When Protein Quality Control Breaks Down 

Proteomic profiling shows exhausted T cells accumulate unfolded proteins despite retaining functional proteasomes 

A proteomics study of exhausted T cells has linked weakened anti-tumor immunity to disrupted proteostasis, revealing how protein buildup may contribute to immune cell dysfunction. Working across tumor-infiltrating lymphocytes and infection models, researchers at the University of California San Diego found that terminally exhausted T cells accumulate unfolded proteins despite retaining functional proteasomes.  

Using low-input, data-independent acquisition mass spectrometry, the team quantified more than 8,000 proteins from ex vivo T cell populations, revealing patterns not captured by transcriptomic data alone. Proteomic profiles showed that exhausted T cells retain active proteasomes but accumulate short-lived and unfolded proteins, alongside elevated markers of endoplasmic reticulum stress. 

“We found that exhausted T cells’ recycling programs are falling apart, leading to damaged and misfolded proteins that pile up with nowhere to go,” said first author Nicole Scharping in a press release.  

The analysis highlighted reduced expression of E3 ubiquitin ligases, including neuralized E3 ubiquitin protein ligase 3 (NEURL3), RING finger protein 149 (RNF149), and WD repeat and SOCS box-containing protein 1 (WSB1), which help tag damaged proteins for degradation. Restoring these ligases in T cells cleared protein accumulation, increased the proportion of stem-like T cell populations, and improved function in tumor models. 

Comparative proteomics across T cell states also showed that progenitor-like and terminally exhausted T cells were more clearly distinguished at the protein level than by transcriptomic profiles alone, revealing proteostasis-related changes that were less apparent from RNA data. 

The researchers suggest that restoring protein quality control could offer a way to strengthen T cell responses in tumors and chronic infection. “We uncovered one of the mechanisms by which T cells lose their ability to fight cancer and now we have a target that we can use to design interventions to improve responses to immunotherapy as well as prevent chronic infection,” said senior author Ananda Goldrath.  

A New Side of Cannabis Chemistry 

Online two-dimensional LC-HR-MS identifies rare flavoalkaloids and 25 previously unreported phenolics in Cannabis 

A detailed analysis of Cannabis leaves and flowers has uncovered rare flavoalkaloids in the plant for the first time, alongside 25 phenolic compounds not previously reported in Cannabis. In a study of three commercially grown South African strains, researchers at Stellenbosch University identified 79 phenolic compounds in leaf and inflorescence extracts. 

To handle the complexity of the extracts, the researchers combined hydrophilic interaction chromatography and reversed-phase liquid chromatography in an online two-dimensional workflow, coupled to ultraviolet detection and high-resolution mass spectrometry. The method separated phenolic classes by complementary chemical properties, helping the team assign structurally similar phenolic acids, flavonoids, glycosides, and rare low-abundance compounds with greater confidence. 

Among the most important findings was the tentative identification of 16 flavoalkaloids, a rare class of compounds containing a nitrogen-bearing group linked to a flavonoid backbone. These compounds were detected mainly in the leaves of one strain, where they appeared alongside higher levels of C-glycosylated flavones such as orientin, vitexin, and cytisoside derivatives. The authors note that the alkaloid portions could not be assigned unambiguously from the available high-resolution mass spectrometry data. 

“We know that Cannabis is extremely complex – it contains more than 750 metabolites – but we did not expect such high variation in phenolic profiles between only three strains, nor to detect so many compounds for the first time in the species,” said first author Magriet Muller in the team’s press release. “Especially the first evidence of flavoalkaloids in Cannabis was very exciting.” 

The findings shift attention away from cannabinoids alone and toward non-cannabinoid plant chemistry, particularly in leaves often treated as lower-value material. Further work will be needed to confirm the structures of the flavoalkaloids, assess how widely they occur across Cannabis strains, and test their biological activity.

Metaproteomics Reveals Microbial Proteins in Fermented Foods 

LC-MS/MS suggests that microbes contribute a measurable share of the proteins present in common fermented foods  

A metaproteomics survey of common fermented foods suggests that the proteins present in yogurt, cheese, bread, and other fermented products may come not only from the original ingredients, but also from the microbes that transform them. 

The analysis combined liquid chromatography-tandem mass spectrometry (LC-MS/MS) with tailored protein databases for each food type, allowing researchers to assign proteins to either microbial communities involved in fermentation or the original substrate. Across 17 fermented foods and three non-fermented controls, the workflow captured both the diversity and relative abundance of microbial proteins, while also estimating microbial proteinaceous biomass across each product. 

The contribution varied widely by food type, reaching up to 11 percent of total protein abundance and, in some products, a much larger share of the proteins identified. Brie cheese contained 1,023 microbial proteins out of 1,573 identified proteins, while microbial proteins accounted for 17–19 percent of identified proteins in bread samples and up to 43 percent in plant-based yogurt. 

“We chose foods that are commonly consumed and are easily accessible at the grocery store,” explained Manuel Kleiner, co-corresponding author of the research. “What we found surprising is that a large proportion of protein being eaten as part of these foods is actually microbially derived.” 

The findings suggest that microbes do more than drive fermentation: they also reshape the protein composition of the finished food. “These results offer future areas for investigation beyond the known probiotic effects of fermented foods, as the microbial proteins consumed as part of these foods may influence the host immune response or interact with the gut microbiota,” said co-corresponding author Ayesha Awan.

Isotope Tracing Reveals Soil as Main Source of Rice Dinitrogen Loss 

Nitrogen-15 tracing and membrane inlet MS suggest most dinitrogen loss in flooded rice comes from soil organic nitrogen  

Most dinitrogen emissions from flooded rice paddies may come from soil organic nitrogen rather than applied fertilizer, according to a recent study led by researchers at the Chinese Academy of Sciences. The finding challenges the long-standing assumption that fertilizer nitrogen is the dominant source of nitrogen gas loss in rice systems. 

Using in situ nitrogen-15 isotope tracing coupled with membrane inlet mass spectrometry, the team measured dinitrogen, ammonia, and nitrous oxide emissions across the rice-growing season and separated soil- from fertilizer-derived sources. The approach helped quantify dinitrogen losses against the high atmospheric background that has long made them difficult to track. 

Soil organic nitrogen accounted for 72–75 percent of dinitrogen emissions across conventional japonica and hybrid rice cultivars. Ammonia losses were mainly fertilizer-derived, while nitrous oxide came from both sources in near-equal proportions. The study also showed a seasonal shift, with ammonia volatilization dominating soon after basal fertilization and dinitrogen becoming the larger loss pathway later in the season. 

The authors propose a “microbial nitrogen pump” mechanism, in which fertilizer-derived ammonium is rapidly assimilated by soil microbes, creating a stoichiometric imbalance that accelerates decomposition of native soil organic matter. This mobilized soil nitrogen is then converted to dinitrogen through nitrification and denitrification. 

“In other words, fertilizer does not directly turn into nitrogen gas. Instead, it activates soil nitrogen pools, indirectly driving larger nitrogen losses,” said Longlong Xia, corresponding author of the study. 

Hybrid rice increased yield by 59 percent and reduced yield-scaled gaseous nitrogen losses by 43 percent, suggesting that cultivar choice could form part of more targeted nitrogen-management strategies. The authors say future work should test whether combining crop breeding with soil-microbe regulation, organic nitrogen replenishment, and tailored fertilizer timing can further reduce losses while maintaining long-term soil fertility.

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