Using ultrafast technology for protein sequencing

Abstract illustration of nanoparticles flowing inside helicoidal nanotube. Credit: Adobe Stock, edited by Karen Arnott/EMBL-EBI

Using ultrafast technology for protein sequencing

2 Aug 2021 - 19:25

Summary 

  • Funding for the Protein-ID (ProID) project was given to seven partner institutes including IIT and EMBL-EBI
  • The project aims to create an ultrafast and convenient method for sequencing proteins
  • This rapid access to individual proteomes could help scientists to predict the onset of diseases and aid the development of medical diagnostics

03 August 2021, Cambridge – The European Union's Horizon 2020 Future and Emerging Technologies program has granted 3 million euros to a research consortium composed of Istituto Italiano di Tecnologia (IIT), Université du Luxembourg, Karlsruher Institut für Technologie, Center National de la Recherche Scientifique, EMBL’s European Molecular Biology Laboratory (EMBL-EBI), Politecnico di Milano, Università di Padova and Micro Photon Devices S.r.l.

The newly funded project – called ProID – aims to create a method to identify proteins in real time and trace their identity using spectroscopic techniques, artificial intelligence and sensors capable of operating at the nanometer scale. The consortium will be coordinated by Dr. Francesco De Angelis, head of IIT's Plasmon Nanotechnologies Lab.

The outcome of this project would help researchers to quickly and easily obtain information about the proteins of an individual or organism – the proteome – by identifying which proteins are present and not just encoded in the genome. Rapid access to proteomes could help scientists to predict the onset of diseases, develop medical diagnostics or even detect toxins and contaminants within food.

Sequencing individual amino acids

The ProID research consortium plans to create a device that can be used to sequence individual amino acid chains and trace the identity of specific proteins. This device would be comparable to long-read sequencing technologies capable of direct, real-time DNA analysis. The information collected by the ProID device will also be used to train machine learning algorithms to help streamline and accelerate the process of identifying proteins.

“This project is possible due to the revolutionary technologies available that we can manipulate to visualise individual amino acids at such speed and precision,” said Nick Goldman, Group Leader at EMBL-EBI. “Once this project is complete the methodology we have created will have an infinite number of uses to further both life science and medical research.”

Ultrafast Raman technology

The revolutionary sensitivity behind the ProID project comes from its use of Raman spectroscopic techniques – an analysis method which provides information about chemical structure – combined with a nanometric sensor capable of optically exciting individual amino acids and reading their response. Using this technology means the device will be capable of ultrafast and precise recording of individual amino acids within a microsecond.

“My part in this project is to decode the ‘light data’ we obtain, which represents the different amino acids that created it, and determine from this which proteins are present,” said Goldman. “Generating this type of data gives a complementary approach to disease diagnosis alongside analysing genomic data in the clinic. Looking directly at protein sequences in this setting is the equivalent to reading speed from a speedometer rather than trying to determine the speed of a car based on its make, model, engine blueprints and how much pressure is applied to the accelerator – it’s much more direct”.  

Contact the news team

Vicky Hatch | Communications Officer

vhatch@ebi.ac.uk

Oana Stroe | Senior Communications Officer

stroe@ebi.ac.uk

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