Back to School: Mass Spectrometry for Proteomics

Mass spectrometry (MS) has been around for decades and has been used for many applications. But in recent years, this technique has made an increasingly large impact on the life sciences, particularly in proteomics and metabolomics. As researchers look beyond genomics (what could be happening in a cell) to proteomics (what is happening in a cell), MS has become a critically important technique for studying the proteome, the range of proteins that can be expressed by a cell, tissue, or organism.

1. MS measures the mass-to-charge ratios of molecules to calculate their molecular weight. First, molecules are converted into a gaseous phase, to keep them stable in a vacuum, and transported with electrical fields. The ions’ mass-to-charge ratios are then analyzed through various algorithms to identify molecular components.
2. MS is incredibly valuable for studying proteins because the technique’s accuracy is off the charts. High resolution instruments can calculate mass down to a single electron. As a result, labs can put complex mixtures into their machines and garner incredible insights.
3. Researchers can perform complete, unbiased discovery because nobody is telling the instrument what to look for, it simply sees what is there. This has become increasingly important, as researchers decipher the mechanisms driving cancer, neurodegenerative diseases, aging, and many other conditions.
4. MS produces rich data. In addition to delivering the mass of each intact peptide, the instrument also hits the mixture with enough energy to break molecules apart, providing information on individual amino acids, as well as protein sequences. This gives researchers a great tool to confidently identify specific peptides.
5. MS instruments have grown exceptionally smart, leveraging algorithms to weed out non-peptide molecules and help scientists focus on proteins.
6. MS is providing insights into proteomics in the same way next-generation sequencing has illuminated genomics, providing a high-throughput, multiplexed technique to rapidly answer biological questions.
7. In the past, MS was often reserved for expert users, making it more of a specialist’s tool. This helped keep mass spec core facilities busy, but it also shaped how research was conducted in many labs. Scientists often gravitated towards genomics and/or transcriptomics – these instruments were just easier to use.
8. But now, advanced machines are making mass spectrometry more accessible, democratizing access to proteomic data. MS is becoming particularly important for drug discovery, providing detailed insights into how proteins react to specific agents.
9. MS instruments have become so sensitive that they can now explore single cell proteomics, helping researchers investigate how protein populations change from cell to cell in a heterogeneous environment.
10. For proteomics, MS is a workhorse because the technique is versatile and can be used to address questions that simply could not be answered before. In addition, there have been enormous advances in both the upstream sample prep and the downstream data analysis. The result is a comprehensive, hyper-accurate methodology for characterizing proteins that is opening new windows into cell biology.

Want to learn more? Earn an A plus by listening to one of Seer’s? field application scientists, Michelle Dubuke , on the SLAS (Society for Laboratory Automation and Screening) New Matter Podcast: https://seer.bio/company/newsroom/?tx_category=podcasts

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