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Thermo Fisher Scientific Inks Pair of Collaborations Around Proteomics Workflows

NEW YORK – Thermo Fisher Scientific announced on Tuesday a pair of collaborations for development of its proteomics tools and workflows.

One agreement, with German informatics firm MSAID, provides Thermo Fisher with an exclusive license to develop and commercialized deep learning tools for proteomics based on MSAID's informatics package, which is based on the Prosit software developed at the Technical University of Munich.

The deep learning tools will be incorporated into Thermo Fisher's Proteome Discoverer 2.5 software package, which the company released this week, and will improve the confidence of mass spec-based protein identifications as well as enable researchers to automatically generate spectral libraries for data-independent acquisition mass spec experiments.

"Increasing the confidence of protein and peptide identifications is a growing need, given that a false discovery rate of even 1 percent means that 1,000 out of every 100,000 peptides might be incorrectly assigned," Mark Sanders, director of life science mass spectrometry software at Thermo Fisher, said in a statement. "Applying deep learning tools enables data-independent analysis (DIA) of proteomics samples with higher confidence and reproducibility, and, when used with Orbitrap technology, reduces the false discovery rate 10-fold, to merely 100 out of every 100,000 peptides."

Thermo Fisher also said on Tuesday that it is extending its collaboration with Swiss proteomics firm Biognosys to advance DIA mass spec workflows. The companies have developed a workflow for rapid quantification of 500 proteins in plasma samples as well as DIA assays using Thermo Fisher's FAIMS Pro ion mobility system for increased proteomic coverage.

"Our continued work with Thermo Fisher aligns with Biognosys' overall mission of transforming life sciences with the next generation of quantitative proteomics solutions," Lukas Reiter, chief technology officer at Biognosys, said in a statement. "With the Thermo Scientific FAIMS Pro interface coupled with the Thermo Scientific Orbitrap Exploris 480 mass spectrometer, Biognosys can profile more than 10,000 proteins from the human HeLa cell line with single-shot FAIMS-DIA. This corresponds to an estimated 80 percent of its expressed proteome."

Thermo Fisher also released a pair of new mass spectrometers this week, the Orbitrap Exploris 240 and the Orbitrap 120, both of which are targeting routine applications in proteomics, small molecule, and biopharma work.

The announcements come in advance of the American Society for Mass Spectrometry annual meeting, which begins next week and is being held virtually due to the SARS-CoV-2 pandemic.

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