Proteomics

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
2018 Sebastian Dorl, Stephan Winkler, Karl Mechtler, and Viktoria Dorfer: PhoStar: Identifying Tandem Mass Spectra of Phosphorylated Peptides before Database Search Journal of Proteome Research , Vol. 17 , pp. 290–295
2018 Viktoria Dorfer, Sergey Maltsev, Stephan M. Winkler, and Karl Mechtler: CharmeRT: Boosting peptide identifications by chimeric spectra identification and retention time prediction Journal of Proteome Research , Vol. 17 , pp. 2581–2589
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 Ana

MS Ana is a scoring system to identify peptides in tandem mass spectrometry data using a library of previously identified spectra. Furthermore, MS Ana can create decoy spectral libraries for validation and run searches for additional modifications not found in the spectral library.

This software is specially designed to work with high accuracy tandem mass spectra and modern spectral libraries build from high accuracy tandem mass spectra. By using a suitable library you can achieve higher sensitivity and increased processing speed compared to traditional database search. Identifications from MS Ana are also highly accurate, as we observe a strong overlap with identifications from database search algorithms like SEQUEST HT, as well as gold-standard spectral library search algorithms like NIST MS Pepsearch.

You can download MS Ana Spectral Library Search Engine for Proteome Discoverer here: http://ms.imp.ac.at/?goto=msana


Head

DI(FH) Dr. Viktoria Dorfer MSc.

Researchers

Sebastian Dorl MSc

DI(FH) Dr. Viktoria Dorfer MSc

Prof.(FH) DI Dr. Stephan Winkler

Duration

2017 - present

Research Areas

Proteomics

Research Institutions

Research Center Hagenberg

University of Applied Sciences, Upper Austria, Hagenberg Campus

Research focus

Software technology and application

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