Manuel Matzinger

Making the Impossible Possible: Uniting TMT and DIA for Scalable Low-Input-Proteomics

This paper combines TMT and DIA proteomics techniques to improve low-input proteomics, showing how to overcome co-isolation interference and enabling TMT quantification with DIA-focused software.

Unified down-stream analysis of crosslinking mass spectrometry results with pyXLMS

pyXLMS simplifies crosslinking mass spectrometry analysis by integrating search engine results with downstream tools, enabling non-experts to perform comprehensive analyses.

Defining Quality Control Standards for Single-Cell Proteomics by Inter-Laboratory Benchmarking

This study establishes quality control standards for single-cell proteomics through inter-laboratory benchmarking, identifying software and technical factors affecting data reliability.

The Single Cell Proteomic blueprint, navigating instrumentation platforms, software tools and high-load libraries in neutrophils, RKO and A549 cells

This study evaluates DIA search engines, high-load libraries, and instrumentation platforms for single-cell proteomics across different cell types.

Pushing the limits of SCP: bacSCP, a proof-of-concept study to investigate heterogeneity of bacteria by single cell proteomics.

This study introduces bacSCP, a single-cell proteomics protocol for bacteria, demonstrating its ability to quantify proteins and reveal stress-response heterogeneity in Bacillus subtilis.

Low-resolution FAIMS for increased peptide coverage in low-load and single-cell proteomics

This paper shows that lowering FAIMS resolution improves peptide identification in low-load and single-cell proteomics by increasing ion transmission and sensitivity.

A journey towards developing a new cleavable crosslinker reagent for in-cell crosslinking

This paper introduces a new cleavable crosslinker, DiSPASO, for in-cell crosslinking and evaluates its performance in different model systems.

In vivo crosslinking and effective 2D enrichment for interactome studies of the nucleosome.

This study improves an in vivo crosslinking workflow to identify protein-protein interactions, finding 56 novel nuclear PPIs and showing increased crosslinking of low-abundance proteins.

Proteome-wide non-cleavable crosslink identification with MS Annika 3.0 reveals the structure of the C. elegans Box C/D complex

The paper introduces an algorithm for non-cleavable crosslink identification in MS Annika, revealing the structure of the C. elegans Box C/D complex and enabling proteome-wide analysis.

Challenging the Astral mass analyzer - up to 5300 proteins per single-cell at unseen quantitative accuracy to study cellular heterogeneity.

This paper introduces a high-throughput single-cell proteomics workflow achieving 5300 protein groups per cell with high accuracy, enabling the study of cellular heterogeneity and lineage differentiation.

Mimicked synthetic ribosomal protein complex for benchmarking cross-linking mass spectrometry workflows

The paper introduces a synthetic peptide library and tool to benchmark cross-linking mass spectrometry workflows and demonstrates the importance of algorithm choice for improving identification rates and FDR.