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Editorial: Advances in mass spectrometry: transforming analytical chemistry in molecular and spatial biology; multimodal omics; and bioanalysis
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DOI：10.3389/fmolb.2026.1926838.png)
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Abstract
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cost-efficient alternative to sequencing techniques; providing global methylome information without the need for extensive bioinformatic analyses. Several studies focused on biomarker discovery in human disease. Zhou et al. applied a nontargeted metabolomics approach with high-resolution mass spectrometry to investigate the mechanisms of icariin in the treatment of rheumatoid arthritis. They identified 31 potential biomarkers to diagnose metabolic disorders in rheumatoid arthritis; 23 of which were regulated by icariin; through pathways including the glutamate; arachidonic acid; pyruvate metabolism; the citrate cycle; glycolysis; etc.; implicating oxidative stress and inflammation. Concomitantly; Masood et al. conducted a complementary investigation of rheumatoid arthritis using untargeted high-resolution mass spectrometry on 122 human plasma samples. They identified 300 dysregulated metabolites; ultimately annotating 60 endogenous metabolites with strong separation between rheumatoid arthritis patients and controls. They found major metabolic changes in the lipid; amino acid; and nucleotide metabolism pathways linked to cytokines; the MAPK pathway; etc.; that supported plasma metabolomics as a phenotyping tool to find candidate biomarkers to diagnose rheumatoid arthritis. Wan et al. examined carotid atherosclerosis using metabolomics; spatial metabolomics; and single-cell transcriptomics with MALDI-MSI. They identified 74 differential metabolites between stable and unstable plaques of the patients; with arachidonic acid as the main inflammation-causing lipid upregulated in unstable plaques and enriched in 22 metabolic pathways. Spatial MALDI-MSI directly localized arachidonic acid with inflammatory macrophages; and single-cell analysis highlighted ELOVL5 and ALOX5 as over-expressed macrophage genes; offering mechanistic information on the linoleic acid -arachidonic acid -leukotriene D4 metabolic axis within atherosclerotic plaques. Dong et al. employed metabolomics to identify early biomarkers to detect acute intra-abdominal infection. They enrolled 30 patients and 20 healthy controls and analyzed their serum and urine samples with high-resolution mass spectrometry. They identified five serum biomarkers linked to fatty acid biosynthesis pathway; and two urinary biomarkers linked to catecholamine biosynthesis pathway. They proposed these candidates as diagnostic biomarkers for the early diagnosis of acute intra-abdominal infection. Zhang et al. developed and validated a rapid triple quadrupole mass spectrometric method for the simultaneous quantification of 11 antimicrobials in human plasma; achieving baseline separation of the components within eight minutes. They validated the method according to regulatory guidelines; meeting the requirements for clinical therapeutic drug monitoring implementation. They successfully applied the procedure to measure plasma samples of pediatric patients receiving mono-or combination antibiotic therapy; building strategies for timely therapeutic drug monitoring in the clinic. From the point of inflammation care; aging; and plant-based therapeutics; Xie et al. used untargeted metabolomics with high-resolution mass spectrometry to investigate Cuscutae Semen in a mouse model of depression-induced ovarian dysfunction. They identified ten differential metabolites from various pathways including arachidonic acid metabolism and steroid hormone biosynthesis; with seven target genes further validating their findings. The results supported Cuscutae Semen as a functional medical food with defined pharmacological mechanisms. Li et al. employed high-resolution mass spectrometry; non-targeted metabolomics; network pharmacology; and molecular dynamics to study Taohong Siwu Decoction in carbon tetrachloride-induced hepatic fibrosis. They identified 45 blood components; 148 differential metabolites; and a target network pointing to PI3K-Akt; MAPK; and estrogen signaling. They found ferulic acid derivatives as emerging key active compounds; with 3-hydroxy-4methoxycinnamic acid showing stable binding to PPARG. Ying et al. took a transcriptomic approach to sarcopenia; integrating several public datasets to identify a three-gene mitochondrial signature; validating them in vitro; and achieving a high diagnostic area-under-the-curve (AUC) score. Their nomogram model emphasized the role of mitochondrial dysfunction in muscle aging and offered a potential clinical tool for early sarcopenia detection. Working on clinical and respiratory applications; Gisler et al. explored real-time breath analysis using secondary electrospray ionization coupled with high-resolution mass spectrometry in 128 children (tobacco-exposed and non-exposed) and found that 71 breath features significantly correlated with the urinary oxidative stress marker 8-iso-PGF2α. They could not detect a strong correlation between predicted and measured values; but the study supported breath metabolomics as a promising non-invasive tool to indicate oxidative stress. Likewise; Shajari et al. monitored the inflammatory bowel disease activity in 174 stool proteomics samples obtained by highresolution mass spectrometry with data-independent analysis. A nine-peptide panel from five proteins; selected within a leakage-free nested cross-validation framework; achieved an outerfold AUC of 0.93. More importantly; the panel retained diagnostic power (AUC 0.80) even in the calprotectin "gray zone; " where current non-invasive tests were unreliable. From the bibliometric perspective; Wu et al. provided a broader context through the analysis of 1; 188 publications on osteosarcoma metabolomics from 1995 to 2024. China leads in output; with growing interest in extracellular vesicles; immune metabolism; and single-cell metabolomics; reflecting a field-wide shift toward higher-resolution metabolic characterization and translational application. Finally; Szeitz et al. hosted a two-part roundtable discussion where they brought together representatives from the mass spectrometry industry to highlight recent developments; research requirements; and regulatory guidelines on mass spectrometry instrumentation and technology. In the first part; the panelists explored current trends in mass spectrometry focusing on research applications and gaps; single-cell analysis; metabolomics; lipidomics; and multi-omics integration; while in the second part; they examined data management; bioinformatics; collaboration and industry needs. They sought to integrate mindsets within scientific research; inspire diverse perspectives; and foster scientific discourse with mass spectrometry transforming the landscape of medical science and molecular research. Taken together; these studies showcase how metabolomics; integrated with genomics; proteomics; spatial imaging; and machine learning; is becoming central to mechanistic biology; clinical diagnostics; and therapeutic discovery through various biological systems. Author contributions AS: Conceptualization; Investigation; Methodology; Writing -original draft; Writing -review and editing. JP: Methodology; Writing -original draft; Writing -review and editing. AP: Methodology; Writing -original draft; Writing -review and editing. Funding The author(s) declared that financial support was not received for this work and/or its publication. Acknowledgments
Keywords:
mass spectrometry
metagenomics
multiomics
spatial biology
analytical chemistry
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