Combined RSS Items
- Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00316
- Data-independent acquisition (DIA) has become the preferred data acquisition method for mass spectrometry-based proteomics, yet, reproducible workflows for differential expression (DE) analysis and reporting results remain limited. We present DiaReport, an R package that performs precursor- and protein-level DE analysis from DIA-NN output using MSqRob and QFeatures, while generating high-quality, interactive HTML reports through Quarto. DiaReport integrates precursor data, filtering of missing values, normalization, protein summarization and statistical modeling within a single function, supporting both simple pairwise as well as […]
- Analyst, 2026, Accepted ManuscriptDOI: 10.1039/D6AN00012F, PaperYinghao Cao, Yuting Tan, Chang Li, Erping Long, Lin WangAchieving high spatial resolution is critical for revealing tissue-specific metabolite distributions in mass spectrometry imaging (MSI), yet practical constraints often limit achievable resolution. While deep learning offers promising post-acquisition enhancement,…The content of this RSS Feed (c) The Royal Society of Chemistry
- XA-Novo: high-throughput mass spectrometry-based de novo sequencing technology for monoclonal antibodies and antibody mixtures
- Ambient metabolomics techniques such as laser-assisted rapid evaporative ionization mass spectrometry (LA-REIMS) enable fast, preparation-free fingerprinting of biological samples but are inherently limited by spectral congestion in the absence of chromatographic separation. While ion mobility spectrometry provides additional gas-phase separation, maintaining ion transmission under the transient signals characteristic of laser desorption remains analytically challenging. Here, we define operating conditions for cyclic traveling-wave ion mobility spectrometry (cIMS) that preserve transmission under LA-REIMS duty-cycle constraints and systematically evaluate how mobility integration reshapes […]
- Environmental Science & TechnologyDOI: 10.1021/acs.est.6c00394
- Publication date: Available online 12 March 2026Source: Journal of Chromatography BAuthor(s): Ibrahim Choucair
- Publication date: 1 August 2026Source: Talanta, Volume 305Author(s): Olha Dushna, Andrzej Gawor, Leszek PÄ czek, Ewa Bulska, Renata Bilewicz
- Doxycycline is a tetracycline-class antibiotic used for malarial prophylaxis and as an occasional partner drug in malaria treatment. Several lines of evidence suggest that doxycycline's antimalarial mechanism of action is through inhibiting the prokaryotic 70S ribosomes of the apicoplast, a non-photosynthetic plastid present in most apicomplexan species including Plasmodium and Toxoplasma. At lower concentrations (10 M) doxycycline has rapid schizonticidal activity via an unknown and likely apicoplast-independent mechanism. In other eukaryotes, and plausibly in Plasmodium, doxycycline inhibits mitochondrial 70S ribosomes. […]
- Chemoproteomics is a popular approach for the identification of small molecule-protein interactions in biological systems. Several chemoproteomics workflows leverage functionalized chemical probes and mass spectrometry to measure protein engagement through direct protein enrichment or competition using a range of small molecule concentrations. Statistical methods for analysis of such dose-response chemoproteomics datasets are limited. For example, existing methods rely on fixed curve shapes and are sensitive to experimental variation, particularly when the number of doses or replicates is limited. Here, we […]
- Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00432
- Analytical ChemistryDOI: 10.1021/acs.analchem.5c06656
- Background: Rapid and accurate identification of urinary tract infection (UTI) pathogens is critical for effective treatment and combating antimicrobial resistance. Conventional culture-based diagnostics are slow, and standard tandem mass spectrometry workflows are resource-intensive. Methods: We present a proof-of-concept workflow that integrates high-resolution data-independent acquisition (DIA) MS/MS on the Thermo Scientific Orbitrap Astral with MS1-only spectra from the Orbitrap Exploris 480. DIA data establish a reference panel of pathogen-specific peptides, which are then identified in MS1 spectra from urine samples. Machine […]
- Analyst, 2026, Advance ArticleDOI: 10.1039/D6AN00119J, Paper Open Access   This article is licensed under a Creative Commons Attribution 3.0 Unported Licence.A. Dawson McLachlan, Rashne Vakharia, Emir NazdrajiÄ, Diana M. CĂĄrdenas-SoracĂĄ, Leslie M. Bragg, Mark R. Servos, W. Scott HopkinsA novel hybrid workflow including chiral LC and differential mobility spectrometry was used to separate and quantify the enantiomers of a set of co-eluting isomers.To cite this article before page numbers are assigned, use the DOI form of citation above.The content of […]
- Protein lipidation is a widespread strategy for anchoring proteins to cellular membranes across all domains of life, yet the mechanisms underlying this process in archaea remain poorly understood. Recently, the first archaeal enzymes involved in lipobox-containing protein (lipoprotein) biogenesis, AliA and AliB, were identified and characterized in the model archaeon Haloferax volcanii. Although these paralogs share significant sequence similarity, distinct deletion phenotypes suggest differences in their substrate specificity and function. Here, we employed large-scale Triton X-114 fractionation followed by quantitative […]
