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This report describes single-cell proteomic analyses of cells dissociated from a complex mammalian tissue using direct label-free mass spectrometry (single-cell proteomics by mass spectrometry, SCP-MS). The nanoDTSC approach was applied to profile individual cells from …
Read PDFMass spectrometry-based immunopeptidomics is a powerful approach for untargeted discovery of peptides presented on MHC molecules, which can guide the selection of vaccine antigens and immunotherapy targets. First-generation immunopeptidomics workflows require processing of hundreds of …
Read PDFAging is asynchronous across cells and organs. Here we tested whether plasma proteomics can be used to analyze cell type-specific aging. From analyses of over 7,000 plasma proteins measured in 60,542 individuals, we developed machine …
Read PDFPolymorphonuclear neutrophils (PMNs) are innate cells that may act as myeloid-derived suppressor cells (MDSCs), most often characterized by their immunosuppressive capacity towards immune cells within the tumor microenvironment. Over the last decade, many studies have …
Read PDF<h4>Rationale</h4>Cardiac fibrosis formation leads to cardiac dysfunction that is mainly caused by a high fat diet accompanied by an increased accumulation of apoptotic cells. MER proto-oncogene tyrosine kinase (MerTK) is a major receptor for efferocytosis, …
Read PDFThe richness of our somatosensory experience is reflected in the functional diversity of somatic sensory neurons. Single-cell RNA sequencing of sensory neurons has revealed a molecular basis for such diversity<sup>1-3</sup>. However, sensory neuron diversity has …
Read PDFSpatial proteomics has become one of the mainstays of spatial biology at an impressive speed. It enables the in-depth study of protein abundance, localization, and microenvironmental context at the levels of tissues, cells, and subcellular …
Read PDF<h4>Background</h4>Recent advances in instrument sensitivity and sample preparation techniques are significantly improving the ability to study the heterogeneity of cell populations at the single-cell level by mass spectrometry-based proteomics. Integrating multiple layers of cellular data …
Read PDFSingle-cell proteomics (SCP) is an exciting new field of study with developments in the areas of sample preparation, instrumentation and informatics. SCP has captured the imagination of biologists and clinicians and the critical interest of …
Read PDFObtaining complete and accurate bacterial genomes is vital for studying the characteristics of uncultured bacteria. Single-cell genomics is a promising approach for the culture-independent recovery of bacterial genomes from individual cells. However, single-amplified genomes (SAGs) …
Read PDFNucleic-acid barcoding is an enabling technique for many applications, but its use remains limited in emerging long-read sequencing technologies with intrinsically low raw accuracy. Here, we apply so-called NS-watermark barcodes, whose error correction capability was …
Read PDFSingle-cell nanopore sequencing of full-length mRNAs transforms single-cell multi-omics studies. However, challenges include high sequencing errors and dependence on short-reads and/or barcode whitelists. To address these, we develop scNanoGPS to calculate same-cell genotypes (mutations) and …
Read PDFDue to remarkably stereotyped development and small numbers of cells, ascidian embryos are invaluable as models for investigating the principles of chordate development at single-cell resolution. Established model species of ascidians, such as Ciona spp. …
Read PDFPlasmodiophora brassicae causes clubroot disease in brassica crops worldwide but cannot be cultured outside its host, complicating its genome sequencing. Previous efforts relied on infected plant tissues and subtracting host DNA, which left microbial contamination …
Read PDF[This corrects the article DOI: 10.3389/fonc.2025.1588514.].
Read PDFMedicinal plants synthesize an immense diversity of specialized metabolites that play crucial roles in ecological interactions and serve as valuable pharmaceutical resources. However, the biosynthetic pathways responsible for this chemical diversity remain largely uncharacterized. These …
Read PDFMacrophages are among the most abundant immune cells in solid tumors, yet how macrophage lineage and spatial organization shape antitumor immunity remains unclear. Here we uncovered a division of labor between tissue-resident CD206<sup>hi</sup> and CD206<sup>lo</sup> …
Read PDFMulti-omics strategies, integrating genomics, transcriptomics, proteomics, and metabolomics, have revolutionized biomarker discovery and enabled novel applications in personalized oncology. Despite rapid technological developments, a comprehensive synthesis addressing integration strategies, analytical workflows, and translational applications has …
Read PDFThe cellular origin and molecular mechanisms underlying therapeutic resistance in colorectal cancer remain largely unclear.This study integrates single-cell transcriptomics, spatial transcriptomics, molecular docking, and multi-cohort public databases to systematically elucidate the epithelial cell-driven drug resistance …
Read PDF<h4>Background</h4>Diabetic kidney disease (DKD) is a severe complication of diabetes mellitus and the leading cause of chronic kidney disease worldwide. Among the many drivers of tubular injury, lipid accumulation and inflammation are emerging as major …
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