bims-mascan 2026-08-23 papers

bims-mascan

Biomed News

on Mass spectrometry in cancer research

Issue of 2026–08–23
twenty-two papers selected by
Giovanny Rodríguez Blanco, Uniklinikum Graz

Resolving Spectral Complexity in 4D Lipidomics Using a Two-Dimensional Deconvolution Framework.
Multi-omic analyses of the same sample using metabolomics, lipidomics, proteomics, phosphoproteomics, and glycoproteomics.
A protocol for untargeted metabolomics using anion-exchange chromatography and high-resolution mass spectrometry.
Quantitative Integration of Targeted and Nontargeted Metabolomics Using Multi-Stable Isotope Chemical Tagging with UHPLC-QToF MS: Application to Myeloid Leukemia Metabolism.
LC-MS-Based Analytical Strategies for Ganglioside Profiling.
Optimizing Oxylipin Analysis with Liquid Chromatography Mass Spectrometry through Bio-Inert Systems and Ion Funnel Adjustments.
SureQuant™ IS-PRM Enables Cross-Species Targeted Quantification of Retinoid Metabolism and Signaling Proteins in the Heart.
Beyond the convergence of metabolic reprogramming in primary liver cancer: a comprehensive review on energy and lipids metabolism.
Decoding the urinary metabolome of aromatic amino acid pathways in Alport syndrome.
Extracellular vesicle lipidomics for disease diagnostics and mechanism-informed discovery.
A Scalable Low-Input Redox Proteomics Workflow Enables High-Throughput Analysis of Cysteine Oxidation in 96-Well Cell Cultures.
Integrated metabolomics data analysis to generate mechanistic hypotheses with MetaProViz.
Protocol for untargeted multi-omics dried blood spot extraction using liquid chromatography-tandem mass spectrometry.
Multi-Organ DIA Proteomics Reveals a Shared Xenobiotic Metabolism Stress Program in a Patient-Derived Xenograft Model.
Spatially Resolved Metabolomics of Optimal Cutting Temperature (OCT) Compound-Embedded Tumors.
New chromatographic and data evaluation approaches for the comprehensive investigation of metal-phytosiderophore-complex dynamics.
Targeted metabolomics of postmortem human cardiac tissue using the Biocrates MxP Quant 500 kit.
High-resolution mapping of osteoblast metabolism and bone matrix turnover in vivo.
Detection of Multiple Medetomidine Metabolites in Clinical Urine Specimens by Liquid Chromatography-Quadrupole Time-of-Flight Mass Spectrometry (LC-qToF-MS).
Isoleucine and valine promote prostate cancer progression via propionyl-CoA-mediated cholesterol metabolism.
An isotope dilution-liquid chromatography-tandem mass spectrometry-based candidate reference measurement procedure for the quantification of gentamicin in human serum.
Nicotinamide nucleotide transhydrogenase directly couples redox homeostasis to proline biosynthesis in human glioma.

Angew Chem Int Ed Engl. 2026 Aug 19. e6117030

Resolving Spectral Complexity in 4D Lipidomics Using a Two-Dimensional Deconvolution Framework.

Yao Qian, Qirui Yu, Zhixu Ni, Zheng Ouyang, Xiaoxiao Ma.

  The application of data-independent acquisition (DIA) in 4D lipidomics has been constrained by spectral interference due to fragment ion overlap, a bottleneck that existing one-dimensional deconvolution methods fail to fully resolve. Here, we overcome this limitation by introducing a two-dimensional liquid chromatography-ion mobility (LC-IM) deconvolution framework that unlocks the full potential of 4D lipidomics. By mathematically modeling the orthogonal LC-IM separation dimensions, our method reconstructs high-quality MS/MS spectra from highly complex DIA data, effectively disentangling co-eluting lipid interferences. We demonstrate the power of this approach by annotating 491 lipids from 1 µL human plasma at a 1% false discovery rate, a two-fold increase in coverage compared to traditional methods. Beyond bulk analysis, we showcase its unique capability for spatial lipidomics, enabling deep profiling of laser-microdissected tissue regions equivalent to only hundreds of cells, revealing metabolic reprogramming in human hepatocellular carcinoma. We further integrate this workflow with six-plex isobaric labeling to achieve high-throughput, high-accuracy quantification in spatial tissue mapping. This transition from one- to two-dimensional deconvolution establishes a robust, sensitive platform for deep lipidome characterization, bridging the gap between proteomics-grade throughput and lipidomic structural complexity.

Keywords:  data‐independent acquisition; deconvolution; ion mobility; lipidomics; mass spectrometry

DOI:  https://doi.org/10.1002/anie.6117030
Chem Commun (Camb). 2026 Aug 20.

Multi-omic analyses of the same sample using metabolomics, lipidomics, proteomics, phosphoproteomics, and glycoproteomics.

Yuefan Wang, Xuejun Peng, Hongyi Liu, Mia Gidley, Beth Kelly, Erika L Pearce, Edward J Pearce, Xianlin Han, Hui Zhang.

