Apply Scop3PTM web-interface to understand post-translational modifications (PTMs) of proteins
6 March, 14h-17:30h (lunch at 12:30)
General context
A common mechanism for protein regulation is through post-translational modifications(PTMs), which can affect the activity, subcellular localization, and stability of proteins. Most of the available databases on protein PTMs collect and integrate PTM information from different resources, but they provide very little or no information on the reliability of the identified PTM sites, experimental condition, pathological status and their functional relevance. In order to remove the hidden layer on the proteomics experiments using different versions of sequence databases with different search settings and FDR controls, and to potentially look for additional modifications that could explain the identified spectra from the original experiments, we created Scop3PTM.
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. Scop3PTM knowledgebase contains 120 different biological modifications (phosphorylation, acetylation etc) and more than 300 non-biological modifications (artefacts and chemical derivatives).
Furthermore, PTM sites are put into sequence, structural and biophysical context by annotating every human protein with per-residue structural propensity, solvent accessibility, disordered probability, backbone and sidechain dynamics, and early folding information. Scop3PTM acts as a much-needed bridge between the fields of proteomics, structural bioinformatics and intrinsically disordered proteins (IDPs), and presents a unique resource for visualization, and to understand the impact of PTM-sites on structure-function relationship of proteins.
A common mechanism for protein regulation is through post-translational modifications(PTMs), which can affect the activity, subcellular localization, and stability of proteins. Most of the available databases on protein PTMs collect and integrate PTM information from different resources, but they provide very little or no information on the reliability of the identified PTM sites, experimental condition, pathological status and their functional relevance. In order to remove the hidden layer on the proteomics experiments using different versions of sequence databases with different search settings and FDR controls, and to potentially look for additional modifications that could explain the identified spectra from the original experiments, we created Scop3PTM. 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. Scop3PTM knowledgebase contains 120 different biological modifications (phosphorylation, acetylation etc) and more than 300 non-biological modifications (artefacts and chemical derivatives). Furthermore, PTM sites are put into sequence, structural and biophysical context by annotating every human protein with per-residue structural propensity, solvent accessibility, disordered probability, backbone and sidechain dynamics, and early folding information. Scop3PTM acts as a much-needed bridge between the fields of proteomics, structural bioinformatics and intrinsically disordered proteins (IDPs), and presents a unique resource for visualization, and to understand the impact of PTM-sites on structure-function relationship of proteins.
- Get to know the PTM data generated by re-processed mass-spectrometry based proteomics experiments from PRIDE
- Hands on experience on Scop3PTM web-interface.
- We will explore your favorite protein (Human proteins) by visualizing all identified PTMs and amino acid variants that are mapped onto the protein structures and understand the predicted biophysical properties of the protein.
- For each modification type, we will explore if the identified modification is biological/non-biological, functional relevance, identified peptides, proteomics projects and experimental conditions, pathological status and tissue types (if any).
This course is intended for researchers working on proteins (and/or PTMs) and would like to know the structure-function relationship of proteins and PTMs.
Basic knowledge on protein and protein structures (1D, 2D and 3D). You are encouraged to use your own laptop.
Trainers
Pathmanaban Ramasamy
I did my masters in Bioinformatics at Saarland University, Germany where I worked on detecting the protein similarity of fast evolving viral proteins using graph mining approach.
In 2016, I joined the CompOmics group and IB2 as a joint PhD student between Prof. Lennart Martens (Ghent University) and Prof. Wim Vranken (Vrije Universiteit Brussel) to work on the FoldMod project, where we try to understand the role of local amino acid interactions in protein folding, fold stability and the location of post-translational modifications. I apply my knowledge on structural bioinformatics and proteomics informatics to understand protein phosphorylation.