The research area Proteomics focuses on the analysis of proteins and peptides in biological data sets. Proteins are essential building blocks for every living organism and over the last years, mass spectrometry has become the method of choice for the analysis of those. To understand and investigate cell processes or gain new insights in illnesses triggered by certain proteins or the absence or oversupply of those, the identification and quantification of proteins in the tissue is of primary importance. Since 2011 and in close collaboration with the Mechtler group at the IMP, Vienna, our research group has focused on the area of computational proteomics and therein on the development of algorithms to identify proteins and peptides in biological samples. This has led to the emergence of the MS Amanda algorithm, a database search engine especially designed for high resolution data sets and perfectly capable of identifying chimeric spectra. In addition, we are currently working on a library search engine, MS Ana, that is able to identify peptides based on a previously created library of mass spectra with known peptide identifications. To complement that, also a search engine for the identification of peptides connected with a cleavable cross-linker, called MS Annika, is in progress.



Selected Publications

2019 Sebastian Dorl, Stephan M. Winkler, Karl Mechtler, and Viktoria Dorfer: MS Ana: A Spectral Library Search Engine Optimized for High-Accuracy Fragment Ion Data European Bioinformatics Community (EuBIC) Winter School 2019
2014 Viktoria Dorfer, Peter Pichler, Thomas Stranzl, Johannes Stadlmann, Thomas Taus, Stephan M. Winkler, and Karl Mechtler: MS Amanda, a Universal Identification Algorithm Optimized for High Accuracy Tandem Mass Spectra Journal of Proteome Research , Vol. 13 , pp. 3679-84

Selected Projects

MS Amanda

The development of the peptide and protein identification algorithm MS Amanda has been started within this project. this scoring system is developed by the Bioinformatics Research Group in close cooperation with the group of Karl Mechtler at IMP Vienna and especially focused on the identification of peptides and proteins of tandem mass spectrometry data.


It is motivated by the fact that only 30-50 % of the spectra of a mass spectrometry run can be satisfyingly interpreted due to various reasons, including – often unknown – posttranslational modifications. In addition, the algorithms used by the majority of the proteomics community have been developed more than 10 years ago and do not provide sufficient results for high resolution tandem mass spectrometers which only emerged recently.


The implementation of MS Amanda for Proteome Discoverer can be found online:


DI(FH) Viktoria Dorfer MSc


DI(FH) Viktoria Dorfer MSc

Sebastian Dorl MSc

Prof.(FH) DI Dr. Stephan Winkler


2011 - present

Research Areas


Research Institutions

Research Center Hagenberg

University of Applied Sciences, Upper Austria, Hagenberg Campus

Research focus

Software technology and application

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