Roman Sakson   Roman Sakson received his MSc degree in Molecular Biotechnology from Heidelberg University (Germany). During his master thesis project at the Core Facility for MS and Proteomics (CFMP) at Heidelberg Molecular Biology Center, Roman started working with Skyline and established an MRM assay for the relative quantification of the human Hsp90 and its cochaperome in hepatocytes. Since 2017, he continued at the CFMP as a Ph.D. candidate under supervision of Dr. Thomas Ruppert and Prof. Matthias Mayer. The main focus of Roman’s work is on relative and absolute quantification of enzymes involved in protein glycosylation using spike-in SILAC in combination with data-dependent and targeted approaches. Together with colleagues, Roman established a recurring hands-on Skyline course for CFMP users and for the members of his graduate school.

Unleashing Versatile Skyline Features for the Everyday Needs of a Proteomics Core Facility

Proteomics Core Facilities need to support a set of robust qualitative and quantitative workflows for a broad customer base. We routinely use Skyline as a versatile, vendor-independent platform that helps us to address two major issues, namely quality control and sharing information between MS experts and users, especially if they are not located in the same place. Customized reports and integrated tools, such as Protter for protein sequence visualization, are extremely helpful while discussing results with customers. Read More
Furthermore, AutoQC in Panorama makes it easy for us to supervise instrumentation performance, even remotely. I will present one study where partially contradicting DDA-based ID results were evaluated in Skyline via MS1 filtering with spectral libraries built from MaxQuant and Proteome Discoverer output files. In a second example, shared customized report templates allow for efficient and remote data analysis by users for MRM studies monitoring hundreds of peptides over hundreds of LC-MRM injections.