MS Annika
Researchers
Prof.(FH) DI(FH) Dr. Viktoria Dorfer MSc.
Prof.(FH) PD DI Dr. Stephan Winkler
Micha Birklbauer MSc.
Georg Pirklbauer MSc. (former)
Duration
Research Areas
Partners
University of Applied Sciences Upper Austria, Hagenberg Campus, RG Bioinformatics
Institute for Molecular Pathology (IMP), Vienna, Austria
Cross-linking mass spectrometry is a powerful tool for the identification of protein–protein interactions and for gaining insight into the structures of proteins. In 2021 we published MS Annika, a cross-linking search engine based on MS Amanda which can accurately identify cross-linked peptides in MS2 spectra from a variety of different MS-cleavable crosslinkers. Since its initial release we have continuously worked on new features and improving the MS Annika search algorithm in collaboration with the Proteomics Tech Hub led by Karl Mechtler, part of the Institute of Molecular Pathology (IMP) in Vienna. In 2023 we presented MS Annika 2.0, an updated version implementing a new search algorithm that, in addition to MS2 level scans, supports the processing of data from MS2–MS3-based approaches for the identification of peptides from MS3 spectra, and introduces a novel scoring function for peptides identified across multiple MS stages. Since 2023 we are now working on tackling non-cleavable crosslink search which poses another challenge, namely that of extremely large search spaces that grow quadratically. MS Annika has time and time again proven to be the cross-linking search engine of choice, outperforming other tools commonly used in the field. MS Annika is available free of charge at https://github.com/hgb-bin-proteomics/MSAnnika
To cite MS Annika and for more information on the MS Annika search algorithm please refer to Birklbauer et al. J Proteome Res. 2023, 22(9):3009-3021 (see cff) and Pirklbauer et al. J Proteome Res. 2021, 20(5):2560-2569.