A common mechanism for protein regulation is through post-translational modifications (PTMs), which can affect the characteristics  of proteins. Most available databases on protein PTMs collect and integrate PTM information from various resources, but provide very little or no information on the reliability of the identified PTM sites, experimental condition, pathological status and their functional relevance. 

To remove the hidden layer from the proteomics experiments using different versions of sequence databases with different search settings and FDR controls, and to potentially search for additional modifications that could explain the identified spectra from the original experiments,  Scop3PTM was created.

Scop3PTM is an interactive knowledge-base on human PTMs built by reprocessing all available human proteomics experiments from PRIDE with the uniform and updated sequence database, search settings and FDR control. The Scop3PTM knowledgebase contains 120 different biological modifications (phosphorylation, acetylation etc) and more than 300 non-biological modifications (artefacts and chemical derivatives).

This course introduces you to PTM data generated by reprocessed mass-spectrometry experiments from PRIDE. Hands-on experience with the Scop3PTM web interface is offered and different modification types are further explored and visualised.

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Organised by VIB Technology Training and ELIXIR Belgium