Martina Samiotaki Research Group

Our research aim is to set up and perform high quality analyses addressing questions mainly in the field of proteomics.

We are continuously trying to improve our mass-spectrometry platform with new methodological, instrumental and software tool developments for the:

• Analysis of proteins in any organism, in any tissue or cell type, using variable sample preparation methods depending on the research question.

• Targeted as well as untargeted proteomic workflows. Label free quantification of proteomes. Labeled based quantification using variable reporter ion chemistries.

• Generation of sensitive results from limited initial material, such as FACS sorted cells and isolated exosomes.

• Studying of protein interaction networks and their visualization.

• Finding and characterizing protein modifications using “Open searches” such as PTM Shepard.

• Characterization of microbial populations taxonomically using metaproteomic platforms as well as functional characterization of altered microbial proteomes.

• Elucidation of drug interactions with proteomes chemo-proteomic approaches.

• Clinical and pre-clinical proteomic projects as well as the proteogenomic-assisted analysis of samples.

• Numerous software solutions often used in parallel in order to extract the most from the experimental data. Main tools in usage are DIA-NN, Proteome Discoverer 2.4 (Thermo), MaxQuant/Perseus, Skyline, MSFragger, EpiProfile, iMetaLab, MSStats.