Viktoria Dorfer

Beyond Delta Masses: MS Andrea Directly Resolves Combinatorial Peptide Modifications in Open Searches

MS Andrea, a tag-filtered open search engine, scores and localizes up to four Unimod modifications per peptide-spectrum match, with identification counts competitive with MSFragger and Sage.

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.

A DIA-based quantitative crosslinking mass spectrometry framework for dynamic structural proteomics

This paper introduces DIA-QCLMS, a framework for quantitative crosslinking mass spectrometry that improves confidence assessment and integrates structural features, showing improved reproducibility in analyzing protein dynamics.

ProteoBench: the community-curated platform for comparing proteomics data analysis workflows

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

Breaking Barriers in Crosslinking Mass Spectrometry: Enhanced Throughput and Sensitivity with the Orbitrap Astral Mass Analyzer

This study compares the performance of Orbitrap Astral and Eclipse mass spectrometers in CLMS, finding the Astral provides higher sensitivity and more unique residue pairs.

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.

A community audit of error control in crosslinking mass spectrometry

The paper audits error control in twelve crosslinking mass spectrometry pipelines using ground-truth designs, finding some pipelines exceed false discovery rates by up to 29-fold.

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.

Universal Spectrum Explorer: A standalone (web-)application for cross-resource spectrum comparison

The paper introduces a web-based tool for cross-resource peptide spectrum comparison and visualization, with a focus on integration and retrieval from spectral databases.