Mass spectrometry (MS)-based multi-omics offers powerful tools to comprehensively characterize proteins, post-translational modifications, metabolites, and lipids. However, these measurements are typically performed using separate sample preparation workflows and modality-specific liquid chromatography mass spectrometry (LC-MS) platforms, limiting integration and constraining applications to small amounts of sample materials, especially scarce clinical specimens. Here, we describe a unified nano-LC-MS framework that enables metabolomic, lipidomic, proteomic, phosphoproteomic, and glycoproteomic analyses from the same starting material using a single nano-LC-MS platform, with only the chromatographic conditions, acquisition methods, and enrichment procedures tailored to each omics. This integrated strategy reduces workflow complexity and sample consumption while improves analytical continuity across molecular layers. By enabling deep multi-omics characterization from the same sample, this platform provides a practical foundation for comprehensive analysis of precious clinical samples.

DOI: https://doi.org/10.1039/d6cc03477b
STAR Protoc. 2026 Aug 19. pii: S2666-1667(26)00437-5. [Epub ahead of print]7(3): 104784

A protocol for untargeted metabolomics using anion-exchange chromatography and high-resolution mass spectrometry.

Marius Jouan, Sylvain Henry, Andrei Turtoi.

  Polar metabolites are challenging to analyze using common reverse-phase chromatography. However, these molecules are most essential for deciphering biological phenotypes. Here, we present a protocol for polar metabolite analysis based on anion-exchange chromatography coupled with high-resolution mass spectrometry (AEC-HRMS). We outline preparation techniques for common biological matrices, instrumental setup for untargeted metabolomics, including sample analysis and essential data treatment.

Keywords:  Mass Spectrometry; Metabolomics; Protocols in Metabolomics and Lipidomics

DOI:  https://doi.org/10.1016/j.xpro.2026.104784
Anal Chem. 2026 Aug 18. 98(32): 23906-23919

Quantitative Integration of Targeted and Nontargeted Metabolomics Using Multi-Stable Isotope Chemical Tagging with UHPLC-QToF MS: Application to Myeloid Leukemia Metabolism.

Takahiro Takayama, Taiyo Tsutsumi, Tomoya Higuchi, Satoshi Takahashi, Yoshihiro Hayashi, Koichi Inoue.

Mass spectrometry-based metabolomics is widely used for comprehensive metabolic profiling. However, most current workflows rely on relative signal intensities, which limit comparability across experiments and prevent quantitative interpretation. This limitation arises from the difficulty in estimating analyte-specific response behavior in the absence of isotopically labeled standards. In this study, we present multistable isotope chemical tagging (MUSIC) as an isotope-resolved internal calibration framework that enables the approximation of response characteristics within a single experimental design. This approach uses multiple isotope-coded tagging reagents as internal calibration points instead of conventional internal standards, enabling the construction of internal calibration curves that account for both tagging efficiency and matrix effects. Internal calibration curves were established for amine-containing metabolites using a dilution series of tagged standard mixtures, enabling robust slope estimation. The resulting calibration framework allows accurate quantification of targeted metabolites and slope-based correction of nontargeted features through reference matching. In validation experiments involving 146 metabolites in serum, the method achieved accuracy and precision within ±15% using only two analytical runs. We further demonstrate that the framework enables the consistent recovery of fold changes across samples and supports comparative metabolic analysis without relying on compound-specific labeled standards. These results establish MUSIC not only as a chemical tagging strategy but also as a quantitative measurement framework that approximates analyte-specific response characteristics for integrated targeted and nontargeted metabolomics for amine-containing metabolites. Following validation, we applied this approach to blood samples to identify the biomarkers of myeloid leukemia.

DOI: https://doi.org/10.1021/acs.analchem.6c04094
Methods Mol Biol. 2026 ;3035 77-89

LC-MS-Based Analytical Strategies for Ganglioside Profiling.

Kazutaka Ikeda.

  Gangliosides, a class of glycosphingolipids containing sialic acid residues, are abundantly expressed in neuronal membranes and play essential roles in cellular signaling and intercellular communication. Impaired ganglioside metabolism contributes to the pathogenesis of lysosomal storage disorders and neurodegenerative diseases. The structural diversity and functional relevance of gangliosides necessitate analytical methods with high sensitivity, resolution, and specificity. In recent years, liquid chromatography-mass spectrometry (LC-MS) has emerged as a powerful tool for comprehensive ganglioside profiling. This review presents current LC-MS-based strategies for ganglioside analysis, with a particular focus on sample preparation methods, chromatographic separation techniques, and mass spectrometric approaches aimed at enabling accurate structural elucidation and pathway-level insights into ganglioside metabolism.

Keywords:  Gangliosides; Glycosphingolipids; LC–MS; Lipidomics; Mass spectrometry

DOI:  https://doi.org/10.1007/978-1-0716-5288-6_7
bioRxiv. 2026 Jul 28. pii: 2026.07.27.741082. [Epub ahead of print]

Optimizing Oxylipin Analysis with Liquid Chromatography Mass Spectrometry through Bio-Inert Systems and Ion Funnel Adjustments.

John T Shuster, Lingshuang Wu, Jericha Mill, Michaela Morhaus, Nina Yu Fan, Fernando Tobias, Dominique Baldwin, Matthew D Bruss, Liam Hurley, Michelle Kimple, Adam R Konopka, Judith Simcox.

