Equipment & Software

Proteomics platform

In detail, we provide the following state-of-the-art MS instrumentation and methods:

Mass spectrometry platforms:

• Two Exploris 480 coupled online to an Ultimate 3000 nanoLC-system (both from Thermo-Fisher Scientific) for discovery-driven and targeted MS workflows

Sample fractionation instruments:

• 3100 OFFGEL Fractionator for peptide separation using isoelectric focusing (Agilent)

Software:

• Database search tools: Mascot (Matrix Science), Sequest (via Proteome Discoverer/Thermo Scientific), Andromeda and Spectromine (Biognosys) for peptide/protein identification
• Scaffold (Proteome software) for exchanging proteomics results with clients
• DIA-NN and Spectronaut (Biognosys) for Data independent acquisition (DIA)
• MaxQuant and Progenesis QI label-free quantification software (Nonlinear Dynamics/Waters) and/or quantification of isotopically labeled samples
• Skyline  and Spectrodive (Biognosys) for targeted acquisitions (PRM) and absolute protein quantification via labelled peptide standards
• SafeQuant and Perseus for statistical analysis of proteomics data sets