bims-metlip 2025-02-16 papers

bims-metlip

Biomed News

on Methods and protocols in metabolomics and lipidomics

Issue of 2025–02–16
fourteen papers selected by
Sofia Costa, Matterworks

Development and Validation of Targeted Metabolomics Methods Using Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) for the Quantification of 235 Plasma Metabolites.
First Dimension Trap-and-Elute Combined with Second Dimension Reversed-Phase Liquid Chromatography Separation Using a Two-Dimensional-Liquid Chromatography-Tandem Mass Spectrometry System for Sensitive Quantification of Human Insulin and Six Insulin Analogs in Plasma: Improved Chromatographic Resolution and Stability Testing.
[Determination of diazepam and its three metabolites in fish by pass-through solid phase extraction purification combined with ultra-performance liquid chromatography-tandem mass spectrometry].
Workflow4Metabolomics (W4M): A User-Friendly Metabolomics Platform for Analysis of Mass Spectrometry and Nuclear Magnetic Resonance Data.
Novel Method for Simultaneously Untargeted Metabolome and Targeted Exposome Analysis in One Injection.
Tackling pressure fluctuations in ultra-high performance liquid chromatography to robustly resolve and analyse polar metabolites.
Development of an Oxylipin Library Using Liquid Chromatography-Ion Mobility Quadrupole Time-of-Flight: Application to Mouse Brain Tissue.
One-Pot Construction of NHS-Activated Magnetic Particles for Chemoselective Capture of Carboxyl Metabolites.
Unveiling Readily Ionized and Robust Anionic Species: A Gateway to Enhanced Ionization Efficiency in ESI-MS Analysis.
Validation of a Novel LC-MS-MS Method for the Separation and Differentiation of Δ8- and Δ9-Tetrahydrocannabinol Isomers and their Major Metabolites in Antemortem Whole Blood.
Molecular Structure and Mass Spectral Data Quality-Driven Processing of High-Resolution Mass Spectrometry for Quantitative Analysis.
Recent advances in analytical methods and bioinformatic tools for quantitative glycomics.
Groomed Fingerprint Sebum Sampling: Reproducibility and Variability According to Anatomical Collection Region and Biological Sex.
An expanded database of high-resolution MS/MS spectra for lichen-derived natural products.

Molecules. 2025 Feb 05. pii: 706. [Epub ahead of print]30(3):

Development and Validation of Targeted Metabolomics Methods Using Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) for the Quantification of 235 Plasma Metabolites.

Kangkang Xu, Franz Berthiller, Barbara U Metzler-Zebeli, Heidi E Schwartz-Zimmermann.

  Plasma contains metabolites with diverse physicochemical properties, ranging from highly polar to highly apolar, and concentrations spanning at least nine orders of magnitude. Plasma metabolome analysis is valuable for monitoring health and evaluating medical interventions but is challenging due to the metabolome's diversity and complexity. This study aims to develop and validate targeted LC-MS/MS methods for quantifying 235 mammalian metabolites from 17 compound classes in porcine plasma without prior derivatization. Utilizing reversed-phase and hydrophilic interaction liquid chromatography coupled with tandem mass spectrometry, each analyte is identified and quantified using two selected reaction monitoring (SRM) transitions. Fast polarity switching and scheduled SRM enhance the metabolome coverage and throughput, enabling the analysis of one sample in about 40 min. A simple "dilute and shoot" sample preparation protocol was employed, with samples injected at two dilution levels to align metabolite concentrations within calibration curve ranges. Validation in porcine plasma included assessments of carryover, linearity, detection and quantification limits, repeatability and recovery. The method was further applied to plasma samples from various animal species, demonstrating its applicability to human and animal studies. This study establishes two robust LC-MS/MS methods for comprehensive porcine plasma metabolome quantification, advancing large-scale targeted metabolomics in biomedical research.

Keywords:  HILIC; animal metabolomics; metabolomics; plasma metabolites; reversed-phase high-performance liquid chromatography; targeted HPLC-MS/MS methods

DOI:  https://doi.org/10.3390/molecules30030706
J Sep Sci. 2025 Feb;48(2): e70092

First Dimension Trap-and-Elute Combined with Second Dimension Reversed-Phase Liquid Chromatography Separation Using a Two-Dimensional-Liquid Chromatography-Tandem Mass Spectrometry System for Sensitive Quantification of Human Insulin and Six Insulin Analogs in Plasma: Improved Chromatographic Resolution and Stability Testing.