Oxylipins are potent signaling lipids that affect inflammation, vascular tone, and metabolism, making them relevant in many diseases. Oxylipins are measured with liquid chromatography-mass spectrometry (LC-MS), but challenges in quantification arise due to low abundance and rapid degradation. In this study, we optimize LC-MS methods to improve the quantification of oxylipins in human plasma given growing interest in oxylipins and their impact on clinical research. Plasma samples were obtained from healthy participants and extracted by solid-phase extraction to concentrate the oxylipins. We then utilized a reversed phase targeted LC-MS/MS method using an Agilent 6495D triple quadrupole with transitions for 248 oxylipin species. Ion funnel voltages were set at 50 or 100 volts. Given the rapid degradation of oxylipins with bio-reactive surfaces, we compared both standard and Altura (bio-inert) columns, as well as standard and bio- inert LC setups. We observed that ion funnel parameters significantly alter detectable levels of oxylipins within LC-MS/MS analysis. By decreasing voltages applied to ions inside the ion funnel, signal was increased for most oxylipin species while peak quality was maintained. We also demonstrated that fully bio-inert setups quantify more compounds and show increased levels of some compounds, but fewer epoxyoctadecadienoic acid (EpODE) species. To explore this further, we injected analytical grade alpha-linolenic acid (ALA), the direct precursor of EpODEs, and observed formation of EpODEs within the instrumentation when using stainless steel columns. Our data shows that oxylipins benefit from fully bio-inert systems and optimized pre-mass analyzer parameters. The stainless-steel components of the column may also be contributing to epoxidation reactions of polyunsaturated fatty acids (PUFAs), generating oxylipin species during analysis. Finally, we utilized this method to perform oxylipin analysis in other human tissues including granulocytes, mononuclear cells, erythrocytes, skeletal muscle, and THP-1 cells, a human derived monocyte cell line.

DOI: https://doi.org/10.64898/2026.07.27.741082
bioRxiv. 2026 Jul 29. pii: 2026.07.27.741027. [Epub ahead of print]

SureQuant™ IS-PRM Enables Cross-Species Targeted Quantification of Retinoid Metabolism and Signaling Proteins in the Heart.

Sogol Sedighi, Robert N O'Meally, Sunayana Begum Syed, Hugo Amadei, Biyi Li, Chulan Kwon, Abhishek Vats, Don Zack, Kenneth B Margulies, Brian O' Rourke, Peter M Abadir, Robert N Cole, D Brian Foster.

Retinoic acid signaling is critical for cardiac development and homeostasis. Dysregulation of all-trans retinoic acid metabolism contributes to vascular atherogenesis, restenosis, calcification, and heart failure. Therefore, assessment of proteins involved in retinoid metabolism and signaling has gained interest for identifying potential biomarkers and therapeutic targets in cardiovascular disease. However, quantifying these proteins remains challenging due to limitations of antibody-based methods. We developed a targeted proteomics approach using SureQuant™ internal standard-triggered parallel reaction monitoring mass spectrometry to profile these proteins. We designed a panel of 80 stable isotope-labeled (heavy) peptides representing proteins involved in retinoid signaling and metabolism, with sequences applicable to human samples and conserved across multiple species. Survey experiments using directed data-dependent acquisition on the Orbitrap Fusion Lumos mass spectrometer determined precursor and product ion masses for each heavy peptide, which were programmed into the SureQuant method for continuous monitoring. Upon detection of these heavy internal standards, the instrument transitions to a targeted PRM acquisition mode in which repeated high-resolution MS/MS spectra of both endogenous (light) and heavy peptides are acquired. Using this method, retinoid pathway-associated proteins were quantified to as low as 10 attomoles for selected targets across multiple tissues and developmental stages. Distinct tissue-specific retinoid metabolic networks were identified across lung, liver, retinal cell lines and cardiac tissues. Developmental profiling of mouse and rat hearts revealed remodeling of retinoid pathway proteins from embryonic to postnatal and adult stages, suggesting a functional transition from retinoid-driven cardiac development toward maintenance of retinoid homeostasis in the mature heart.

DOI: https://doi.org/10.64898/2026.07.27.741027
Front Cell Dev Biol. 2026 ;14 1890663

Beyond the convergence of metabolic reprogramming in primary liver cancer: a comprehensive review on energy and lipids metabolism.

Galina S Stupnikova, Igor A Popov, Stanislav I Pekov.

  Hepatocellular carcinoma and cholangiocarcinoma, the most common primary liver cancers, are usually considered quite different pathologies. However, convergent metabolic reprogramming across different progenitor cells can result in similar molecular alterations and, even in a combined form of cancer that is characterized by transitional features and a shared phenotype. In this review, we summarize essential steps in glucose and lipid metabolism to distinguish similarities in glucose and energy metabolism reprogramming from divergent lipid remodeling in different types of primary liver cancers. We show the convergent nature of metabolic alterations in glucose decomposition and related mitochondrial enzymes. Also, we outline the essential role of lactate in promoting cell viability, adaptation to increased biomass synthesis, and fueling surrounding cancer cells to support their growth and proliferation. Lipid metabolism, in contrast, was found to be dramatically different between primary liver cancers. Hepatocellular carcinoma relies on de novo fatty acids synthesis, for which mitochondrial activity shifts from energy production to citrate efflux. Cholangiocarcinoma, in contrast, relies on fatty acids uptake from the extracellular space and, at later stages, even engages in beta-oxidation, which is uncharacteristic of hepatocellular carcinoma. This yields an altered lipid portrait for these pathologies despite the overall convergent alterations in energy metabolism. With this review, we provide not only fundamental insights for further primary liver tumor metabolism investigation, but also an emphasis on the independence of lipid alterations from energy metabolism reprogramming, vital for further basic and translational applications of metabolomics and lipidomics to a broad range of cancers.

