Unlocking the potential of mass spectrometry-based protein analysis

Proteins are a fundamental unit of biological systems. They determine cell structure and activity, facilitate signaling between cells and tissues, and catalyze chemical reactions.1 However, proteins are not just a simple amino acid sequence. They assemble into 3D structures and undergo post-translational modifications like glycosylation, resulting in tens of thousands of possible variations.2 Furthermore, most proteins do not function in isolation; there are millions of potential combinations when they interact with each other or form complexes.3,4

Image Credit: S. Singha/Shutterstock.com

Image Credit: S. Singha/Shutterstock.com

Historically, these factors have made the identification of proteins incredibly challenging. The advent of mass spectrometry (MS) and MS-based proteomics helped to change that.2 MS is an analytical technique used to ascertain the molecular weight of compounds via the separation of molecular ions based on their mass and charge (m/z).5 This method provides researchers with a better understanding of proteins to determine the molecular mechanisms of disease, identify potential therapeutic targets, and discover biomarkers that could aid in early disease detection.

As bioanalytics and life sciences are one of the main tracks at this year’s Pittcon, attendees will have the opportunity to learn about the latest innovation in MS-based methods of protein analysis from researchers and manufacturers who are leading the way in pushing forwards the next wave of MS innovation in the life sciences.

Surface Protein Glycosylation

At Pittcon, Dr. Ronghu Wu, associate professor in the School of Chemistry and Biochemistry at Georgia Institute of Technology, will host a symposium on the latest advance in biological mass spectrometry. Dr. Wu’s group has worked on the development of MS-based chemical and enzymatic methods for analyzing protein modifications, with a particular focus on glycosylation. These surface glycoproteins regulate almost all extracellular events, including cell-cell communications. This is particularly important as errors in glycosylation tend to be linked to illnesses, including cancer and infectious diseases.

Dr. Wu will present research conducted by his lab, in which they developed an approach for the targeted analysis of surface glycoproteins with MS. The team used metabolic labeling and biorthogonal chemistry to specifically tag and selectively enrich surface glycoproteins. Using MS-based proteomics, they performed site-specific global identification and quantification of surface glycoproteins. As part of this talk, Dr. Wu will outline this approach was applied to the study of surface glycoproteins on monocytes and macrophages, allowing them to identify novel surface glycoproteins in these cells in response to infection.

Protein Cross-Talk

Professor of Cancer Biology from the University of Kansas Medical Center, Michael Washburn, will also be at Pittcon. His research focuses on applying innovative proteomic and cellular technologies to study chromatin remodeling complexes in cancer. Washburn will present an abstract outlining his lab’s research into the development of a novel approach for studying human protein-protein interactions (HPPIs).

Researchers face huge challenges in understanding the structural and functional significance of HPPIs, which can exist in millions of combinations, differing between different cells and disease states within the human body.3 At present, the established approach for analyzing HPPIs is affinity purification with MS (AP-MS). However, this strategy does not selectively isolate specific protein complexes but rather provides a representation of the average population of the complexes that contain a specific protein within a cell.

Therefore, Dr. Washburn’s novel approach, known as Serial Capture Affinity Purification (SCAP), means that researchers will be able to study any pair of proteins that might directly associate.3 In this method, two proteins of interest are introduced simultaneously as baits to reduce the complexity and increase the purity of protein complexes. Label-free quantitative MS is then applied to help identify the protein complexes that contain the two proteins of interest. This method of combining SCAP with cross-linking MS can then be used with other data and computational methods to build integrative structural models. The team advocates that this approach can be used to analyze any protein complex in human tissue culture cells.3

Designing Innovation

Alec Valenta from Thermo Fisher Scientific will also be presenting at Pittcon. Dr. Valenta will discuss new approaches to low-flow LC-MS that will minimize residual analyte, or carryover, between runs. One approach uses ZebraWash, an automated, optimized, easy-to-use solution to remove carryover while maintaining throughput, even with large volume injections.6 Another harnesses the multi-draw functionality of the company’s Vanquish Neo, with trifluoroacetic acid in the loading buffer as a strong ion-pairing reagent.7 The team’s data demonstrated 100% sample recovery with 500 µL sample injections.

