Thermo Fischer & TUM announce milestone on human proteomes

Report on synthesis of a library of over 330,000 reference peptides to analyse human proteomes

Thermo Fisher and the Technical University of Munich (TUM) announced a milestone for analysis of human proteomes. In an online manuscript in Nature Methods, ProteomeTools scientists report on the synthesis of a library of over 330,000 reference peptides (termed PROPEL) representing essentially all canonical proteins of the human proteome. All peptides were analysed by multi-modal liquid chromatography-tandem mass spectrometry (LC-MS/MS), creating a compendium of millions of high quality reference spectra (termed PROSPECT). The study illustrated utility of these reagents and data to verify protein identifications from sparse observations and to predict the behaviour of peptides during LC-MS.

The data has been made freely available to the scientific community via data analytics platform ProteomicsDB and the data repository PRIDE.

The ProteomeTools project intends to generate a further one million peptides and corresponding spectra with a focus on splice variants, cancer mutations and post-translational modifications like phosphorylation, acetylation and ubiquitinylation. Using new resources, ProteomeTools scientists will study human proteomes to turn the vast amount of molecular information on the human proteome into new reagents, equipment, workflows, assays and software to enhance the application of proteomics in both science and medicine.

Professor Bernhard Kuster, Chair, Proteomics and Bioanalytics, TUM, and coordinator of the project said, “Representing the human proteome by tandem mass spectra of synthetic peptides alleviates some of the current issues with protein identification and quantification. The libraries of peptides and spectra now allow us to develop new and improve upon existing hardware, software, workflows and reagents for proteomics. Making all the data available to the public provides a wonderful opportunity to exploit this resource beyond what a single laboratory can do. We are now reaching out to the community to suggest interesting sets of peptides to make and measure as well as to create LC-MS/ MS data on platforms not available to the ProteomeTools consortium.”

The project is funded in part by the German Federal Ministry of Education and Research (BMBF), JPT Peptide Technologies, SAP, Thermo Fisher Scientific and TUM.