Keywords:  cholangiocarcinoma; glycolysis; hepatocellular carcinoma; lipid metabolism; metabolic reprogramming; primary liver cancer

DOI:  https://doi.org/10.3389/fcell.2026.1890663
Anal Bioanal Chem. 2026 Aug 19.

Decoding the urinary metabolome of aromatic amino acid pathways in Alport syndrome.

Domniki Gallou, Jaime Morillas-Armenta, Miguel Fernández-García, Belen Requena, Santiago Angulo, Olga Begou, Helen Gika, Georgios Theodoridis, Gema Fernández-Juárez, Amir Shabaka, Ana Gradillas, Coral Barbas, Víctor González-Ruiz, Alma Villaseñor.

  Chronic kidney disease (CKD) has been associated with alterations in plasma-free aromatic amino acids (AAA)-tryptophan (Trp), phenylalanine (Phe), and tyrosine (Tyr)-and some downstream metabolites. However, AAA metabolism comprises a wider set of compounds, including microbiome-derived and sulfate-conjugated metabolites excreted in urine with potential biological implications. Alport syndrome (AS), a genetic condition defined by progressive renal impairment, frequently advances to CKD, suggesting that disturbances in AAA-related metabolism may also be relevant in this disorder. Nevertheless, a comprehensive quantitative method covering AAA-derived metabolites enabling an assessment of their implications in AS has not been established. Here, we introduce a novel method for the quantification of up to 43 AAA-derived metabolites in urine, including sulfated metabolites. The method is based on liquid chromatography coupled to tandem mass spectrometry and includes six deuterated internal standards to achieve reliable quantitation. A pooled healthy urine sample was characterized, and the method was validated in terms of linearity, matrix effect, accuracy, precision and sensitivity. The method was applied to urine samples from AS patients-with CKD and non-CKD-and controls. Significant alterations across groups in the concentrations of metabolites from Trp, Phe, and Tyr pathways were observed, including 4-OH-phenylacetic acid-O-sulfate. Notably, the urinary kynurenic acid (KYNA)/Trp ratio emerged as a potential indicator of renal function, showing a marked increase in AS patients with CKD, consistent with enhanced kynurenine pathway activation. Overall, this analytical platform represents a valuable tool for clinical research and for advancing the understanding of AAA-related metabolic dysregulation in renal diseases.

Keywords:  Aromatic amino acids; Kidney disease; MS/MS targeted metabolomics; Microbial metabolites; Sulfatome

DOI:  https://doi.org/10.1007/s00216-026-06707-8
Curr Opin Biotechnol. 2026 Aug 15. pii: S0958-1669(26)00135-7. [Epub ahead of print]101 103570

Extracellular vesicle lipidomics for disease diagnostics and mechanism-informed discovery.

Danielle Maundy, Fernanda Sousa Monteiro, Adriana Zardini Buzatto.

Extracellular vesicles (EVs) are cell-released nanoparticles whose lipid membranes enclose molecular cargo and contribute to vesicle stability, uptake, and biological activity. EV composition encodes and transmits biological information, reflecting cellular origin, membrane remodeling, metabolism, and disease-associated stress. This makes EV lipidomics highly relevant for diagnostics, therapeutics, mechanism-informed discovery, and emerging biotechnology. Recent advances in isolation, characterization, and lipidomics approaches are making EV lipid profiles increasingly interpretable. At the same time, low sample biomass, heterogeneity, co-isolated particles, extraction bias, and variable confidence in lipid detection, annotation, and quantification remain important design considerations. In this review, we discuss how recent EV lipidomics studies are moving beyond untargeted biomarker discovery toward mechanistic questions about membrane adaptation, cellular origin, intercellular communication, and function. We then examine applications in cancer and neurodegeneration, where recent work illustrates the biological and biotechnological potential of EV lipidomes. We argue that the next phase of EV lipidomics will require stronger integration of EV characterization, quality controls, matched biofluid comparisons, and functional assays. With rigorous analytical design, EV lipidomics is evolving into a powerful platform for mechanistic discovery, diagnostic development, and therapeutic delivery.

DOI: https://doi.org/10.1016/j.copbio.2026.103570
Mol Cell Proteomics. 2026 Aug 17. pii: S1535-9476(26)00137-4. [Epub ahead of print] 101641

A Scalable Low-Input Redox Proteomics Workflow Enables High-Throughput Analysis of Cysteine Oxidation in 96-Well Cell Cultures.

Adam M Kabza, Rosey Chu, Jesse Trejo, Xiaolu Li, Matthew J Gaffrey, David Hall, Wei-Jun Qian, Tong Zhang.

