ProteomeTools Peptide Library now open to scientists

Researchers led by the Technical University of Munich (TUM) have synthesised a library of more than 330,000 reference peptides, representing essentially all canonical proteins of the human proteome. The library was created as part of the ProteomeTools project, which aims at translating human proteome information into new molecular and digital tools with the potential for use in drug discovery, personalised medicine and life science research.

All peptides in the ProteomeTools Peptide Library (PROPEL) were analysed by multimodal liquid chromatography-tandem mass spectrometry (LC-MS/MS), creating a compendium of millions of high-quality reference spectra (ProteomeTools Spectrum Compendium, or PROSPECT). The researchers’ study, published in the journal Nature Methods, illustrates the utility of these reagents and data to verify protein identifications from sparse observations and to predict the behaviour of peptides during liquid chromatography and tandem mass spectrometry.

Going forward, the ProteomeTools project will generate a further one million peptides and corresponding spectra with a focus on splice variants, cancer mutations and post-translational modifications such as phosphorylation, acetylation and ubiquitinylation. ProteomeTools scientists will study human proteomes with the aim of turning 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.

“Representing the human proteome by tandem mass spectra of synthetic peptides alleviates some of the current issues with protein identification and quantification,” said ProteomeTools coordinator Professor Bernhard Kuster, chair of Proteomics and Bioanalytics at TUM. “The libraries of peptides and spectra now allow us to develop new and improve upon existing hardware, software, workflows and reagents for proteomics.”

The TUM researchers and their collaborators at JPT Peptide Technologies, SAP and Thermo Fisher Scientific have now made the vast quantity of their data freely available to the scientific community via data analytics platform ProteomicsDB and data repository PRIDE to enable scientists and to foster collaboration around the globe. As noted by Professor Kuster, “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,” Professor Kuster concluded.

Image caption: Mathias Wilhelm, Professor Bernhard Küster and Daniel Paul Zolg in discussion about the ProteomeTools Peptide Library (PROPEL). Image credit: Andreas Heddergott/TUM.