Next-Gen Proteomics: High-Fidelity Enrichment, New Mass Spec, and Single-Molecule Fingerprinting
Mass spectrometry (MS) has long been a bedrock tool in proteomics investigations, with liquid chromatography mass spectrometry (LC-MS) especially key in analyzing the presence, identity, and quantity of proteins in a complex sample. But the expanding scope of proteomics research requires higher resolution than traditional MS techniques can offer, and as such, new sample preparation techniques that supplement and enhance MS workflows as well as novel MS approaches constitute a large swath of the next-gen proteomics market.
Several types of sample prep strategies have been designed to enhance enrichment and throughput. One broad class of methods employs particles to bind to and enrich for proteins in a sample that is subsequently analyzed by LC-MS or other MS techniques. Other approaches use subcellular fractionation to separate cellular components, while still others utilize depletion to remove abundant proteins from samples via immunoaffinity to boost detection of less abundant ones. High-fidelity enrichment tools are typically applied to drug target discovery and development, clinical biomarker discovery, and population-scale studies. Key companies include Evosep, which provides tips and columns designed to improve binding and sensitivity in chromatography, and Seer, which offers a magnetic nanoparticle panel and automated liquid handler compatible with most LC-MS instruments. This market, while nascent today, is expected to grow by an order of magnitude by 2027, driven by the technique’s ability to simplify workflow, increase throughput, and quicken turnaround time.
In addition to these turnkey sample prep solutions, novel MS methods that improve upon the sensitivity and resolution of conventional approaches have become available. If MS can be thought of as comprising three dimensions—retention time, peptide mass, and spectral peak intensity—an approach known as “4D proteomics” seeks to add a fourth. By using ion mobility separation to segregate ions in the gas phase before coupling with MS, users can interrogate a sample for proteins of lower abundance and decrease acquisition time. Bruker leads the market with its disruptive timsTOF instruments, and other major providers of ion mobility mass spec instruments include Agilent, Waters, and Thermo Fisher.
Another novel MS strategy, limited proteolysis mass spectrometry (LiP-MS), enables users to chart structural changes across the entire proteome. The LiP-MS technique is proprietary to Switzerland-based company Biognosys, which offers the approach as a contract research service. Biognosys made a splash at the American Association of Cancer Research (AACR)’s 2022 annual meeting presenting drug discovery data derived from its proteomics platforms, and has several collaborations with pharmaceutical firms, most notably AstraZeneca.
While these novel MS methods provide high resolution and sensitivity, they still require specialized expertise and centralized equipment like traditional MS, and other drawbacks include their complexity and length of workflow. These approaches are typically applied to drug studies, clinical biomarker discovery, proteome atlas creation, and in situations where particular proteins have to be interrogated deeply. These technologies comprise a substantial market today that is expected to double over the next six years, driven by adoption by biopharma.
An emerging strategy known as single-molecule fingerprinting is also well suited to these applications. This class of approaches aims to identify the entire chemical character of individual protein molecules via an end-to-end platform. One player is Nautilus Biotechnology, which offers a single molecule platform that involves preparation of protein arrays, cycled application of fluorescent affinity probes, and analysis with machine learning software. Another is Erisyon, whose “fluorosequencing” workflow labels amino acids on peptides in a sample with fluorophores, images the sample before and after an Edman reaction is performed to remove the N-terminal amino acid, and infers sequence information based on changes in fluorescence intensity when compared to a reference database. Single molecule fingerprinting technologies are still emerging and do not yet have a market. TDA expects these approaches to show high growth driven by the technique’s ability to interrogate proteins deeply at potentially lower cost; however, it is unproven if its accuracy will equal that of MS.