  Reversible oxidation of cysteine residues (redox modifications) plays a crucial role in regulating protein function, signaling, and cellular homeostasis. These dynamic modifications act as molecular switches that transduce redox signals and modulate stress responses, metabolism, and pathogenesis. Redox proteomics enables systematic profiling of these modifications, quantifying the oxidation levels of tens of thousands of cysteine sites across the proteome and providing rich data to understand redox-regulated networks. However, conventional redox proteomic workflows are often limited by low throughput and high sample requirements. Here, we present a high-throughput sample processing workflow for redox proteomics analysis from as little as 2 μg of protein, enabling, for the first time, rapid redox-state profiling of cells cultured in 96-well plates. The workflow integrates 96-well plate-based cell culture, lysis, digestion, and cysteine-peptide enrichment, substantially increasing throughput and reducing hands-on processing time. Incorporating field asymmetric ion mobility spectrometry (FAIMS) further enhances redox proteome coverage by removing singly charged species in low-input samples, thereby increasing the signal of cysteine-containing peptides. Applying the workflow to RAW264.7 cells cultured in 96-well plates (40,000 cells per well), DIA identified >10,000 cysteine sites and revealed a global increase in cysteine oxidation upon diamide treatment. To assess robustness, we repeated the 96-well experiment across three independent batches processed on different days and observed consistent coverage, reproducible quantification, and comparable diamide-induced oxidation of heat shock proteins, transcription factors, and protein kinases. Together, this workflow and new data acquisition scheme enable comprehensive redox proteomics from minimal inputs, paving the way for high-throughput sophisticated studies of redox modifications in cell signaling, disease, or large-scale screening of redox-modulating compounds.

Keywords:  Cysteine oxidation; Enrichment; High-throughput; Low-input; Proteomics; Redox

DOI:  https://doi.org/10.1016/j.mcpro.2026.101641
Mol Syst Biol. 2026 Aug 17.

Integrated metabolomics data analysis to generate mechanistic hypotheses with MetaProViz.

Christina Schmidt, Jannik Franken, Denes Turei, Dimitrios Prymidis, Macabe Daley, Christian Frezza, Julio Saez-Rodriguez.

The lack of standardised workflows and ambiguous metabolite annotations hampers metabolomics integration with prior knowledge, thus limiting the extraction of meaningful biological insights. We present MetaProViz (Metabolomics Processing, functional analysis and Visualization), an open-source Bioconductor R package for metabolomics data analysis that integrates prior knowledge to generate mechanistic hypotheses ( https://saezlab.github.io/MetaProViz/ ). MetaProViz operates on annotated intensity values and offers a flexible framework consisting of five modules: processing, differential analysis, prior knowledge integration, functional analysis and visualisation, applicable to intracellular and exometabolomics experiments. To improve functional analysis, we created the Metabolism Signature Database (MetSigDB), a collection of annotated metabolite sets. MetSigDB includes pathway-metabolite, metabolite-receptor, metabolite-transporter sets, and chemical class-metabolite sets. MetaProViz enables the conversion of gene sets to metabolite sets, metabolite identifier expansion and analyses mapping ambiguities. The MetaProViz functional analysis toolkit includes sample metadata analysis, enrichment analysis and biologically informed clustering. By applying MetaProViz to kidney cancer metabolomics data, we identified increased methionine usage in line with decreased methionine levels in tumour samples. In summary, MetaProViz facilitates and improves the analysis and interpretation of metabolomics data.

DOI: https://doi.org/10.1038/s44320-026-00231-8
STAR Protoc. 2026 Aug 19. pii: S2666-1667(26)00436-3. [Epub ahead of print]7(3): 104783

Protocol for untargeted multi-omics dried blood spot extraction using liquid chromatography-tandem mass spectrometry.

Esabella R Powers, Timothy J Garrett.

  Dried blood spots (DBS), most notably employed in newborn screening, present a valuable opportunity to analyze whole blood via a stable and simplified sample collection. DBS are generally used to evaluate one class of compounds at a time. Herein, we present a protocol to semi-quantitatively evaluate metabolites and lipids from the same DBS using a multi-omics approach. We describe steps for extracting both metabolites and lipids from the paper-based sample and analyzing them via liquid chromatography-tandem mass spectrometry. For complete details on the use and execution of this protocol, please refer to Li et al.1.

Keywords:  Health sciences; Metabolomics; Protocols in metabolomics and lipidomics

DOI:  https://doi.org/10.1016/j.xpro.2026.104783
Proteomics. 2026 Aug 17. e70171

Multi-Organ DIA Proteomics Reveals a Shared Xenobiotic Metabolism Stress Program in a Patient-Derived Xenograft Model.

Julia Osaki, Yomogi Shiota, Kazuyoshi Yanagihara, Masaki Matsumoto, Tadashi Kondo.

  Cancer cachexia is a devastating systemic syndrome characterized by progressive body weight loss and multi-organ dysfunction, yet the proteome-level mechanisms driving synchronized organ remodeling remain incompletely defined. Here, we applied large-scale data-independent acquisition (DIA) proteomics to a reproducible xenograft model using cachexia-inducing human neuroendocrine carcinoma cells (AkuNEC). Compared with non-implanted controls, AkuNEC-bearing mice developed severe wasting of the heart, liver, kidney, and skeletal muscle. Quantitative profiling revealed extensive multi-organ proteome remodeling, with xenobiotic metabolism emerging as a recurrently altered program across all tissues. This shared "chemical stress" signature was overlaid with distinct organ-specific alterations. The liver, heart, and kidney exhibited convergent suppression of mTORC1 signaling, with the liver displaying additional complex reprogramming involving interferon responses and fatty acid metabolism. In contrast, skeletal muscle showed unique stress features, with coagulation emerging as the most prominent signature alongside xenobiotic metabolism. These findings establish a comprehensive multi-organ proteomic framework for cachexia, identifying systemic remodeling of xenobiotic and endobiotic stress pathways as a unifying pathophysiological feature. This pan-organ alteration implies a fundamental compromise in the host's capacity to detoxify endobiotics and therapeutics, providing a molecular rationale for the unpredictable pharmacokinetics and heightened drug toxicity frequently complicating cachexia management.

