A couple collaborations

Thermo Fisher inks a new deal and extends an existing agreement

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SAN JOSE, Calif.—Thermo Fisher Scientific is closing out May with word of a new collaboration and the extension of an existing partnership.
The former is a newly announced exclusive license agreement with software company MSAID GmbH, under which the partners will develop and commercialize deep learning tools for proteomics and make MSAID's Prosit-derived framework accessible to proteomics labs. This is expected to boost confidence in proteomics results in areas such as protein profiling using label-free or tandem mass tag-based quantification.
"At MSAID, we reinvent the way proteomic data is acquired and analyzed by using state-of-the-art deep learning. Through our collaboration with Thermo Fisher Scientific, we can bring this technological revolution to laboratories around the world and empower the scientific community to gain exceptional insight into new and existing data," said Martin Frejno, CEO of MSAID GmbH.
The new algorithm will be released as part of Thermo Fisher's latest Thermo Scientific Proteome Discoverer 2.5 software release, which enables users to access deep learning-based prediction of tandem mass spectra and thereby form spectral libraries on demand, facilitate the identification of peptides with up to 10 times higher confidence, and extract more identifications from datasets thanks to intensity-based rescoring. Together with Thermo Scientific Orbitrap technology, the combination is expected to open the way for emerging approaches such as immunopeptidomics and metaproteomics.
"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," commented Mark Sanders, director of life science mass spectrometry software for Thermo Fisher Scientific. "Applying deep learning tools enables data-independent analysis 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."
As for Thermo Fisher's renewed partnership, which also involves proteomics, Thermo Fisher and Biognosys are extending their collaboration to advance data-independent acquisition (DIA) mass spectrometry-based workflows. The partners have developed a workflow to enable accurate, flexible, label-free protein quantitation and proteome profiling in plasma matrices.
The two organizations have combined their respective technologies—specifically the Thermo Scientific Orbitrap Exploris 480 mass spectrometer, Thermo Scientific Orbitrap Exploris 240 mass spectrometer and Biognosys PQ500 kit—to create a streamlined, simplified workflow that gives users increased depth of coverage and sensitivity for analyzing blood-derived samples. Adding the Thermo Scientific FAIMS Pro interface, which uses field asymmetric ion mobility spectrometry (FAIMS), adds greater selectivity and reproducibility, while the Biognosys PQ500 kit can be used to implement Thermo Scientific SureQuant Targeted Assay Kits for more refined quantitative analyses.
"Researchers are delving into the proteome more than ever before, opening doors into potential new therapies and study areas, but revealing complex analytical challenges to overcome," stated Daniel Lopez-Ferrer, senior manager, proteomics, Thermo Fisher Scientific. "Through our ongoing collaboration with Biognosys, we are now able to offer the FAIMS-DIA and SureQuant workflows which, used in conjunction with the Biognosys PQ500 kit, simplify experimental processes."
Lukas Reiter, chief technology officer at Biognosys, added, "Our continued work with Thermo Fisher aligns with Biognosys' overall mission of transforming life sciences with the next generation of quantitative proteomics solutions. 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 Scientific plans to present the outcomes of both collaborations this week at its virtual event, vLC-MS.com, from May 26-28, 2020, as well as at the American Society for Mass Spectrometry Reboot Program being held from June 1-12, 2020.
SOURCE: Thermo Fisher Scientific press release

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