Publication date: Available online 10 October 2025 Source: Journal of Mass Spectrometry and Advances in the Clinical Lab Author(s): Joon Hee Lee, Kyunghoon Lee, Sun-Hee Jun, Yun Jeong Lee, Choong Ho Shin, Young Ah Lee, Junghan Song

Publication date: Available online 10 October 2025 Source: Journal of Mass Spectrometry and Advances in the Clinical Lab Author(s): Mahdiyeh Shahi, R. Graham Cooks

ABSTRACT Validated assays are vital to support the accurate reporting of pharmacokinetics for parent drug/metabolite(s), regardless of the stage of drug development. One of the recent nuances in the field has focused on the selection of an appropriate stable isotopically labeled internal standard (SIL-IS) with a sufficient mass difference from the target analyte as a panacea to render unambiguous quantitation of the target analyte(s) in liquid chromatography–tandem mass spectrometry methods (LC–MS/MS). Although the intent of using SIL-IS is well supported, there are potential issues that may arise because of cross-signal contributions due to various factors, which could potentially lead to nonlinearity in the standard curves and further contribute to wider assay biases. This perspective article presents the available knowledge in the field pertaining to potential issues with the use of SIL-IS and provides insights/commentary on these situations, as a means to both understand and manage such issues during the development of assays.

ABSTRACT The introduction of mass spectrometry in the analysis of pesticide residues has significantly enhanced analytical efficiency, reduced analysis times, and enabled ultra-trace detection. However, the matrix effect—wherein target analytes experience interference from the matrix during ionization—remains a critical issue. In multiresidue pesticide analysis via LC-MS/MS, matrix effects are typically addressed by preparing calibration standards through the dilution of matrix extracts with buffers (organic solvents) or by diluting the sample, which must be manually performed by the analyst. This study developed an automated matrix dilution injection (AMDI) method that leverages the autosampler built-in automatic dilution injection feature in liquid chromatography (LC) to prepare matrix-corrected dilutions and quantify analytes without manual manipulation. The AMDI method was validated by analyzing 71 pesticides in four agricultural commodities, where linearity, accuracy, and precision were assessed using two LC systems with different performances (HPLC-MS/MS and UHPLC-MS/MS). The AMDI method exhibited superior linearity in UHPLC analyses compared with conventional matrix-matched calibration standards. Furthermore, most of the pesticides analyzed exhibited measurement accuracies of 70%–120% and precision with relative standard deviations below 10%.

ABSTRACT An innovative approach combining electrochemistry with online quadrupole time-of-flight-mass spectrometry (EC-MS/MS) was employed to study the oxidative products and metabolic pathways of three bioactive compounds found in Phellodendri Chinensis Cortex, including phellodendrine, obaculactone, and obacunone. This advanced analytical technique provided detailed insights into their transformation processes. The simulation of phase I metabolism reactions was conducted within an electrochemical microreactor system. The heart of this apparatus was a reliably performing boron-doped diamond electrode. Meanwhile, a defined concentration of glutathione (GSH) was injected into the reaction system to obtain phase II metabolites. The metabolites were collected and concentrated for offline electrochemistry-ultra-high-performance liquid chromatography-quadrupole-time of flight-mass spectrometry analysis (EC-UHPLC-MS/MS). The main converted products and metabolic pathways were further verified through in vitro liver microsome incubation experiments. It was revealed that the simulated metabolic process based on the electrochemical system effectively produced a variety of metabolites from the compounds, which were subsequently compared with those obtained from rat liver microsomal incubations. Without matrix interference, the drug metabolic process could be effectively simulated and analyzed using the electrochemical system. The findings underscore the utility of electrochemistry as a robust tool for preliminary investigations into the metabolism of natural products, offering a reliable and efficient alternative to traditional methods.

Publication date: Available online 9 October 2025 Source: Journal of Proteomics Author(s): José Ángel Huerta-Ocampo, Robert Winkler, Aldo Moreno-Ulloa, Sergio Encarnación-Guevara

Analytical ChemistryDOI: 10.1021/acs.analchem.5c04367

Analytical ChemistryDOI: 10.1021/acs.analchem.5c04933

Analytical ChemistryDOI: 10.1021/acs.analchem.5c02331

Neuronal morphogenesis is guided by filopodia, dynamically generated plasma membrane protrusions filled with parallel actin filaments. However, how filopodial actin filaments are locally produced, organized, and maintained remains unclear. The transmembrane protein PLPPR3 induces filopodia in neurons and other cells. We find that the intracellular domain (ICD) of PLPPR3 forms liquid condensates, which exhibit strong co-partitioning of actin monomers. These condensates promote actin polymerization within the condensates at the expense of actin monomers in the environment, consistent with thermodynamic coupling of actin partitioning and polymerization, which we recapitulate in a modified polymerization kinetics model. This mechanism requires favorable actin partitioning into the condensate relative to the environment. Using crosslinking mass spectrometry, we identify a WH2-like actin-affinity domain within the PLPPR3 ICD. Deleting this domain lowers actin partitioning in vitro and decreases filopodia formation in vivo. Our findings establish a previously unrecognized mechanism for actin network remodeling, in which condensates act as actin sinks, locally boosting monomer concentrations and facilitating polymerization of actin filaments.

Publication date: Available online 10 October 2025 Source: Analytica Chimica Acta Author(s): Cheng-Chia Chen, Yu-En Lin, Mei-Chich Hsu, Yu-Chuan Lin, William Chih-Wei Chang

Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00174

Chemistry – A European Journal, Volume 31, Issue 56, October 8, 2025.

Chemistry – A European Journal, Volume 31, Issue 56, October 8, 2025.

