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

PROTrEIN

PROTrEIN is a European Innovative Training Network composed of 11 beneficiaries, and 6 partner organizations, from the academic and non-academic sectors (including two SMEs and two large companies).

The network’s mission is to train a new generation of computational proteomics researchers by providing them an inter-sectoral and interdisciplinary set of skills to tackle the main challenges in the field and improve their future employability.

 

PROTrEIN has developed a highly multi-and inter-disciplinary translational research and training network that will exploit the integrated analysis of several state-of-the-art technologies to achieve these ambitious goals:

We need a new generation of researchers that can delve into the complexity of the computational proteomics field. PROTrEIN aims to nurture this new generation of computational proteomics scientists by training them on the mastering of i) the mass spectrometry raw data nature, structure and information content, ii) mass spectrometry acquisition methods, iii) algorithms, gamification and machine learning tools, iv) data integration and visualization, v) science communication, vi) data management and vii) research integrity and innovation (RRI).

To successfully achieve the goal described above, we have designed a comprehensive research program around the development of new proteomics predictors using machine and deep learning technologies, new raw data processing algorithms that enable new proteomics applications, and omics data integration and visualization.

For more information please visit the PROTrEIN website: protrein.eu

 

 


Head

DI(FH) Dr. Viktoria Dorfer MSc.

Researchers

DI(FH) Dr. Viktoria Dorfer MSc.

Prof.(FH) DI Dr. Stephan Winkler

Duration

2021 - present

Research Areas

Proteomics

Research Institutions

UNIVERSITY OF APPLIED SCIENCES UPPER AUSTRIA, Hagenberg, Austria

CENTRE FOR GENOMIC REGULATION, Barcelona, Spain

NATIONAL CENTER FOR GENOMIC ANALYSIS, Barcelona, SpainUNIVERSITY OF SOUTHERN DENMARK, Odense, Denmark

THE MAX PLANCK INSTITUTE OF BIOCHEMISTRY, Martinsried, Germany

THE FLEMISH INSTITUTE FOR BIOTECHNOLOGY, Ghent, Belgium

THE CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE, Toulouse, France

THE TECHNICAL UNIVERSITY OF MUNICH, Munich, Germany

ANAXOMICS BIOTECH S.L., Barcelona Spain

THE EBERHARD KARLS UNIVERSITAET TUEBINGEN, Tuebingen, Germany

THERMO FISHER SCIENTIFIC, Bremen, Germany

TAMPERE UNIVERSITY, Tampere, Finland

Funding

Marie Skłodowska-Curie ITN - EU Horizon 2020

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