Keywords:  DIA proteomics; cancer cachexia; multi‐organ proteomics; xenobiotic metabolism; xenograft model

DOI:  https://doi.org/10.1002/pmic.70171
Int J Cancer. 2026 Aug 19.

Spatially Resolved Metabolomics of Optimal Cutting Temperature (OCT) Compound-Embedded Tumors.

Joseph Monaghan, Nicholas Woytowich, Tian Zhao, Kiera Nguyen, Emily Mahony, Julian J Lum, Kyle D Duncan.

  Mass spectrometry imaging (MSI) is emerging as a powerful tool for uncovering the distribution of metabolites in the tumor microenvironment and studying tumor metabolism in vivo. To date, MSI of biobanked tissues contextualized by patient data has been limited to peptides, proteins, and glycans-with few examples for metabolites. This is because most biobanked fresh-frozen tissue required for spatial metabolomics is embedded in optimal cutting temperature (OCT) compound to preserve structural features and mitigate thermal decay. However, OCT introduces abundant polyethylene glycol and polyvinyl alcohol interferents. Herein, we use nanospray desorption electrospray ionization (nano-DESI) to demonstrate MSI of metabolites in OCT-embedded tissue. Metabolite coverage and sensitivity for tissue mimetic homogenates embedded in OCT and an MSI-compatible material, carboxymethylcellulose (CMC), exhibited excellent agreement. We apply our ambient MSI workflow to study the impact of methionine-restriction in a preclinical mouse model undergoing adoptive T-cell therapy. After tumor incubation (8 days), lymphoma-bearing mice were maintained on a complete or methionine-restricted diet for 2 days. Nano-DESI MSI revealed a heterogeneous tumor microenvironment, with multiple methionine-cycle intermediates (S-adenosylmethionine, S-adenosylhomocysteine) and related metabolites, including known T-cell modulators (1-methylnicotinamide, polyamines) localizing to tumor subregions. Methionine-restricted tumors exhibited reduced methionine and elevated S-adenosylmethionine, relative to the control group. Overall, this work establishes the potential for spatial metabolomics of fresh-frozen OCT-embedded tumors, unlocking the wealth of information stored in primary tissue biobanks and consequently accelerating our understanding of cancer metabolism and treatment.

Keywords:  ambient ionization; mass spectrometry imaging; nanospray desorption electrospray ionization; spatial metabolomics; tissue preparation

DOI:  https://doi.org/10.1002/ijc.70707
Anal Chim Acta. 2026 Oct 15. pii: S0003-2670(26)00915-3. [Epub ahead of print]1419 345965

New chromatographic and data evaluation approaches for the comprehensive investigation of metal-phytosiderophore-complex dynamics.

Laura Zellner, Andreea Spiridon, Sangeeta Kumari, Simone Braeuer, Nicolas Kratena, Christian Stanetty, Eva Oburger, Tim Causon, Christian W Klampfl, Stephan Hann.

   BACKGROUND: Phytosiderophores (PS) are root exudates released by graminaceous plants that play a crucial role in micronutrient acquisition. This is particularly relevant for iron, but PS can also complex other transition metals in the rhizosphere, influencing their bioavailability and uptake. However, characterizing intact metal-PS complexes remains analytically challenging, and studies have largely relied on targeted approaches using a limited number of selected PS.
RESULTS: We developed a liquid chromatography electrospray ionization high resolution mass spectrometry (LC-HRMS) workflow using a mixed-mode stationary phase to separate 2'-deoxymugineic acid, mugineic acid and 3″-epi-hydroxymugineic acid along with their Fe(III), Cu(II) and Ni(II) complexes. Complex integrity was preserved under mild gradient conditions, enabling quantification in negative ionization mode across a working range of 1 to 15 μmol L-1. In parallel, we utilized MetalPicker, a novel software tool for non-targeted detection of metal complexes in LC-HRMS data. By leveraging the distinctive isotopic distribution of transition metals, MetalPicker enables the discovery of metal-PS features in a non-targeted fashion. Validation of MetalPicker against a manufacturer software for targeted quantitative analysis yielded comparable results, demonstrating the accuracy and applicability of MetalPicker for non-targeted metal complex analysis. Our approach was applied for competitive complexation experiments in model samples, revealing a strong affinity of the PS towards Cu(II), potentially limiting iron bioavailability for plants.
SIGNIFICANCE: Our study presents the first chromatographic method separating metal-PS complexes alongside free PS, integrated with the novel non-targeted metal-complex detection software MetalPicker. Together, these advances enable the determination of coexisting metal-PS complexes in samples, expanding analytical capabilities for studying rhizosphere metal dynamics and nutrient mobilization.

Keywords:  LC-MS; Metal-complexes; Micronutrients; Phytosiderophores

DOI:  https://doi.org/10.1016/j.aca.2026.345965
PLoS One. 2026 ;21(8): e0356269

Targeted metabolomics of postmortem human cardiac tissue using the Biocrates MxP Quant 500 kit.

