Rescore improves peptide identification and taxonomic specificity in metaproteomics by using machine learning-based rescoring, achieving lower false discovery rates with minimal sensitivity loss.

PathwayPilot is a web tool for visualizing and comparing metabolic pathways using metaproteomic data, demonstrating its effectiveness in analyzing enzyme expression shifts in gut microbiota under caloric restriction.

MultiStageSearch improves viral strain identification by combining proteomic and genomic databases, outperforming existing methods without relying on NCBI taxonomy.

PepGM infers viral taxonomy from proteomic data with confidence scores, showing strain-level resolution and accurate species-level assignments in some cases.