Publications ​

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

Micha J. Birklbauer, Louise M. Buur, Sabrina Kaser, Fränze Müller, Manuel Matzinger, Karl Mechtler, Stephan Winkler & Viktoria Dorfer

Nature Communications, 2026, Volume 17, Issue 10508

10.1038/s41467-026-77407-1

Breaking barriers in crosslinking mass spectrometry with enhanced throughput and sensitivity using Orbitrap Astral

Fränze Müller, Micha J. Birklbauer, Julia Bubis, Karel Stejskal, Viktoria Dorfer & Karl Mechtler

Nature Communications, 2025, Volume 16, Issue 9877

10.1038/s41467-025-64844-7

Developing a new cleavable crosslinker reagent for in-cell crosslinking

Fränze Müller, Bogdan R. Brutiu, Iakovos Saridakis, Thomas Leischner, Micha J. Birklbauer, Manuel Matzinger, Mathias Madalinski, Thomas Lendl, Saad Shaaban, Viktoria Dorfer, Nuno Maulide & Karl Mechtler

Communications Chemistry, 2025, Volume 8, Issue 191

10.1038/s42004-025-01568-1

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

Micha J. Birklbauer, Fränze Müller, Sowmya Sivakumar Geetha, Manuel Matzinger, Karl Mechtler & Viktoria Dorfer

Communications Chemistry, 2024, Volume 7, Issue 300

10.1038/s42004-024-01386-x

MS2Rescore 3.0 Is a Modular, Flexible, and User-Friendly Platform to Boost Peptide Identifications, as Showcased with MS Amanda 3.0

Louise M. Buur, Arthur Declercq, Marina Strobl, Robbin Bouwmeester, Sven Degroeve, Lennart Martens, Viktoria Dorfer & Ralf Gabriels

Journal of Proteome Research, 2024, Volume 23, Issue 8

10.1021/acs.jproteome.3c00785

MS Annika 2.0 Identifies Cross-Linked Peptides in MS2–MS3-Based Workflows at High Sensitivity and Specificity

Micha J. Birklbauer, Manuel Matzinger, Fränze Müller, Karl Mechtler & Viktoria Dorfer

Journal of Proteome Research, 2023, Volume 22, Issue 9

10.1021/acs.jproteome.3c00325

MS Ana: Improving Sensitivity in Peptide Identification with Spectral Library Search

Sebastian Dorl, Stephan Winkler, Karl Mechtler & Viktoria Dorfer

Journal of Proteome Research, 2023, Volume 22, Issue 2

10.1021/acs.jproteome.2c00658

MS Amanda 2.0: Advancements in the standalone implementation

Viktoria Dorfer, Marina Strobl, Stephan Winkler & Karl Mechtler

Rapid Communications in Mass Spectrometry, 2021, Volume 35, Issue 11

10.1002/rcm.9088

CharmeRT: Boosting Peptide Identifications by Chimeric Spectra Identification and Retention Time Prediction

Viktoria Dorfer, Sergey Maltsev, Stephan Winkler & Karl Mechtler

Journal of Proteome Research, 2018, Volume 17, Issue 8

10.1021/acs.jproteome.7b00836

PhoStar: Identifying Tandem Mass Spectra of Phosphorylated Peptides before Database Search

Sebastian Dorl, Stephan Winkler, Karl Mechtler & Viktoria Dorfer

Journal of Proteome Research, 2017, Volume 17, Issue 1

10.1021/acs.jproteome.7b00563

MS Amanda, a Universal Identification Algorithm Optimized for High Accuracy Tandem Mass Spectra

Viktoria Dorfer, Peter Pichler, Thomas Stranzl, Johannes Stadlmann, Thomas Taus, Stephan Winkler & Karl Mechtler

Journal of Proteome Research, 2014, Volume 13, Issue 8

10.1021/pr500202e