Publication date: 1 February 2026 Source: Talanta, Volume 298, Part B Author(s): Ana Justo-Vega, Raquel Domínguez-González, Pilar Bermejo-Barrera, Antonio Moreda-Piñeiro, Javier Jiménez-Lamana

Journal of Mass Spectrometry, Volume 60, Issue 11, November 2025.

Journal of Mass Spectrometry, Volume 60, Issue 11, November 2025.

PIWI-interacting RNAs (piRNAs) are critical for transposon silencing and genome integrity, as well as gene expression regulation and antiviral immunity in metazoans, yet the molecular mechanisms governing their biogenesis remain incompletely understood. The participation of the splicing-associated process in piRNA biogenesis has been emphasized in multiple species, but the key factors and mechanisms remain elusive. Here, we identified SUGP1 (SURP and G-Patch Domain Containing 1) in BmE (a unique model cell system with a complete piRNA biogenesis pathway) as a key splicing factor that functions in piRNA biogenesis. Through CRISPR-Cas9-mediated gene knockdown in cultured cells combined with RNA-seq, small RNA-seq, and IP-mass spectrometry (IP-MS), our results reveal that SUGP1 deficiency disrupts piRNA accumulation, alters mature piRNA length distributions, and activates transposon expression. Immunofluorescence and Western blot (WB) analyses further demonstrate that SUGP1 interacts with Y-box protein (YBP), which is key regulators of RNA metabolism. Functional validation in Drosophila SUGP1-RNAi lines highlights evolutionary conserved and species-specific roles of SUGP1 in piRNA maturation. Collectively, our data uncover a dual role for silkworm SUGP1 in coordinating YBP-dependent piRNA biogenesis, thus elucidating a novel mechanistic framework for piRNA pathway regulation. Our work also underscores the silkworm as a unique model for studying non-canonical piRNA biogenesis mechanisms, with implications for treating transposon dysregulation-linked diseases.

Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00324

Publication date: Available online 9 October 2025 Source: Journal of Chromatography A Author(s): Rui Wang, Wei Wei, Man Yang, Yang Liu, Xue Meng, Shiming Fang, Jin Li, Kunze Du, Yanxu Chang

Publication date: Available online 8 October 2025 Source: Journal of Chromatography A Author(s): Hira Zulfiqar, Maria Llompart, Natalia Montero, Andres Duque-Villaverde, Daniele Fabbri

Protein identification by mass spectrometry is a pivotal step in proteomics. Numerous methods have been developed to securely and effectively identify proteins derived from experimentally detected peptides by mass spectrometry. The dominant approach is based on the assumption that each experimentally identified peptide can be matched with a peptide included in a database of peptide sequences, generated by in silico digestion of proteins with a specific proteolytic enzyme. In this way, the protein containing the peptide can be identified. In a more advanced approach, the proteins and their in silico digested peptides in the database are transformed into theoretical mass spectrometry spectra, and search engines match the experimentally obtained spectra to these theoretical spectra generated from protein and peptide sequences. We developed an alternative method for protein identification using Core Unique Peptides (CrUPs) and the Uniquome, termed as Uniquome-Based Protein Identification Method (UB-PIM). According to this method, instead of searching for peptides in the database of in silico_digested peptides, we search for CrUPs within the experimentally obtained peptides by mass spectrometry. If a peptide contains at least one CrUP, it can be directly correlated to the protein from which the CrUP is derived. Because of the unique nature of CrUPs, peptides obtained by MS can securely and uniquely identify the protein of origin. This provides a reference space in which even single-peptide identifications can achieve high specificity, reducing the ambiguity caused by shared or homologous sequences and improving the interpretability of MS data. Furthermore, UB-PIM can be applied to any type of peptide and is effective with both Data-Independent Acquisition (DIA) and Data-Dependent Acquisition (DDA) approaches, as well as with top-down and bottom-up proteomics. This allows confident protein identification from minimal evidence, expands the scope of detectable proteins, and remains computationally efficient, rapid, and universally applicable.

Halogenated natural products (HNPs) are a diverse group of organohalogen compounds, predominantly found in the marine environment. Selected HNPs show structural similarity to persistent organic pollutants (POPs), but data on their occurrence is limited. An analytical method for the detection of 17 commonly reported HNPs, as well as selected POPs, using gas chromatography with electron-capture negative ionisation mass spectrometry (GC/ECNI-MS) was established and validated for salmon and blue mussel. The validation confirmed the applicability of the method with recovery rates and inter-day coefficients of variations of 52–101% and 3.7–16%, respectively. The subsequent application of the method to 17 samples of frequently consumed seafood products from the German retail market demonstrated its suitability for a wide variety of matrices. HNPs were detected in all analysed samples, with contents ranging from 

J. Anal. At. Spectrom., 2025, Accepted Manuscript DOI: 10.1039/D5JA00232J, PaperPierre-Emmanuel Peyneau, Léonard Seydoux, Mickael Tharaud Single particle inductively coupled plasma-mass spectrometry (sp-ICP-MS) produces time series - time scans - that require processing to extract meaningful information regarding the nanoparticles that are analysed. In this work,... The content of this RSS Feed (c) The Royal Society of Chemistry

J. Anal. At. Spectrom., 2025, Accepted Manuscript DOI: 10.1039/D5JA00309A, Critical ReviewChufan Zhou, Qiang Huang, Minming Cui, Xun Wang, Xinbin Feng The rapid advancement of artificial intelligence (AI), particularly machine learning (ML), is revolutionizing stable isotope geochemistry, enhancing mass spectrometry-based analytical techniques and unlocking transformative capabilities in data interpretation and geochemical... The content of this RSS Feed (c) The Royal Society of Chemistry