The world’s first proteomics database, rooted in VIB: Something to take pride in

14 December 2017
​Many VIB collaborators are familiar with PRIDE, the public data repository of mass spectrometry-based proteomics data. Maintained by the European Bioinformatics Institute, the PRoteomics IDEntifications database was conceived by Lennart Martens of the VIB-UGent Center for Medical biotechnology during his Marie Curie Fellowship in 2003.

The idea of PRIDE grew alongside the rapid improvement of mass spectrometers. Increasingly more data was obtained, but the bulk of it couldn’t be interpreted at the time. Instead of throwing 85% of this research output away, Lennart believed that making all the ‘redundant’ data accessible via a public database could benefit the entire proteomics community. He got the ball rolling, and in 2005, he established PRIDE as the first real proteomics repository. Other, similar open data initiatives were emerging around the same time, such as PeptideAtlas and the Global Proteome Machine Database.

PRIDE data as building blocks
PRIDE’s importance in research cannot be underestimated. A considerable number of papers on genome annotation benefitted from PRIDE data, such as studies on long non-coding RNAs and genome re-annotation. Another example is the study of O-linked glycosylation, which used phosphorylation data in PRIDE to show
surreptitiously co-enriched O-linked glycosylated peptides.

Finally, a very recent example is the VIB-UGent project titled ‘the online Tabloid Proteome’. Based on thousands of PRIDE datasets, this approach maps out co-occurrences of proteins. This enables researchers to discover biological associations between pairs of proteins that are strongly complementary to binary interactions. As you may have guessed, the Tabloid Proteome is freely available at

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©VIB-Ine Dehandschutter