- Structural dynamics and immunogenicity of the recombinant and outer membrane vesicle-embedded Meningococcal antigen NadA
- Anal. Methods, 2026, Advance ArticleDOI: 10.1039/D5AY01489A, Paper Open Access   This article is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported Licence.Hans S. A. Yates, James F. Carter, Jiali Zhang, Mary T. Fletcher, Viviene S. Santiago, Natasha L. HungerfordThe analysis of rare or atypical sugars is not encompassed by standard sugar methodology. With greater selectivity, this new method covers 80 sugars for their analysis.To cite this article before page numbers are assigned, use the DOI form of citation above.The content […]
- J. Anal. At. Spectrom., 2026, Accepted ManuscriptDOI: 10.1039/D5JA00415B, PaperZhekun Wang, Zhongjun Zhao, Zhihao He, Xiaoqin Jiang, Yanting Yang, Jianxiong Dai, Ziqiu Su, Xing Guo, Yixiang DuanIon mobility spectrometry-mass spectrometry (IMS-MS) is a powerful tool used in the separation, detection, and characterization of ions. Electrospray ionization (ESI) coupled with IMS-MS has been widely employed in metabolomics,…The content of this RSS Feed (c) The Royal Society of Chemistry
- Publication date: Available online 11 March 2026Source: Journal of Chromatography BAuthor(s): Apurva Patil, Michaela Austel, Michael G. Bartlett
- ABSTRACT Rationale Protein phosphorylation plays a central role in regulating cellular signaling, and its dysregulation is closely linked to diseases such as cancer and neurodegeneration. Mass spectrometryâbased phosphoproteomics allows comprehensive mapping of phosphorylation; however, detecting low-abundance and poor ionization phosphopeptides remains a challenge. High-field asymmetric waveform ion mobility spectrometry (FAIMS) offers orthogonal gas-phase fractionation, enhancing phosphopeptide detection. However, FAIMS and conventional non-FAIMS (noFAIMS) analyses often identify partially overlapping yet complementary subsets of phosphopeptides. This suggests that integrating both approaches could […]
- ABSTRACT Rationale Nitrogen mustards (HN1, HN2 and HN3) and N,N-dialkylaminoethyl-2-chlorides (where alkylâ=âmethyl, ethyl, isopropyl, or propyl) contain reactive chloride bonds that react with phenol in environmental samples to form phenolic reaction products. Identifying these products is crucial for the Chemical Weapons Convention (CWC) verification, as they serve as markers for the presence of scheduled chemicals. Methods Phenolic reaction products of nitrogen mustards (1â3) and N,N-dialkylaminoethyl-2-chlorides (4â13) were analysed using direct ESIâMS and LCâESIâMS/MS on an Agilent Q-TOF system. Product ion […]
- We developed a novel domino polymerization to synthesize reductively degradable poly(disulfide)s with tunable side chains. A novel monomer bearing thiolactone and pyridyl disulfide groups reacts with various amines, enabling continuous ring-opening and disulfide exchange. The resulting polymers show reductive degradability, pH-responsive solubility, and can form degradable gels, offering versatile applications. ABSTRACT The environmental persistence of conventional plastics has driven the development of degradable polymers with functional versatility. Poly(disulfide)s are particularly attractive due to their reductive degradability and environmentally triggered disassembly. […]
- Protein phosphorylation is a key regulator of signaling, with mass spectrometry (MS) based phosphoproteomics serving as the premier technology for its analysis. However, phosphorylation profiling is hindered by acquisition biases: Data-Dependent Acquisition (DDA) suffers from stochastic undersampling and missing values, while Data-Independent Acquisition (DIA) faces computational bottlenecks and inefficiencies from vast spectral libraries. We present PhosSight, a unified deep learning framework designed to augment identification depth and accelerate search efficiency. PhosSight features PhosDetect, a model that explicitly encodes phosphorylation specific […]
- Background: Low-dose aspirin (LDA) reduces preeclampsia (PE) risk by up to 40%, yet its molecular effects on chorion trophoblast cells (CTCs) a fetal membrane lineage at the feto-maternal interface remain obscure. CTCs form a structural and immunoregulatory barrier whose dysfunction drives inflammation-associated membrane pathology in PE. Extracellular vesicles (EVs) released by CTCs may encode cellular stress and adaptation states, offering a molecular window into aspirin's timing-dependent effects on PE risk modification. Methods: Human CTCs were challenged with cigarette smoke extract […]
- Liquid chromatography-tandem mass spectrometry (LC-MS/MS) based proteomics, particularly data-independent acquisition (DIA), has become widely adopted across in One Health approaches for biological and clinical research for quantitative protein characterization. Among the many computational tools available, DIA-NN has demonstrated superior performance; however, the primary output of the current versions is provided as a compact, compressed PARQUET file that can be difficult to interrogate without programming expertise. To address this limitation, we developed DIA-NN EasyFilter (DEF), a fast, user-friendly, KNIME-based workflow for […]