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 from a variety of sample types (e.g. mammalian tissue, cell culture cells, body fluids etc), processing steps such as cell lysis, protein proteolysis and optional fractionation or even labelling steps must be tailored and optimized to fit individual project needs. 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 are mainly acquired in DIA-Pasef measurement mode, with identification and quantification rates of up to 10000 proteins per sample at a throughput of 25 samples per day.
Even larger serum and plasma cohorts can be measured in reasonable timeframes, due to short gradients (50 samples per day) and newest enrichment sample preparation methods, allowing for the identification of up to 3000 proteins from plasma. Applying different search engines and software solutions (like Spectronaut (Biognosis) and DIA-NN), we can 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.

Our new Bruker timsTOF HT and Bruker timsTOF Ultra2 can be coupled to a VanquishNeo or EvoSep One HPLC, depending on the specific requirements of the project. The timsTOF HT is primarily dedicated to robustly and reproducibly analyze bulk cell and tissue samples, whereas the Ultra2 is a highly sensitive mass spectrometer capable of analyzing samples with extremely low protein concentrations even down to single cells.