Oscar Emil Puntervold, Pia Johansson Heinsvig, Mads Gustav Skytte, Kristine Boisen Olsen, Jytte Banner, Jacob Tfelt-Hansen, Kristian Linnet, Marie Mardal.

AIM: This proof-of-concept study aimed to evaluate the feasibility and analytical performance of the Biocrates MxP® Quant 500 kit, originally developed for biofluids, to postmortem human cardiac tissue obtained from forensic autopsies, evaluating its potential as a standardized, cost-effective alternative to complex, resource-intensive metabolomics workflows.
METHODS: Left ventricular tissue samples were collected from 40 forensic autopsy cases, comprising 10 decedents with type 2 diabetes, 20 decedents with ischemic heart disease without type 2 diabetes, and 10 control cases without cardiac pathology. Cases were selected to represent the range of myocardial conditions commonly encountered in forensic practice, enabling assessment of analytical feasibility across heterogeneous postmortem cardiac tissue. Samples were analyzed using the MxP® Quant 500 kit following the standard protocol and using liquid chromatography-tandem mass spectrometry and flow injection analysis methods, measuring and quantifying a total of 630 endogenous metabolites across diverse classes.
RESULTS: Out of the 630 metabolites, 463 (74%) were within the quantifiable range. Lipid-related metabolites were notably well represented, with sphingomyelins (100% retained), phosphatidylcholines (93% retained), triacylglycerols (82% retained), and fatty acids (83% retained) showing the highest retention. Other metabolite classes such as acylcarnitines (45% retained) demonstrated greater variability, with some measurements falling below the limit of detection (e.g., 47% of acylcarnitines below this limit) or exceeding the upper limit of quantification (e.g., 35% of amino acids above this limit). Univariate analyses showed nominal group differences among specific metabolite subclasses (unadjusted p < 0.05). However, no metabolites remained statistically significant after correcting for false discovery rate. Multivariate analysis using PERMANOVA or PCA showed no strong global separation.
CONCLUSION: The Biocrates MxP® Quant 500 kit demonstrated technical feasibility for postmortem cardiac tissue analysis, enabling quantification of a broad range of metabolites, particularly lipids. While variability was observed across certain metabolite classes, the approach provides a promising basis for standardized metabolomic investigations in forensic and cardiovascular research.

DOI: https://doi.org/10.1371/journal.pone.0356269
Proc Natl Acad Sci U S A. 2026 Aug 25. 123(34): e2533109123

High-resolution mapping of osteoblast metabolism and bone matrix turnover in vivo.

Kai Chen, Jinyu Guo, Xiaojun Chen, Buran Chen, Heng Qiu, Hui Yang, Paul Guagliardo, Sitao Hu, Chau Bui, Kavishadhi Chandrasekaran, Qiongxiang Lin, Bo He, Qi Chen, Jiake Xu, Stephen G Young, Matthew B Greenblatt, K Swaminathan Iyer, Nathan J Pavlos, Haibo Jiang.

  Understanding how osteoblasts build and remodel bone matrix in vivo remains a fundamental challenge because cellular metabolism and matrix turnover are difficult to resolve across time and space within mineralized tissues. Here, we developed an integrated imaging platform combining stable isotope labeling with correlative electron microscopy and nanoscale secondary ion mass spectrometry (NanoSIMS) to visualize bone cell metabolism and matrix dynamics at nanometer resolution in vivo. This approach revealed rapid incorporation of dietary amino acids into osteoblast subcellular compartments within minutes of oral administration, followed by deposition of newly labeled extracellular matrix within hours. By linking elemental composition, isotope incorporation, and ultrastructure, we further show that cellular phosphorus signal is associated with early osteoblast amino acid incorporation. Multiday labeling revealed that newly deposited matrix is spatially associated with local osteocyte process architecture. Long-term amino acid tracing uncovered localized matrix turnover at osteocyte and osteoclast interfaces, including osteocyte-associated pericellular matrix remodeling and osteoclast association with newly formed, old, and mixed matrix regions. Finally, aging was associated with reduced osteoblast amino acid incorporation, diminished matrix deposition, and impaired osteocyte process-associated activity. Together, this work establishes a high-resolution platform for linking bone cell metabolism with matrix deposition and turnover in vivo, providing a broadly adaptable strategy to investigate skeletal aging, tissue remodeling, and metabolic dysfunction in disease.

Keywords:  NanoSIMS; bone; bone matrix; metabolism; osteoblast

DOI:  https://doi.org/10.1073/pnas.2533109123
Clin Chem. 2026 Aug 17. pii: hvag096. [Epub ahead of print]

Detection of Multiple Medetomidine Metabolites in Clinical Urine Specimens by Liquid Chromatography-Quadrupole Time-of-Flight Mass Spectrometry (LC-qToF-MS).

Kenichi Tamama, Delaney Morrow, Todd Rates.

DOI: https://doi.org/10.1093/clinchem/hvag096
Nat Metab. 2026 Aug;8(8): 1772-1790

Isoleucine and valine promote prostate cancer progression via propionyl-CoA-mediated cholesterol metabolism.

Zhongchi Li, Shuchen Liu, Wenbing Jin, Leyi Xiao, Olivia Kester, Nayah Bullen, Xuanrong Chen, Un In Chan, Jude Owiredu, Zhucui Li, Rabia Khan, Jennifer Endress, Moniquetta Shafer, Vivien Low, Nikolaos Koundouros, Sungyun Cho, Christopher Barbieri, Chun-Jun Guo, John Blenis.

