Our main research aim is to enable comprehensive proteome comparisons using liquid chromatography - mass spectrometry (LC-MS). To accomplish this we develop new strategies and tools for analysis of MS data from different types of workflows. Depending on biological question and sample type, we utilise data-dependent (DDA, shotgun proteomics) , data-independent (DIA, SWATH), as well as targeted (SRM) acquistion methods. We have, and are, developing software tools for all these methods, and focus on quantification using label-free strategies. We aim at fine-grained quantification of individual protein variants, and to put the results into a functional context to increase our understanding of biological systems.
We are driving developement of the Proteios Software Environment for management and analysis of proteomics data. The Proteios applcation is now integrated with a MS data storage workflow developed within the Swedish NBIS infrastructure, and enables integrated quantitative analysis, as well as sharing of data using standards developed by the Proteomics Standards Initiative (PSI) of the Human Proteome Organisation (HUPO.
Our team has developed several standalone software tools that are available for download. Logos with links to some of these are available below.A list of tools is available at quantitativeproteomics.org.
We are always interested in new collaborative projects in different biological domains.