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Innovative approach redefines data analysis in proteomics research

Thermo Fisher Scientific

Thermo Fisher Scientific and MSAID continue their collaboration to deliver transformative deep learning tools for proteomics data analysis

3 Nov 2021
Dora Wells
Clinical Content Editor

Industry news

Thermo Fisher Scientific, a world leader in serving science, and MSAID, a leader in proteomics artificial intelligence, have collaborated to provide proteomics researchers with advanced mass spectrometry software that generates market-leading biological insight from acquired data by substantially increasing peptide identification and quantitation capabilities using artificial intelligence (AI) and deep learning.

Thermo Scientific Proteome Discoverer 3.0 software with CHIMERYS by MSAID leverages artificial intelligence (AI) to substantially enhance the identification rate and number of unique peptide identifications in proteomics data. CHIMERYS identifies a minimal set of peptides that can explain the acquired tandem mass spectrum, in comparison to existing methodologies, which typically assume all peaks in a tandem mass spectrum are derived from a single peptide. This innovative approach provides a 1.8-fold increase in the number of unique peptide identifications and a 1.5-fold increase in the number of protein identifications for typical proteomics data sets when compared to existing tools. In addition to improved protein coverage and quantitation capabilities, Proteome Discoverer 3.0 software paired with CHIMERYS also facilitates faster data acquisition for increased sample throughput.

Thermo Fisher Scientific and MSAID are showcasing their new software solution during the 69th American Society for Mass Spectrometry (ASMS) Conference on Mass Spectrometry and Allied Topics, held October 31-November 4, in the Pennsylvania Convention Center, Philadelphia, Pennsylvania.

"Previous technologies have been unable to fully interpret data generated using mass spectrometry, as mass spectra can contain fragments from multiple co-isolated peptides that cannot be identified using current algorithms," said August Specht, vice president, research and development, chromatography and mass spectrometry, Thermo Fisher Scientific. "By using Proteome Discoverer 3.0 software and CHIMERYS, scientists can now leverage AI for deeper mining of proteomic data. This not only improves proteomic coverage, but also expands the ways in which proteomics scientists can acquire and apply their data."

Martin Frejno, chief executive officer, MSAID said, "Chimeric spectra were a long-standing problem in mass spectrometry-based proteomics. With CHIMERYS, we reimagined the analysis of tandem mass spectra from the ground up using AI to solve it."

The Proteome Discoverer 3.0 software release also includes an updated INFERYS prediction model, extending support to tandem mass tagging (TMT), collisionally induced dissociation (CID), and providing improved results for immunopeptidomics. By pairing intelligent data analysis through Proteome Discoverer 3.0 software and CHIMERYS with leading hardware technology in the Thermo Scientific Vanquish Neo Ultra-High Performance Liquid Chromatography (UHPLC) system and Thermo Scientific Orbitrap mass spectrometry platforms, researchers will be empowered to continue pushing the boundaries of proteomics research.

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Mass SpectrometryMass spectrometry (MS) is a powerful analytical technique used to identify and quantify molecules based on the mass-to-charge ratio of gas-phase ions. It provides detailed information about the structure, composition, and properties of compounds and is widely used across fields such as environmental monitoring, materials science, drug discovery and development, food and beverage testing, and wider chemical research. Key MS techniques include tandem mass spectrometry (MS/MS), liquid chromatography–mass spectrometry (LS-MS) and inductively coupled plasma (ICP-MS). Choosing from these wide range of techniques and technologies can be a daunting task, so keep up to date with scientific applications, performance expectations, and customer reviews here all in one place. Visit our product directory to receive quotes direct from the manufacturer. ProteomicsProteomics is the systemic bioinformatics study of proteins and amino acids, including their structure, size, function and identification. Tools used in proteomics include chromatography, blotting and gels, protein arrays, mass spectrometry and ELISA and associated analysis software. Analyzers and proteomic systems should be sensitive, high resolution, fast and may be automated for high-throughput.Software PlatformsSoftware platforms are useful for various stages of laboratory experiments from data collection to data storage and processing. For instance lab software is available for system control, data management, data analysis and qualification / validation.Automation Supplies / AccessoriesAutomated accessories and consumables make lab processes fast, efficient and reliable. Useful automation accessories include microplate sealers, label printers and reagent reservoirs.Protein QuantificationThe detection and quantification of proteins in a sample is vital across life sciences, pharmaceutical research and clinical diagnostics, and a variety of equipment is available to scientists to simplify the workflow. Proteins of interest can be easily labeled and detected on light-based detection instruments. Immunoassay kits allow you to identify a specific protein of interest and protein detection beads or antibody microarrays allow you to identify multiple specific proteins at once. Protein interactions and enzyme activity can also be monitored with protein-protein interaction assays. Additionally, the biophysical characterization of proteins is made easy with biokinetic analyzers. Find the best protein detection and quantification products in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.UHPLC and HPLCHigh performance liquid chromatography (HPLC) and ultra high performance liquid chromatography (UHPLC), also known as UPLC, are analytical techniques used to separate, identify and quantitate components of complex mixtures including biological samples such as proteins and lipids as well as chemical mixtures of pesticides, drugs and oils. Both techniques are liquid chromatographic methods but differ by operating pressures (HPLC < 6000 psi < UHPLC ). Components of HPLC and UHPLC systems include columns, detectors, pumps, autosamplers and column heaters. Explore a range of UHPLC and HPLC columns for your specific sample needs including reverse phase, normal phase, ion exchange, HILIC, ion exclusion and size exclusion columns. For more specialized HPLC, explore FPLC, countercurrent LC and simulated moving bed systems. Find the best UHPLC and HPLC equipment in our peer reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.AutomationAutomation in laboratories and manufacturing processes enhances efficiency, precision, and scalability by reducing the need for manual intervention. It plays a critical role in improving productivity, minimizing human error, and accelerating workflows in fields like diagnostics, drug development, and industrial testing. Automation technologies include robotic systems, automated liquid handlers, and process control systems that streamline complex tasks and ensure consistent, reproducible results. Explore our peer-reviewed product directory to discover the best automation solutions, compare options, read user reviews, and get prices directly from manufacturers.Protein DetectionProtein detection techniques are essential for understanding protein expression, localization, and function. Methods such as western blotting, ELISA, and mass spectrometry are commonly used in research and diagnostics. Browse our peer-reviewed product directory to find the best tools for protein detection, compare products, check reviews, and get pricing directly from manufacturers.ProteomicsProteomics refers to the analysis of proteins through a variety of different experiments in order to understand structure and functionality. Typical techniques include protein purification and mass spectrometry. HPLCHigh-performance liquid chromatography (HPLC) is a technique for separating, identifying, and quantifying components in mixtures. It is widely used in chemical, pharmaceutical, and environmental analysis to ensure purity and identify unknown compounds. Explore the best HPLC systems in our peer-reviewed product directory; compare products, read reviews, and get pricing directly from manufacturers.

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Innovative approach redefines data analysis in proteomics research