Pavel Sistik, Romana Urinovska, Klara Handlosova, Petr Handlos, Katerina Andelova, Jan Jurica, David Stejskal.

  Multidimensional chromatography coupled to tandem mass spectrometry (MS/MS), including simple sample preparation with protein precipitation, anion conversion with ammonium hydroxide, and solid-phase extraction using mixed-mode anion exchange in a 96-well plate format, has been validated for rapid simultaneous analysis of human insulin and its six analogs (lispro, glulisine, glargine, degludec, detemir, and aspart) in human plasma. This method is critical for clinical diagnostics, forensic investigations, and anti-doping efforts due to the widespread use of these substances. In the present study, improved chromatographic resolution was achieved using a first-dimension trap-and-elute configuration with an XBridge C18 (2.1 × 20 mm, 3.5 µm) trap column combined with second dimension separation on a Cortecs Ultra-High-Performance Liquid Chromatography (UHPLC) C18+ (2.1 × 100 mm, 1.6 µm) analytical column implemented within a two-dimensional-LC-MS/MS system. The total chromatographic run time was 11 min. This setup increases both the resolution and sensitivity of the method. A mobile phase consisting of 0.8% formic acid (FA) in water and 0.7% FA in acetonitrile was used for gradient elution. Bovine insulin was used as the internal standard. MS detection was performed in positive electrospray ionization mode, and the ion suppression due to matrix effects was evaluated. Validation criteria included linearity, precision, accuracy, recovery, lower limit of quantitation, matrix effect, and stability tests with and without protease inhibitor cocktail under different conditions (short-term stability, long-term stability, and freeze-thaw stability). The concentration range for all insulins was 50-15 000 pg/mL, with limits of quantification below the therapeutic reference range for all analytes. Intra-run precision ranged from 1.1% to 5.7%, inter-run precision from 0.7% to 5.9%, and overall recovery from 96.9% to 114.3%. The validated method has been implemented successfully by the Department of Forensic Medicine at our hospital for the investigation of unexplained deaths.

Keywords:  human plasma; insulins; liquid chromatography; mass spectrometry; method validation; stability studies

DOI:  https://doi.org/10.1002/jssc.70092
Wei Sheng Yan Jiu. 2025 Jan;54(1): 129-135

[Determination of diazepam and its three metabolites in fish by pass-through solid phase extraction purification combined with ultra-performance liquid chromatography-tandem mass spectrometry].

Ping Ouyang, Junlin Wang, Nianhua Zhang, Pinggu Wu, Dingnan Wang, Yang Wang.

   OBJECTIVE: A stable isotope dilution-through solid phase extraction(SPE)-ultra-performance liquid chromatography-tandem mass spectrometry(UPLC-MS/MS) method was established for rapid determination of diazepam and its three metabolites(nordiazepam, temazepam and oxazepam) in fish.
METHODS: Sample was extracted with acetonitrile, then salted out with sodium chloride and degreased by freezing centrifugation. The acetonitrile layer diluted to a ratio of 90 percents with pure water, and through C_(18)/PSA SPE column for purification. Purification solution was collected with the first 1 mL discarded, and nitrogen blow to near dry.1.0 mL initial mobile phase was used for reconstitution, and then separated by BEH C_(18)(100 mm × 2.1 mm, 1.7 μm) chromatography column using 0.1% formic acid aqueous and 0.1% formic acid methanol at gradient elution, and detected with triple quadrupole mass spectrometry.
RESULTS: One-step purification with C_(18)/PSA SPE column would effectively reduce matrix interference, simplify operation and improve work efficiency. The linear ranges of 4 target compounds were 0.2 to 10.0 ng/mL and the correlation coefficients were greater than 0.999. The recoveries were in the range of 92.0%-120.0% with the relative standard deviations ranging from 4.5%-10.7%(n = 6). The method limits of detection were 0.2 μg/kg. Then the established method was used for the determination of 10 positive fish samples, and the content of diazepam and nordiazepam were 68.4%-100% in fish samples, and it indicated that diazepam and nordiazepam were the main biomarker.
CONCLUSION: The established method is simple, rapid, sensitive and selective, which is suitable for the simultaneous determination of diazepam and its three metabolites in fish.

