Pieter Verschaffelt

Effects of UniProtKB restructuring and taxonomic database restrictions on downstream Unipept peptide-centric profiling

The paper examines how changes to UniProtKB and taxonomic restrictions affect metaproteomics analysis, finding reduced peptide mapping coverage but stable dominant taxonomic profiles.

The Peptonizer2000: bringing confidence to metaproteomics

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.

Direct construction of sparse suffix arrays with Libsais

The paper introduces a method to directly construct sparse suffix arrays with reduced memory and time usage, using a text encoding and Libsais library for bioinformatics applications.

Machine learning-based rescoring with MS2Rescore boosts peptide identification and taxonomic specificity in metaproteomics

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: A User-Friendly Tool for Visualizing and Navigating Metabolic Pathways

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.

Unipept in 2024: Expanding metaproteomics analysis with support for missed cleavages, semi-tryptic and non-tryptic peptides

The paper updates the Unipept software to support analysis of non-tryptic and semi-tryptic peptides, improving performance while maintaining accuracy.

Unipept Desktop 2.0: construction of targeted reference protein databases for proteogenomics analyses

Unipept Desktop 2.0 enables the construction of targeted protein reference databases for proteogenomics analyses, improving taxonomic and functional resolution while enhancing privacy and analysis speed.

UMGAP: the Unipept MetaGenomics Analysis Pipeline

UMGAP is a metagenomics analysis pipeline that provides fast, memory-efficient, and accurate taxonomic profiling of shotgun metagenomes using protein code regions.

Pout2Prot: an efficient tool to create protein (sub)groups from Percolator output files

Pout2Prot converts Percolator output files into protein group files compatible with Prophane, using weighted spectral counts and multiple grouping strategies.

MegaGO: a fast yet powerful approach to assess functional similarity across meta-omics data sets

MegaGO assesses functional similarity between meta-omics datasets using semantic GO term similarity, offering fast and scalable analysis.