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The importance of sharing proteomics data. Detecting nitrotyrosine-containing proteins. Analyzing yeast proteasomes. Read about articles on these topics recently published in the journal Molecular & Cellular Proteomics.

Importance of sharing proteomics data

Proteomics encompasses the study of protein function, structure and expression. Proteomics data sharing can help reduce the cost of research and fast-track scientific discoveries by promoting data reproducibility. The importance of sharing proteomics data is evident from the recent example of international collaboration to develop the SARS-CoV-2 vaccine. Since 2003, the National Institutes of Health have required public data-sharing for research associated with their grants of over $500,000, and some scientific journals require data sharing. These practices have led to increased data-sharing in the last 20 years. However, proteomics data sharing is not prevalent and lacks organizational regulations.

In a recent published in the journal Molecular & Cellular Proteomics, Mahasish Shome and colleagues at Stanford University found that researchers are reluctant to share data for several reasons: They have no incentive for data sharing, although it requires a lot of time to organize the data, and some scientists fear possible financial loss associated with sharing raw data or are ignorant of the regulations in place. However, some sources of proteomics data exist, and the authors provided examples of proteomics data repositories including the Protein Data Bank, Biological Magnetic Resonance Data Bank and ProteomicsDB.

Based on the literature, the authors concluded that the benefits of sharing data include improving data accuracy, creating a common megadata repository, enhancing collaborations and reducing research costs and time. However, the authors stated that data sharing also has potential negative outcomes: It may lead to data compromise and misuse. The authors assert that researchers first need data use and sharing training, which includes data validation and citation. The authors concluded that if researchers share proteomics data responsibly by safeguarding the privacy of individuals, then they can use this common repository of data leading to faster discoveries with reduced cost.

Detecting nitrotyrosine-containing proteins

Proteins and peptides undergo post-translational modifications, or PTMs, which can change their structure, function and cellular localization. One of these PTMs, the nitration of tyrosine, is irreversible. Nitrotyrosine-containing peptides and proteins are associated with inflammatory, neurodegenerative and cardiovascular disorders as well as cancer. These modified proteins and peptides are also oxidative stress markers. However, due to their low abundance, researchers cannot easily identify them using conventional lab techniques.

Recently, Firdous Bhat of the Mayo Clinic and an international team of researchers developed a technique to detect nitrotyrosine-containing proteins and peptides using four commercial monoclonal antibodies to enrich their abundance. The published their the journal Molecular & Cellular Proteomics.

The authors tested the technique in a multiple myeloma cell line and then analyzed the peptides using liquid chromatography–mass spectrometry. They identified more than 2,600 nitrotyrosine-containing peptides and proteins — the largest number containing nitrotyrosine identified to date. The authors synthesized and validated 101 novel peptides using a synthetic library and showed that 70% of their results were accurate. The researchers suggest that this method can be used to investigate the pathological implications behind nitrotyrosine-containing peptides and proteins in various diseases.

Analyzing yeast proteasomes

In eukaryotic cells, protein complexes called proteasomes break down misfolded and damaged proteins. The proteasome is made up of core proteolytic subunits that degrade peptides as well as regulatory subunits that facilitate this process. Fluctuations in cellular proteasome levels can disrupt protein homeostasis and lead to diseases, such as Alzheimer’s disease, Huntington’s disease, cystic fibrosis and more.

In a recent published in Molecular & Cellular Proteomics, Manisha Priyadarsini Sahoo, Tali Lavy and a team from the Technion–Israel Institute of Technology investigated proteasome activity in normal and mutant yeast strains lacking the proteasome integral subunits Sem1 and α3. They used a novel technique called activity-guided proteomic profiling to isolate and analyze active proteasome complexes. In this method, the researchers used a fluorogenic peptide substrate of the proteasome as an indicator to select the active proteasome complexes for analysis. They found that the mutant strains exhibited reduced proteasome activity, which was attributed to increased binding of Fub1, a proteasome inhibitor, and incomplete maturation of the β2 and β5 proteolytic subunits.

The authors suggest that these immature subunits may be important mediators of proteosome quality control. Future directions will investigate the role of other immature proteosome subunits and their potential binding partners. These studies could inform how to treat disorders associated with aberrant proteosome expression or function.