For many, a pill to suppress stomach acid is a routine solution for heartburn. Proton pump inhibitors (PPIs)-including common medications like omeprazole, lansoprazole, esomeprazole, pantoprazole, and rabeprazole-are among the most widely used drugs globally. However, a study published in the European Journal of Hospital Pharmacy suggests that when these medications are used long-term, the effects may extend far beyond the digestive system. The research indicates a statistical link between taking PPIs for more than 30 days and an increased risk of cardiovascular events. According to the data, individuals using these drugs for over a month were 58% more likely to experience a cardiovascular problem, such as a heart attack or cardiac arrest, compared to those who did not take them. The risk of death from cardiac causes was found to be 38% higher. Interestingly, the study found no statistically significant increase in the risk of stroke. Understanding the risk It is important to distinguish between a statistical association and a proven cause. This was an observational study, meaning it identified a pattern but did not definitively prove that the medication caused the heart issues. Researchers from the National University of Malaysia have proposed several biological hypotheses to explain the link. One theory focuses on nitric oxide (NO), a molecule essential for helping blood vessels relax and expand; PPIs might reduce NO levels, potentially impairing vascular health. Other theories suggest that altering gut microbiota could trigger systemic inflammation or that PPIs may interact with anticoagulants (blood thinners).

Motivation Analysis of context-specific protein-protein interactions (PPIs) provides deeper insight into protein function, revealing how cellular pathway components interact in certain perturbation conditions. However, identifying such interactions experimentally often requires combining affinity purification with mass spectrometry, proving costly and time-consuming. On the other hand, it has been shown that an increase in protein abundance does not always correspond to an increase in protein interaction, making it an unsuitable surrogate for interaction studies. Results To address this, a random forest model was created using PPI-specific MINT embeddings and condition-specific mass spectrometry protein abundance information to predict differential interactions across two experimental conditions. The model was trained and tested on validated context-specific PPIs from eight distinct cell-lines, demonstrating proficiency in predicting differential PPIs for both novel proteins and cell lines. To our knowledge, we provide the first computational model that predicts differential PPIs between experimental conditions. Availability and implementation The code is available on GitHub and backed up on Zenodo (DOI: 10.5281/zenodo.23758127). The model is freely available on Zenodo (DOI: 10.5281/zenodo.23757927).

Background:Proton pump inhibitors (PPIs) have been linked to hyponatremia, but evidence based on laboratory-confirmed sodium measurements remains...

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Crosslinking mass spectrometry (XL-MS) enables residue-level characterization of protein-protein interactions (PPIs) in both purified assemblies and complex biological systems. Cleavable crosslinkers such as DSSO are widely used to facilitate analysis of complex samples, yet there remains limited consensus on how best to leverage their properties in both acquisition and data analysis workflows. In part, this reflects differences in scoring, classification, and false discovery rate (FDR) estimation across analysis pipelines. Therefore, an integrated XL-MS data analysis pipeline that enables confident identification of MS-cleavable cross-linked peptides through improved scoring and rigorous FDR assessment is essential for systematically comparing and benchmarking workflows across different sample preparations. To this end, we implemented a new capability within the Protein Prospector search engine to improve MS2-based identification of MS-cleavable cross-linked peptides. Next, we developed Touchstone, a framework for re-scoring, classification, FDR-controlled summarization, and visualization of Prospector XL-MS search results. Using this approach, we evaluate the contributions of DSSO-specific fragmentation features and compare multiple acquisition strategies across datasets ranging from purified macromolecular assemblies to proteome-scale samples. We find that the primary advantage of DSSO arises from enhanced backbone fragmentation of both linked peptides, rather than from diagnostic ion formation, and that incorporating diagnostic ion pairs into MS2-based scoring or filtering does not improve identification performance. Benchmarking against established datasets shows that Prospector-Touchstone performs comparably to leading methods for non-cleavable crosslinkers and provides improved performance for DSSO analysis. We further compare acquisition strategies and find that for purified protein assemblies, MS2.stHCD characterizes more residue-pairs than ETD-based, MS3-based, and hybrid methods. In contrast, for proteome-scale XL-MS, MS3-based acquisition yields similar numbers of inter-protein PPIs with lower error rates despite reduced sampling depth. Together, these results highlight complementary strengths of MS2- and MS3-based workflows and provide practical guidance for MS-cleavable XL-MS experiments with varying sample complexities.

A new Bentley study, published in JAMA Health Forum, shows that the amount invested per approved drug by the NIH is comparable to that of reported investment by the biopharmaceutical industry.

13 October 2026 (Navroze Bureau) Omeprazole is widely prescribed to manage acid-related digestive conditions, including gastroesophageal reflux disease (GERD), heartburn and stomach ulcers. However, research suggests that prolonged use of proton pump inhibitors (PPIs), the class of medicines to which omeprazole belongs, may be associated with an increased risk of small intestinal bacterial overgrowth (SIBO). SIBO occurs when excessive numbers of bacteria accumulate in the small intestine, potentially causing bloating, abdominal discomfort, gas and changes in bowel habits.