In addition to ThermoFisher, an array of representatives from other companies delivering innovation in MS for life sciences will be presenting as part of the Pittcon Expo. This includes Bruker, who has an extensive MS product line that includes timsTOF, MALDI-TOF/TOF, and UHR-QTOF. Bruker also offers industry-leading software solutions for MS, including SCiLS Lab for MS Imaging, MetaboScape®, and Biopharma Compass®. Waters will also be in attendance to discuss its MS systems and solutions. This includes quantitative MS, time-of-flight MS, tandem quadrupole MS and their portfolio of medical devices for the clinical laboratory.

MS in the Life Sciences at Pittcon

Innovation in MS plays an ongoing role in understanding the complex structures and dynamics of proteins in living organisms. With the critical role that proteins play in human health and disease, these advances have the potential to inform new understanding of illnesses and discover new ways to diagnose and treat them.

As one of the main tracks at Pittcon, attendees will have the opportunity to gain insight into the latest advances in the field first-hand from leading researchers and manufacturers.

Visit the Pittcon website to find out more about Pittcon, or check out the Session Gallery to see which talks and symposia are on offer throughout the week.

References and further reading

  1. Timp W, Tim G. (2020) Beyond mass spectrometry, the next step in proteomics. Sci Adv., 6, p. eaax8978. doi: 10.1126/sciadv.aax8978.
  2. Noor Z, Ahn SB, Baker MS, et al. (2021) Mass spectrometry-based protein identification in proteomics-a review. Brief Bioinform., 22, pp. 1620-1638. doi: 10.1093/bib/bbz163.
  3. Suttapitugsakul S, Sun F, Wu S. (2020) Recent Advances in Glycoproteomic Analysis by Mass Spectrometry. Anal Chem., 92, pp. 267-291. doi:10.1021/acs.analchem.9b04651.
  4. Iwamoto N, Shimada T. (2018) Recent advances in mass spectrometry-based approaches for proteomics and biologics: Great contribution for developing therapeutic antibodies. Pharmacol Ther., 185, pp. 147-154. doi: 10.1016/j.pharmthera.2017.12.007.
  5. Meštrović, D.T. (2019) What is mass spectrometry?, [Online] News. Available at: https://www.news-medical.net/life-sciences/What-is-Mass-Spectrometry.aspx#:~:text=Reviewed%20by%20Susha%20Cheriyedath%2C%20M,prior%20knowledge%20of%20its%20composition.
  6. Schaffer LV, Millikin RJ, Miller RM, et al. (2019) Identification and Quantification of Proteoforms by Mass Spectrometry. Proteomics., 19, p. e1800361. doi: 10.1002/pmic.201800361.
  7. Liu X, Zhang Y, Wen Z, et al. (2020) Driving integrative structural modeling with serial capture affinity purification. Proc Natl Acad Sci USA., 117, pp. 31861-31870. doi: 10.1073/pnas.2007931117.

About Pittcon

Pittcon® is a registered trademark of The Pittsburgh Conference on Analytical Chemistry and Applied Spectroscopy, a Pennsylvania non-profit organization. Co-sponsored by the Spectroscopy Society of Pittsburgh and the Society for Analytical Chemists of Pittsburgh, Pittcon is the premier annual conference and exposition on laboratory science.

Proceeds from Pittcon fund science education and outreach at all levels, kindergarten through adult. Pittcon donates more than a million dollars a year to provide financial and administrative support for various science outreach activities including science equipment grants, research grants, scholarships and internships for students, awards to teachers and professors, and grants to public science centers, libraries and museums.

Visit pittcon.org for more information.

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Last updated: Feb 1, 2024 at 7:22 AM


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