The Fundamentals of Mass Spectrometry-Based Proteomics

Mass spectrometry is one of the mainstays of proteomics. Technical advances in the field of mass spectrometry such as data analytics, instrumentation, and general workflow improvements have enabled greater depth, robustness, and scalability in proteomics, empowering researchers to quantify proteins on a proteome-wide scale.

Mass spectrometry-based proteomics includes an expanding collection of technologies that provide a way for high throughput characterization and quantification of proteins in a biological system. While the genome sequence provides a detailed snapshot of the biological complexity of an organism, activity that occurs at the protein-level cannot be deduced by genome analysis. Therefore, a proteomics approach can be used in combination, or in place of, genomics analysis — bridging the gap between genotype and phenotype — and providing the most comprehensive approach for the profiling proteins, including their interactions and modifications.

How Does Mass Spectrometry Proteomics Work?

The most common mass spectrometry method for studying proteins is described as “bottom-up” proteomics, which begins by cleaving a mixture of proteins into peptides. This mixture is separated via liquid chromatography before being ionized and analyzed in the mass spectrometer.

The first thing to understand about how mass spectrometry works is the basic principles of mass spectrometers. These comprise three main components: an ion source, a mass analyzer, and a detector. Using a high voltage, liquid phase peptides are converted into gaseous ions that are fed into the mass analyzer, where they are separated by their mass-to-charge ratios (m/z). An electrical detector records what is known as a spectrum pattern, which represents the number of ions per m/z. This can be interpreted to identify the molecules that make up proteins in the original sample.

In the context of proteomics, mass spectrometry is an invaluable tool as it enables unprecedented specificity and outstanding depths of quantification. Additionally, tandem mass spectrometry, whereby multiple analyzers are coupled together to maximize the number of identified peptides in complex mixtures, can provide exquisitely detailed information on amino acid sequence.

Clinical Applications of MS

Mass spectrometry-based proteomics has a vast array of descriptive and quantitative applications. For example, in the clinical field, it is being applied to define drug targets, aid in the discovery of disease biomarkers and map aberrant pathways that underlie disease, thereby revolutionizing the field of diagnostics. This is having a significant impact in the field of oncology where it is expediting cancer detection, improving risk stratification, and facilitating the accurate monitoring of patient conditions and response to treatment by providing proteomic profiles of responders vs non-responders. This can enable the exploration of whole panels of biomarkers for accurate predictions of clinical responses.

Enhancing Proteomics Workflows with Biognosys

The previous decade witnessed extensive development of mass spectrometry-based proteomics, expanding coverage of the proteome, improving data quality and strengthening identification confidence and quantification accuracy. The future of this technology looks very promising with advancements in set to enable a greater depth of coverage of the proteome with identification of over 13,000 proteins and continual advances each year approaching total coverage of all cell line proteins. Furthermore advances in quality workflows result in data reproducibility which make Biognosys next generation proteomics ideal for analysis of longitudinal clinical study samples. Interested in learning more about mass spectrometry proteomics and how it can enhance your research? Simply contact a member of the Biognosys team today.