Combined RSS Items
- The study of microbial volatile organic compounds (mVOCs) is a growing area of research, with applications ranging from agriculture to human health. The majority of the mVOC data are from in vitro liquid cultures, while few analyses of bacterial and fungal volatilomes on solid media cultures exist. Studies comparing liquid versus solid cultures of bacteria and fungi show significant changes to the soluble metabolites that are produced, suggesting that large differences would be observed for mVOCs based on the culture […]
- Spectral similarity is widely used as a proxy for structural similarity in tandem mass spectrometry (MS/MS) analyses, including library matching and molecular networking. However, the relationship between spectral similarity scores and true structural similarity remains imperfect, limiting compound identification in metabolomics studies. Here, we present BertMS, a spectral similarity framework based on bidirectional encoder representations from transformers (BERT), which learns contextualized representations of fragment ions from large scale MS/MS data. Using datasets from MoNA and GNPS comprising over 100,000 unique […]
- Okay, so maybe what we actually need is 500 parallel ion traps within our instruments!!! This is just an early proof of concept of teeny tiny ion traps operating under the control of individual (or individual clusters?) of GPU (CUDA-type?) cores. I've never seen anything at all like this so it jumped the queue of things I meant to type about this week.
- Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.6c00017
- Accurate genome annotation is fundamental to modern biology, yet distinguishing authentic protein-coding sequences from prediction artifacts remains challenging, particularly in complex plant genomes where automated methods are error-prone and manual curation is rarely feasible due to prohibitive time and costs. Here, we present GAP-MS (Gene model Assessment using Peptides from Mass Spectrometry), an automated proteogenomic pipeline that leverages mass spectrometry evidence to systematically validate the protein-level accuracy of predicted gene models. Applied across 9 major crop species, GAP-MS consistently improved […]
- Analytical ChemistryDOI: 10.1021/acs.analchem.5c07216
- Anal. Methods, 2026, Accepted ManuscriptDOI: 10.1039/D5AY01988E, CommunicationGui Ying Kang, Wei Cheng, Jin Li, Dahua Zhang, Yufeng LiuThe high-temperature detergency of alkyl salicylates (ASs) as lubricant detergents is influenced by their composition and molecular structure. Analysis via normal-phase liquid chromatography (LC) combined with mass spectrometry (MS) reveals…The content of this RSS Feed (c) The Royal Society of Chemistry
- Journal of Mass Spectrometry, Volume 61, Issue 4, April 2026.
- Mammalian development takes place inside the maternal uterus, creating technological constraints that make difficult the study of embryogenesis in live developing embryos. A central challenge for understanding the role of metabolism in mammalian development is discriminating placental and uterine-regulated signals from embryo-intrinsic processes independent of maternal influence, a process that until now has remained inseparable during gastrulation and organogenesis. Ex utero culture systems allowing continuous growth of embryos during pre-gastrulation to organogenesis offer a promising solution to this challenge. Here, […]
- Paired electrolysis enables para-C–H amination of phenols with nitroarenes and mechanistic visualization via multifunctional electrochemical mass spectrometry
- Yikes. Okay, so if there is legitimate instrument competition across the board, I think there should be some seriously competitive pricing in the LCMS space this year. If you're not seeing it, demo something else and let them know about it because – holy cow…I had a super early version of the 7600. I had it before it could do ZenoPulsing/ ZenoTrapping in DIA. It was a nice instrument and super ridiculoulsy great at targeted proteomics. That PRM thing (mRmHR?) […]
- Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00429
- Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.6c00028
- Analytical ChemistryDOI: 10.1021/acs.analchem.5c06318
- Analytical ChemistryDOI: 10.1021/acs.analchem.5c06392
- Motivation: An unprecedented amount of mass spectrometry-based proteomics data is publicly available through repositories such as the PRoteomics IDEntifications Database (PRIDE), and the field is increasingly leveraging machine learning approaches. However, the available data is not ready to be reused in a scalable way beyond the original acquisition purpose. Existing machine learning models commonly rely on a few manually curated datasets that require deep domain expertise and tedious technical work to construct. Importantly, these datasets have not been updated in […]
