Combined RSS Items
- The de novo design and assembly of a DNA genome represents an important milestone toward the construction of a minimal synthetic cell. The genome must contain all the instructions to enable primary cellular functions, probably comprising over 150 genes with a total size over 200 kb. Here, we designed and built a partial synthetic genome that satisfies the requirements for its expression in PURE system–a minimal transcription-translation machinery reconstituted from purified elements–and its replication by the protein-primed {varphi}29 DNA replication […]
- Volatile organic compounds (VOCs) in urine have shown increasing promise as non-invasive biomarkers for the early detection and monitoring of diseases. However, their volatile nature may make them highly susceptible to pre-analytical factors, presenting significant challenges for consistent biomarker discovery and reproducibility within metabolomic workflows. This study aimed to assess the impact of four critical pre-analytical variables, including fasting state, centrifugation procedures, room temperature (RT) stability, and freeze-thaw (FT) cycles, as well as intra- and inter-individual variability on the profiles […]
- Publication date: Available online 15 October 2025Source: Journal of ProteomicsAuthor(s): Hiba Salim, Ruben Almey, Laura Pont, Fernando Benavente, Maarten Dhaenens, Estela Giménez
- Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00251
- Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00331
- Motivation: Hydrogen-deuterium exchange/mass spectrometry (HX/MS) is a rapidly expanding technique used to investigate protein conformational ensembles. The growing popularity and utility of HX/MS has driven the development of diverse instrumentation and software, resulting in inconsistent, non-standardized data analysis and representation. Most HX/MS data formats also employ only centroid-level representations of the data rather than full isotopic mass spectra, reducing the information content of the data and limiting downstream quantitative analysis. Results: Inspired by reliable protein structure and genomics data formats, […]
- PROTEOMICS, EarlyView.
- PROTEOMICS, EarlyView.
- ABSTRACT Rationale Light stable isotopes (δ 13C, δ 15N, δ 2H, and δ 18O) of Ectropis grisescens (Lepidoptera: Geometridae), a destructive tea leaf-eating pest, were measured at different developmental stages. Isotope values of larval instars, pupae, and adult moth body tissues were determined to understand fractionation patterns at different life stages and to evaluate dietary isotopic change from food to insect to excrement. Methods Young Ectropis grisescens larvae (collected before the first instar) were raised on Camellia sinensis tea leaves […]
- Mass spectrometry imaging (MSI) is a powerful tool in both basic and clinical research, enabling spatial visualization of biomolecules and drugs in tissue sections. However, factors influencing mass spectrometric response during imaging are increasingly recognized for their impact on apparent molecular distribution. Quantitative mass spectrometry imaging (qMSI) addresses this variability by incorporating analytical standards that undergo the same processes as analytes. While qMSI sample preparation protocols for omics-scale quantitative lipidomics are actively evolving, software solutions for downstream data processing remain […]
- Tauopathies are a group of neurodegenerative disorders, including Alzheimer disease, that are neuropathologically defined by deposition of pathological forms of tau in the brain. While tau is reported to drive neurotoxicity by negatively affecting cytoskeletal, nucleoskeletal, and genomic architecture, the mechanisms mediating tau-induced dysfunction of the cytoskeleton and nucleoskeleton are incompletely understood. Based on proteomic profiling, we identify a suite of cytoskeletal and nucleoskeletal proteins with differing abundance in a cellular model of tauopathy, iTau. Building upon previous findings that […]
- Ubiquilin-2 (UBQLN2) is a ubiquitin (Ub)-binding shuttle protein that is mutated in X-linked forms of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). ALS/FTD-linked mutations in UBQLN2 disrupt its conformation, increasing its tendency to form cytoplasmic aggregates that may disrupt cellular regulation through loss-of-function (LOF) and gain-of-function (GOF) effects. To explore how ALS-associated mutations impact UBQLN2 function, we performed quantitative mass spectrometry (MS)-based interactome analysis using affinity-purified UBQLN2 from inducible pluripotent stem cells (iPSCs) and induced motor neurons (iMNs) expressing […]
