Deep proteome profiling

One of the biggest challenges in discovery proteomics is the identification and precise quantification of protein abundances in highly complex samples that can consist of thousands of proteins. Starting with a numerous variety of sample types (e.g. mammalian tissue, cell culture cells, body fluids, whole plants …), cell lysis, protein proteolysis and optional fractionation or even labelling steps have to be tailored and optimized to fit the individual needs of your specific sample of interest. More than 100,000 released peptides then need to be separated and measured on state-of-the-art LC-MSMS systems (reversed phase liquid chromatography online coupled to a highly sensitive mass spectrometer). Precursor and fragment spectra can be acquired in a variety of measurement modes (data dependent acquisition (DDA) or data independent acquisition (DIA) or parallel reaction monitoring (PRM)), in order to fit the project-specific needs. Applying different search engines and software solutions, we will obtain identifications, differential quantification and statistics values for thousands of proteins comparing your sample conditions of interest. Furthermore, follow-up analyses like volcano plots, networks, heatmaps and pathway enrichment analyses can facilitate a detailed understanding of differential phenotypes and give indications for following experiments.