The VIB Proteomics Core (PRC) provides contemporary mass spectrometry (MS)-based proteomics services to academic and non-academic users. Located at the VIB-UGent Center for Medical Biotechnology in Ghent, Belgium, the PRC started in 2005 as a spin-off service unit from the proteomics laboratory of Prof. Dr. Kris Gevaert. Today, the PRC has evolved from a research-oriented facility into a service-oriented platform and has become a reference center for proteome research in Belgium and beyond.
Six state-of-the-art orbitrap mass spectrometers coupled to nano-LC chromatography systems are available for LC-MS/MS analyses carried out at the PRC. These instruments run 24/7 and allow to process several 100s of samples/month. In addition, the PRC disposes of a triple quadrupole mass spectrometer for targeted proteomics, as well as a MALDI-TOF MS/MS instrument.

As part of its routine service portfolio, the PRC offers three main types of proteomics applications in modern life sciences. As a first application, shotgun analyses generate comprehensive proteome profiles that reveal differences in protein levels associated with a particular cellular state or experimental condition. Second, affinity purification mass spectrometry (AP-MS) experiments allow to characterizate protein complexes and to discover novel protein interactions. Third, the PRC has extensive experience in mapping common protein post-translational modifications such as acetylation, phosphorylation and ubiquitination. Next to these routine applications, custom services include the identification of proteolytic processing sites, the development of targeted proteomics assays (e.g. by SRM/PRM) and mass determination of intact proteins. Samples can be isotopically labeled (e.g. by SILAC or TMT labeling) for optimal quantitation accuracy or sample multiplexing, in addition to standard labelfree workflows.

Significant maturation of LC-MS/MS instrumentation and data analysis software over recent years has set the stage for clinical proteomics. To cope with these developments and to play an active role in biomarker discovery, the PRC recently implemented a novel analysis pipeline based on data independent acquisition (DIA). This pipeline ensures improved detectability and quantitation of proteins, ideally suited for high-throughput screening of patient samples.

The PRC is operated by an experienced, international team composed of MS engineers, biochemists and data analysts, and operates under permanently surveilled conditions that include daily MS quality control and continuous benchmarking of implemented protocols. The facility is ready to deliver high quality services at all times, encompassing every step of a proteomics experiment. Users are guided from sample collection to data analysis and are assisted by the PRC team to formulate biological conclusions that are easy to interpret for the non-proteomics expert.