Tim Van Den Bossche

The paper introduces mzQC, a standard for representing quality control metrics in mass spectrometry, enabling interoperable and machine-readable QC reporting.

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

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.

The paper presents the E. coli PeptideAtlas build, a comprehensive pan-proteome resource covering 4,755 proteins and over 10,000 PTM sites from 40 datasets.

ProteoBench provides a centralized platform for comparing proteomics data analysis workflows, enabling benchmarking and community collaboration.

CAMPI-2 evaluates five fecal sample stabilization methods for metaproteomics, finding one commercial device offers the best reproducibility and stability during room-temperature storage.

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

This study compares DIA-MS and DDA-MS for metaproteomics, finding DIA-MS provides more reproducible and accurate protein and peptide identifications across laboratories.

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.

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

TIMS2Rescore is a data-driven rescoring pipeline optimized for DDA-PASEF data that improves protein identification in proteomics analyses.

The paper presents open-source software libraries for processing mzQC data in Python, R, and Java, enabling QC analysis and integration in mass spectrometry workflows.

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.

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

The paper introduces a standardized metadata format for proteomics datasets to improve reusability and integration across public repositories.

The paper introduces the Universal Spectrum Identifier (USI) to standardize referencing mass spectra in proteomics repositories, enabling transparent traceability of spectral evidence in publications.

The paper evaluates integrating Percolator into COSS for improved peptide identification sensitivity and specificity using multiple datasets and search tools.

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

The paper introduces PEFF, a new format for proteomics data that enhances FASTA with metadata for sequence variants and PTMs, enabling better analysis in proteogenomics and top-down proteomics.