Enhanced cholesterol synthesis and lipid droplet accumulation are hallmarks of aggressive prostate cancer, yet how tumour cells sense metabolic inputs to dynamically regulate cholesterol homeostasis remains poorly defined. Here we uncover a metabolic signalling mechanism in which prostate cancer cells remodel propionyl-CoA metabolism to support stress adaptation during disease progression. We show that the catabolism of branched-chain amino acid, specifically isoleucine and valine, is the primary source of intracellular propionyl-CoA in prostate cancer cells. Beyond its metabolic role, propionyl-CoA functions as a signalling molecule that stabilizes nuclear sterol regulatory element-binding protein 2 (SREBP2) through site-specific lysine propionylation, thereby enhancing its transcriptional activity. This activation promotes cholesterol biosynthesis, fuels de novo androgen production, and sustains androgen receptor signalling under metabolic and therapeutic stress, including androgen deprivation. Together, our findings establish propionyl-CoA as a key metabolic signal linking amino acid catabolism to cholesterol-driven oncogenic programmes and highlight targeting isoleucine and valine metabolism as a potential strategy to disrupt lipid reprogramming in prostate cancer.

DOI: https://doi.org/10.1038/s42255-026-01583-z
Clin Chem Lab Med. 2026 Aug 19.

An isotope dilution-liquid chromatography-tandem mass spectrometry-based candidate reference measurement procedure for the quantification of gentamicin in human serum.

Jo Anne Wright, Neeraj Singh, Annika Brauch, Friederike Bauland, Andrea Geistanger, Judith Taibon, Elie Fux.

   OBJECTIVES: Therapeutic drug monitoring (TDM) of gentamicin is critical to ensure efficacy and minimize toxicity. We report a candidate reference measurement procedure (RMP) to quantify gentamicin in biological matrices, establishing an unbroken traceability chain to the International System of Units (SI).
METHODS: An isotope dilution-liquid chromatography-tandem mass spectrometry (ID-LC-MS/MS) method was validated using quantitative nuclear magnetic resonance (qNMR) spectroscopy to replace historical biological activity-based standardization with gravimetric mass. Strict ID-MS principles were applied to the major congeners (C1, C1a, and C2). Isomers C2a and C2b, eluting at distinct retention times, were quantified using C2-D3 as a structural analog internal standard. Pharmacokinetic-based analytical performance specifications set the maximum allowable standard measurement uncertainty (k=1) at ≤6.7 %.
RESULTS: The RMP demonstrated high analytical control, with trueness (bias 1.0-2.8 %) and within-run precision (CV 0.2-0.9 %) fulfilling clinical requirements. Expanded measurement uncertainties (k=2) for target value assignment ranged from 2.0 to 2.4 %. Comparison with the current JCTLM-listed RMP revealed a systematic negative bias of -9.2 %. A three-way method correlation confirmed these differences as a direct result of the metrological transition from activity to SI-traceable mass units.
CONCLUSIONS: This candidate RMP provides a robust, highly precise SI-traceable foundation for gentamicin quantification. While the resulting downward shift in reported concentrations may necessitate re-evaluating established clinical decision thresholds and TDM protocols, the clinical requirement for such adjustments remains to be fully determined.

Keywords:  SI units; gentamicin; isotope dilution-liquid chromatography-tandem mass spectrometry; qNMR characterization; reference measurement procedure; traceability

DOI:  https://doi.org/10.1515/cclm-2026-0593
Mol Cell. 2026 Aug 21. pii: S1097-2765(26)00517-4. [Epub ahead of print]

Nicotinamide nucleotide transhydrogenase directly couples redox homeostasis to proline biosynthesis in human glioma.

Lisa A Vettore, Adam Boufersaoui, Yingying Lyu, Anaïs Oudin, Keene L Abbott, Sonu Subudhi, Yetiş Gültekin, Katherine L Eales, Ishana Rajgopal, Cristina Escribano-Gonzalez, Rahatil A Chowdhury, Himani Rana, Victoria Wykes, Rakesh K Jain, Anna Golebiewska, Matthew G Vander Heiden, Daniel A Tennant.

  Cancer cell proliferation requires a precise balance between biomass production and nutrient catabolism. The pyridine nucleotide cofactors nicotinamide adenine dinucleotide NAD(H) and NAD phosphate NADP(H) are central to this process, but their compartment-specific regulation is incompletely understood. Using in vivo isotope-labeled metabolite tracing in an orthotopic xenograft model, we find that human gliomas extensively synthesize proline, an amino acid previously associated with hypoxia tolerance. In glioma cells, we identify a hypoxia-enhanced proliferative sensitivity to environmental proline dependent on NADH to NADPH transhydrogenation from a spatially compartmentalized mitochondrial pool by the enzyme nicotinamide nucleotide transhydrogenase (NNT). We demonstrate NNT-dependent generation of mitochondrial NADPH is important for proline accumulation, maintenance of antioxidant systems, and reductive metabolism in hypoxic glioma cells in vitro and tumor progression in vivo. Collectively, these results highlight proline accumulation as a marker of mitochondrial NAD(P)(H) homeostasis and NNT as a specific metabolic dependency in human glioma.

Keywords:  NNT; glioma; hypoxia; proline; redox

DOI:  https://doi.org/10.1016/j.molcel.2026.07.031