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We offer a selection of papers on a variety of topics recently published in the journal Molecular & Cellular Proteomics.

Using co-elution to study protein interactions

Studying how the vast network of proteins and molecules in a cell interact, a discipline known as interactomics, is crucial to researchers’ fundamental understanding of biological processes and for the development of new medicines and biotechnology. Among the technical strategies for mapping the interactome, co-elution is a global protein interaction mapping method. However, strategies vary across studies that utilize co-elution, depending on experimental considerations.

In in the journal Molecular & Cellular Proteomics, Daniela Salas and colleagues at the University of British Columbia delineate co-elution methods used to map protein–protein interaction networks and discuss important considerations in designing co-elution studies, such as the choice of separation method and how to analyze co-elution profiling studies. The researchers also discuss the benefits of co-elution versus other mapping methods, including the time and resources required to perform the protein mapping and the number of protein interactions that can be explored.

Confident identification of citrullinated peptides

Citrulline is an amino acid not encoded in the genome. It is generated by a post-translational modification to the amino acid arginine, a process known as citrullination. In recent years, scientists concerned with the immune system have been paying attention to citrullination because of its role in inducing anti-citrullinated proteins/peptide antibodies, which results in an autoimmune reaction where the host’s immune system attacks its healthy tissue. The bacteria Porphyromonas gingivalis generates citrullinated epitopes in the periodontium, which contributes to chronic periodontitis and recently has been linked to rheumatoid arthritis.

Using a new two-dimensional heptafluorobutyric acid–based separation system combined with liquid chromatography–mass spectrometry, Daniel Larsen and colleagues at the University of Southern Denmark analyzed the outer membrane vesicles and other related elements of P. gingivalis to identify 79 citrullinated proteins with 161 citrullination sites. These results were reported in published in the journal Molecular & Cellular Proteomics. This work establishes a method for identifying citrullinated proteins that will advance development of treatments for human autoimmune and inflammatory diseases.