- Peptergent is a novel class of amphipathic peptides that enable detergent-free extraction and purification of membrane proteins (MPs). These designed peptides self-assemble around hydrophobic transmembrane regions of proteins, forming stable, water-soluble assemblies that can be isolated directly from biological membranes. By doing so, Peptergent bypass the limitations imposed by traditional detergents, which often destabilize proteins and restrict downstream analyses. Since detergents are completely avoided, Peptergent-isolated MPs are directly amenable to structural and mass spectrometry (MS) analysis, thereby addressing their persistent […]
- Phytohormones are key players in the regulation of plant development and metabolism. The different phytohormone classes comprise numerous chemically very diverse compounds, which are often present at very low concentrations. The chemical properties of phytohormones range from acidic to basic and from polar to non-polar. Furthermore, concentration varies strongly among different phytohormones, between plant species, tissues and developmental stages. Challenges often arise when only small amounts of plant material are available and when plant species are investigated in which the […]
- RNA 5-methylcytidine (m5C) is a prevalent modification that drives RNA stability and function. In humans, m5C is deposited on distinct RNA substrates by DNMT2/TRDMT1 and the NSUN family, to regulate diverse cellular processes, but how m5C writers recognise their substrates remains unclear. NSUN2 is a major m5C methyltransferase with broad roles in cell physiology and strong links to cancer and neurodevelopmental disorders 1. Here, we reconstitute an active human NSUN2-tRNA complex and capture its post-catalytic, tRNA- bound structure at 3.1 […]
- Chemistry – A European Journal, Volume 32, Issue 10, 9 March 2026.
- Astrocyte-mediated cell-cell interactions at synapses are essential for circuit formation, yet the molecular mechanisms underlying astrocyte-mediated regulation of hippocampal synapse development remain incompletely characterized. Here, we take a systematic cross-modal approach to identify novel astrocytic cell surface proteins (CSPs) at the tripartite synapse. By using single-cell spatial transcriptomics (scST) targeting CSPs identified in a previous hippocampal synaptic dataset, we find 10 potential candidate astrocytic CSPs. Subsequent systematic protein-level profiling using multiple antibody-based assays establishes GPR37L1, HepaCAM, and VCAM1 as astrocytic […]
- The SWI/SNF chromatin remodelling complex controls proliferation and cell fate determination by regulating chromatin accessibility at promoters and enhancers, thereby modulating programs of gene expression, and has roles in DNA damage response, replication, splicing, and translation, and cell plasticity. The cBAF-exclusive subunit ARID1A acts as scaffold for the assembly of cBAF SWI/SNF complexes through its C-terminal globular domain and is the most frequently mutated SWI/SNF subunit in cancer. More than half of the ARID1A protein sequence contains regions of intrinsic […]
- Entosis is a cell-in-cell (CIC) invasion process in which one living cell actively invades into another, with important implications for tumor evolution, cell competition, and responses to cellular stress. Both the initiation and progression of entosis require extensive actin cytoskeletal remodeling, as one cell must physically accommodate the complete internalization of another viable cell, which can subsequently migrate, divide, undergo degradation, or escape. Nearly two decades after its discovery, mechanistic insight into how cytoskeleton organization is regulated during entosis remains […]
- Histone Deacetylase (HDAC) 1 and 2 are key enzymatic components in multiple large chromatin remodeling complexes including NuRD, SIN3, and CoREST. In addition, both HDAC 1 and 2 contain a large intrinsically disordered region (IDR) within their C-terminal domain (CTD). How HDAC1/2 assemble into these complexes and the structure of the CTD IDR remains poorly understood. Here, we used HDAC1/2 to isolate their protein interaction networks from cells and used crosslinking mass spectrometry (XL-MS) coupled with the Integrative Modeling Platform […]
- …well…this is frustratingly brilliant….So why we're all messing around trying to figure out how to do a better job deep learning endogenous peptides, this group decided to just cut out the middle of the plan completely.This system relies on using E.coli to generate the peptides that you think are there which can be directly informed from your genomics data – to actually make the endogenous peptides that you might be able to see – if they are there. Double dash! Then […]