- The identification of bacteria is central to the microbiological sciences. While gene sequencing methods have been the standard to identify bacteria, use of MALDI-TOF mass spectrometry (MS) in clinical microbiology provides high-throughput identification to the subspecies level. However, biotyping has yet to be adopted outside of clinical settings due to the lack of a centralized public database of MS protein signatures that would facilitate strain identification via spectral comparison. Herein we present the IDBac web platform, a crowd-sourced central knowledgebase […]
- Anal. Methods, 2025, Advance ArticleDOI: 10.1039/D5AY01057H, Paper Open Access   This article is licensed under a Creative Commons Attribution 3.0 Unported Licence.Fiona Regan, Catherine Allen, Jenny LawlerA sensitive contaminantion-controled LC-MS/MS workflow quantifies 11 phthalate diesters in environmental samples with sub ng L−1 limits.To cite this article before page numbers are assigned, use the DOI form of citation above.The content of this RSS Feed (c) The Royal Society of Chemistry
- N-glycosylation is a post-translational modification of proteins that represents a critical quality attribute (CQA) for therapeutics like monoclonal antibodies (mAbs), directly affecting drug efficacy, safety, and stability. Real-time CQA monitoring analytical platforms depend on rapid N-glycan release and fluorophore labeling chemistries to support automated bioprocess analytics during mAb manufacturing. Procainamide is a well-known fluorophore used for released N-glycans reducing sugar aldehydes labeling that offers both high fluorescence and mass spectrometry detection sensitivity comparable to several commercial reagents available in the […]
- Analytical ChemistryDOI: 10.1021/acs.analchem.5c04349
- [ASAP] A Universal Spectrum Annotator for Complex Peptidoforms in Mass Spectrometry-Based ProteomicsAnalytical ChemistryDOI: 10.1021/acs.analchem.5c02832
- Publication date: Available online 14 October 2025Source: International Journal of Mass SpectrometryAuthor(s): Sarah J. Madlener, Bowei Yuan, Marc Reimann, Shaodong Zhou, Martin K. Beyer, Joost M. Bakker, Christian van der Linde
- A study was conducted to validate the gas chromatography-triple quadrupole mass spectrometry (GC-QqQ-MS) method as a cost-effective method for the analysis of polychlorinated dibenzo-p-dioxins/dibenzofurans (PCDD/Fs) in sediment samples. The instrument sensitivity for 17 PCDD/Fs congeners was determined to be in the range of 0.201 to 1.45 ng/mL. The four-point calibration curve exhibited high linearity, with the mean relative response factors (RRFs) for PCDD/Fs ranging from 0.81 to 1.88, and RSD
- The aggregation of the protein alpha-synuclein (Syn) is a common feature of multiple neurodegenerative diseases collectively called synucleinopathies, for which the pathobiology is not well understood. The different phenotypic characteristics of the synucleinopathies Parkinson's disease (PD), Dementia with Lewy Bodies (DLB) and Multiple System Atrophy (MSA) have been proposed to originate from the distinct structures adopted by Syn in its amyloid forms. Here, using covalent labeling and limited proteolysis coupled to mass spectrometry (LiP-MS) in vitro and in situ within […]
- Journal of Proteome ResearchDOI: 10.1021/acs.jproteome.5c00540
- J. Anal. At. Spectrom., 2025, Advance ArticleDOI: 10.1039/D4JA00324A, Paper Open Access   This article is licensed under a Creative Commons Attribution 3.0 Unported Licence.Dalia Morcillo, Alexander Winckelmann, Marcus Oelze, Robert Leonhardt, Anita Schmidt, Silke Richter, Sebastian Recknagel, Jochen Vogl, Ulrich Panne, Carlos AbadBattery aging leaves a lithium-isotope signature. Mass spectrometric, using a microwave-induced cold nitrogen plasma ionization source, detects subtle 7Li/6Li shifts between electrodes, revealing Li-ion cell health and cycling history.To cite this article before page numbers are assigned, use […]
- Spatial biology using single-cell mass spectrometry imaging and integrated microscopy
- Subcellular mass spectrometry imaging of lipids and nucleotides using transmission geometry ambient laser desorption and plasma ionisation
- Insight into the influence of various cultivation regions on the identification of metabolites from Capsella bursa-pastoris via a clustering algorithm