Keywords:  UPLC-MS/MS; diazepam; fish; metabolites; solid phase extraction

DOI:  https://doi.org/10.19813/j. cnki.weishengyanjiu.2025.01.023
Curr Protoc. 2025 Feb;5(2): e70095

Workflow4Metabolomics (W4M): A User-Friendly Metabolomics Platform for Analysis of Mass Spectrometry and Nuclear Magnetic Resonance Data.

Cédric Delporte, Marie Tremblay-Franco, Yann Guitton, Cécile Canlet, Ralf J M Weber, Helge Hecht, Elliott James Price, Jana Klánová, Charlotte Joly, Céline Dalle, Julien Saint-Vanne, Etienne Thévenot, Isabelle Schmitz, Sylvain Chéreau, Sylvain Dechaumet, Binta Diémé, Franck Giacomoni, Gildas Le Corguillé, Mélanie Pétéra, Florence Souard.

  Various spectrometric methods can be used to conduct metabolomics studies. Nuclear magnetic resonance (NMR) or mass spectrometry (MS) coupled with separation methods, such as liquid or gas chromatography (LC and GC, respectively), are the most commonly used techniques. Once the raw data have been obtained, the real challenge lies in the bioinformatics required to conduct: (i) data processing (including preprocessing, normalization, and quality control); (ii) statistical analysis for comparative studies (such as univariate and multivariate analyses, including PCA or PLS-DA/OPLS-DA); (iii) annotation of the metabolites of interest; and (iv) interpretation of the relationships between key metabolites and the relevant phenotypes or scientific questions to be addressed. Here, we will introduce and detail a stepwise protocol for use of the Workflow4Metabolomics platform (W4M), which provides user-friendly access to workflows for processing of LC-MS, GC-MS, and NMR data. Those modular and extensible workflows are composed of existing standalone components (e.g., XCMS and CAMERA packages) as well as a suite of complementary W4M-implemented modules. This tool suite is accessible worldwide through a web interface and is hosted on UseGalaxy France. The extensible Virtual Research Environment (VRE) provided offers pre-configured workflows for metabolomics communities (platforms, end users, etc.), as well as possibilities for sharing among users. By providing a consistent ecosystem of tools and workflows through Galaxy, W4M makes it possible to process MS and NMR data from hundreds of samples using an ordinary personal computer, after step-by-step workflow optimization. © 2025 Wiley Periodicals LLC. Basic Protocol 1: W4M account creation, working history preparation, and data upload Support Protocol 1: How to prepare an NMR zip file Support Protocol 2: How to convert MS data from proprietary format to open format Support Protocol 3: How to get help with W4M (IFB forum) and how to report a problem on the GitHub repository Basic Protocol 2: LC-MS data processing Alternate Protocol 1: GC-MS data processing Alternate Protocol 2: NMR data processing Basic Protocol 3: Statistical analysis Basic Protocol 4: Annotation of metabolites from LC-MS data Alternate Protocol 3: Annotation of metabolites from NMR data.

Keywords:  GC–MS; LC–MS; NMR; annotation; chemometrics; statistics; untargeted metabolomics

DOI:  https://doi.org/10.1002/cpz1.70095
Anal Chem. 2025 Feb 12.

Novel Method for Simultaneously Untargeted Metabolome and Targeted Exposome Analysis in One Injection.

Pengwei Guan, Yuting Wang, Tiantian Chen, Jun Yang, Xiaolin Wang, Guowang Xu, Xinyu Liu.

Serum endogenous metabolites and coexisting exogenous compounds are closely related to human health. Metabolomics often uses high-resolution mass spectrometry (HRMS), but current exposomics studies typically rely on triple quadrupole tandem mass spectrometry due to lower concentrations in the body. As a result, metabolome-exposome-wide association studies (mEWAS) require a combination of untargeted metabolomics and several targeted exposomics methods to measure more exposures, leading to increased time and sample consumption. In this study, a novel method was proposed by leveraging the advantages of recently introduced Zeno MRMHR technology; it allows for the simultaneous acquisition of the metabolome in HRMS and the exposome in multiple reaction monitoring (MRM) modes in one injection. The signal responses for exogenous compounds in MRM were comparable to those of metabolites in HRMS. This method was rigorously validated, and all exogenous standards had relative standard deviations (RSDs) below 20% for intraday and interday repeatability. Over 90% of metabolic features exhibited RSDs below 20% in these assessments. The method also had a broad quantification range, with lower limits of quantification (LLOQ) from 0.1 to 25 ng/mL and higher limits of quantification (HLOQ) from 2.5 to 1000 ng/mL. This approach was demonstratively applied to a type 2 diabetes mellitus cohort to identify serum risk factors and study the metabolome-exposome association. To our knowledge, this study is the first implementation of a unified method for the simultaneous analysis of endogenous metabolites in the untargeted mode and 210 exogenous compounds in the targeted mode in one injection, offering a novel tool for mEWAS research.

