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- Iron is crucial for cellular metabolism and cell growth. Nevertheless, in humans, both iron deficiency and disorders of iron overload are widespread. How cellular iron content varies depending upon iron availability, and how this influences cell function is poorly characterised. We developed a method to quantify metals in hundreds of cells per minute via single-cell inductively-coupled plasma mass spectrometry (sc-ICP-MS), and used this to explore iron usage by immune cells. Activated murine T-cells exposed to a 625-fold titration of extracellular […]
- Viral RNAs (vRNAs) interact with hundreds of host proteins, but how these interactions shape viral infection remains largely unknown. Here we developed a mass-spectrometry approach to identify cellular RNA-binding proteins (RBPs) that enhance or inhibit infection by modulating vRNA translation. We identified 130 RBPs that associate with polysomes in human cells infected with poliovirus, including known regulators of cap-independent translation from the viral internal ribosome entry site (IRES). We find that adenosine deaminase acting on RNA (ADAR1) is recruited to […]
- Covalent inhibitors are an emerging class of therapeutics, but methods to comprehensively profile their binding kinetics and selectivity across the proteome have been limited. Here we introduce COOKIE-Pro (COvalent Occupancy KInetic Enrichment via Proteomics), an unbiased method for quantifying irreversible covalent inhibitor binding kinetics on a proteome-wide scale. COOKIE-Pro uses a two-step incubation process with mass spectrometry-based proteomics to determine kinact and KI values for covalent inhibitors against both on-target and off-target proteins. We validated COOKIE-Pro using the BTK inhibitors […]
- Lung tissue is composed of various functional units, each essential for maintaining the intricate functions of the lung. Disruptions in the molecular and cellular mechanisms in the lung can cause tissue fibrosis, inflammation, and severe breathing difficulties, which are common in conditions such as bronchopulmonary dysplasia (BPD). BPDs molecular changes are not well understood, which hinders effective diagnosis and treatment. Here, we present a new multimodal imaging workflow for detailed molecular and metabolic characterization of tissues at multiple spatial scales. […]
- Lepidopteran-infecting baculoviruses represent one of the most promising alternatives for pest biocontrol. In particular, Spodoptera frugiperda granulovirus (SfGV) infects the fall armyworm Spodoptera frugiperda, an increasingly important pest for maize and other crops around the world. SfGV has been investigated due to its capacity to enhance other baculovirus infectivity and as a biopesticide itself. Although the proteome of SfGV occlusion bodies (OB) is fundamental for their infectivity properties, we still lack a detailed understanding of its protein components and how […]
- This came up when some old friends were visiting my lab this week. Where do I get these estimates for how much protein concentration should be in each single human cell? A couple of places, but the best organized place to start is the amazing Human Cell Tree Map – https://humancelltreemap.mis.mpg.de/Is is the topic of this recent PNAS paper. Now – they did this the hard way. They took tissue from people counted the cells and weighed them. For real. It was an amazing amount […]
- There is a lot to love in this short new preprint! Let's count them!1) This uses a NIST reference material and uses a very standard analytical approach to tell if one of these "next gen" proteomics things actually has quantitative accuracy. As an aside – this is one way to approach the easy and obvious SomaScam experiment that I've been searching for and pleading for – for nearly a decade. The authors spiked in a some proteins into plasma and then used the […]
- Cell-free expression systems have gained considerable attention for their potential in biomanufacturing, biosensing, and circuit prototyping. All these endeavors make use of the innate metabolic activity of cell lysates. However, our knowledge of the underlying nature of cell-free metabolism remains lacking. In this work, we use non-targeted mass spectrometry to generate time-course measurements of small molecules in E. coli cell lysates (metabolomics) during cell-free protein synthesis (CFPS) to show that the majority of E. coli's metabolism is active in cell […]
- Gliomas are the most common primary intracranial tumors, comprising 81% of malignant brain tumors, and currently lack effective therapies. Recent advances in molecular biology have shown that cancer cells exploit microtubule-associated proteins (MAPs) under stress to activate various signaling pathways. This study investigates the role of Doublecortin (DCX) in glioma metabolism and its impact on tumor proliferation. In this study, CRISPR-engineered glioma models with DCX overexpression or knockdown were analyzed using integrated genomic, transcriptomic, and metabolomic approaches. Metabolic activity was […]
- AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAHHHH!!!One of the biggest challenges in adopting a new piece of hardware is that you might lose access to software that you've used for years and are very comfortable using. Losing MetaMorpheus by adopting TIMSTOFs hurt. For real. And this isn't a dig on other great software out there – I just know how to use MM and how to read the data and how to make MM do what I want it to do. I have whole downstream pipelines […]
- Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00070
- Single-particle mass spectrometry (SPMS) has the potential to identify bacterial species. However, this crucial topic has received limited attention in research. This investigation aims to fill this gap by combining SPMS with supervised learning algorithms to distinguish six bacterial species. The study begins by collecting particle size and mass spectra data for six bacteria and four biomass combustion products (BCPs) using SPMS. These data are used to compare particle sizes and create a comprehensive dataset containing mass spectra for all […]
- Environmental Science & TechnologyDOI: 10.1021/acs.est.4c11600
- Publication date: Available online 21 June 2025Source: Analytica Chimica ActaAuthor(s): Riin Rebane, Ivo Leito
- Journal of Proteome ResearchDOI: 10.1021/acs.jproteome.5c00219
- A mechanistic basis for luciferase bioluminescence provides a glimpse into its evolutionary role for organism survival, as it provides a blueprint to engineer luciferase enzymes for advanced technological applications. Gaussia Luciferase is among the brightest natural luciferases, but (1) the evolutionary development of its luminescence behavior remains unclear, (2) recent fundamental studies utilized E. Coli expression systems instead of eukaryotic expression systems, and (3) notable mutants have been discovered but not integrated into comprehensive mechanistic analysis. We describe new mechanistic […]
- Publication date: 1 January 2026Source: Talanta, Volume 296Author(s): Peng Gan, Xin Zhang, Yu Wang, Qianru Zhou, Xiaoli Zou
- Publication date: 1 January 2026Source: Talanta, Volume 296Author(s): Fabrice Saintmont, Yoann Ladner, Catherine Perrin, Sébastien Dutertre, Claudia Bich
- Hydrogen deuterium exchange mass spectrometry (HDX-MS) is a powerful technique to probe changes in protein structural dynamics. In differential settings, HDX-MS compares dynamics between protein states, such as conformational changes resulting from antibody-antigen binding or the effects of mutations. As the method becomes more high-throughput, the number of comparisons between peptides and states grows, creating a multiple hypothesis testing challenge where some observed changes may result from statistical randomness rather than biological differences. While this problem can be addressed by […]
- Matrix-assisted laser desorption/ionization coupled with time-of-flight mass spectrometry (MALDI-TOF MS) is a fast emerging and robust method for rapid and accurate characterization of arthropod vectors. Correct identification of ticks is key in monitoring medically or veterinary relevant species and associated pathogens. It has been extensively used for tick identification based on leg proteins; however, in North America, MALDI-TOF MS has not been explored for comprehensive identification of ticks, except for a few studies focusing on a limited number of species. […]
- This isn't the first study of it's type but this digs into more variations of how to fix cells. Something everyone doing single cell proteomics (SCP) has struggled with is HOW TO GET THE FREAKING CELLS TO THE MASS SPEC LAB.At ASMS, I detailed my adventures preparing EvoTips and driving them across the completely insane and poorly maintained Pennsylvania Turnpike. In case you were wondering – I have far better luck keeping the tips at a stable temperature and being on […]
- Dengue virus (DENV) causes a wide variety of dengue diseases that threaten over half of the world's population. At present, there is no antiviral therapeutics against dengue. Virus infection and its associated pathologies are the result of a myriad of interactions between the virus and its host, of which most are protein-protein interactions (PPIs). Virus-encoded proteins modulate the host environment for the virus' benefit by interacting with host proteins during infection. Thus studies of these virus-host PPIs are most informative […]
- Untargeted mass spectrometry measures many spectra of unknown molecules. Tandem mass spectrometry (MS/MS) generates fragmentation patterns representing common substructures termed Mass2Motifs. However, MS/MS-based substructure identification is limited by computational efficiency and interpretability. Here, we introduce a complete overhaul of MS2LDA, overcoming limitations of its predecessor. We report an up to 14x speed improvement for unsupervised Mass2Motif discovery, allowing it to process larger datasets. Furthermore, the new automated Mass2Motif Annotation Guidance (MAG) aids in structurally identifying Mass2Motifs. Using three curated MotifDB-MotifSets […]
- Publication date: Available online 19 June 2025Source: Journal of ProteomicsAuthor(s): Rafael F. Castelli, Haroldo C. de Oliveira, Marlon D.M. Santos, Amanda C. Camillo-Andrade, Flavia C.G. Dos Reis, Paulo C. Carvalho, Marcio L. Rodrigues
- Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00088