DOI: https://doi.org/10.1021/acs.analchem.4c05565
J Biol Chem. 2025 Feb 10. pii: S0021-9258(25)00131-0. [Epub ahead of print] 108283

Tackling pressure fluctuations in ultra-high performance liquid chromatography to robustly resolve and analyse polar metabolites.

James R Krycer, Manuel Plan, Thomas Stoll, Andrew R Laskary, Mark P Hodson, James E Hudson.

The success of modern metabolomics analysis depends on the separation of metabolites in complex samples using methods such as liquid chromatography and mass spectrometry. Herein, we present a protocol for resolving a broad range of polar metabolites, based on hydrophilic interaction liquid chromatography with a zwitterionic bonded phase (HILICz). In optimising this protocol, we encountered pressure fluctuations, a widespread problem that impacts metabolite analysis, restricts batch sizes, and imposes instrument downtime, ultimately incurring substantial time and financial expense. Thus, we use this opportunity as a case study to demonstrate the steps taken to overcome such pressure fluctuations, resulting in a protocol that robustly and consistently resolves polar metabolites in large batches of samples (>100 samples, equating to >40 hours of run-time). This consistency is essential to address the growing demand for repeatable in-depth metabolomics analysis of complex samples.

DOI: https://doi.org/10.1016/j.jbc.2025.108283
Anal Chem. 2025 Feb 09.

Development of an Oxylipin Library Using Liquid Chromatography-Ion Mobility Quadrupole Time-of-Flight: Application to Mouse Brain Tissue.

Maria Moran-Garrido, Ameer Y Taha, Ángel Gaudioso, Maria Dolores Ledesma, Coral Barbas.

Oxylipins are bioactive lipid mediators derived from polyunsaturated fatty acids (PUFAs) that play crucial roles in physiological and pathological processes. The analysis and identification of oxylipins are challenging due to the numerous isomeric forms. Ion mobility (IM), which separates ions based on their spatial configuration, combined with liquid chromatography (LC) and mass spectrometry (MS), has been proven effective for separating isomeric compounds. In this study, we developed an extensive oxylipin library containing information on retention time (RT), m/z, and CCS values for 74 oxylipin standards using LC-IM-QTOF-MS in positive and negative ionization modes. The oxylipins in the library were grouped into 15 isomer categories to evaluate the efficacy of IM in isomeric separation. Various adducts were investigated, including protonated, deprotonated, and sodiated forms. The ΔCCS% for more than 1000 isomeric pairs was calculated, revealing that 30% of these exhibited a ΔCCS% greater than 2%. Positive ionization mode demonstrated superior separation capabilities, with 274 isomer pairs achieving baseline separation (ΔCCS% >  4%). Sodium adducts significantly improved isomer separation. With the inclusion of LC separation, only nine oxylipins coeluted, forming six different isomeric pairs. CCS values for the adducts [M+Na]+ and [M+2Na-H]+ separated three of these isomeric pairs. The CCS values were compared to experimental libraries, confirming the high reproducibility of CCS measurements, with average errors below 2%. Applying this library to mouse brain samples, 19 different oxylipins were identified by matching RT, m/z, and CCS values. Coeluting isomers, 9- and 13-HODE, 8- and 12-HETE, and 15-oxo-ETE and 14(15)-EpETrE, were successfully separated and identified using drift time separation.

DOI: https://doi.org/10.1021/acs.analchem.4c06265
Adv Sci (Weinh). 2025 Feb 11. e2413830

One-Pot Construction of NHS-Activated Magnetic Particles for Chemoselective Capture of Carboxyl Metabolites.

Shuai Liu, Meng Yu, Xin-Yao Luo, Jie Liu, Zhong-Mei Zou.

  Chemoselective probes immobilize on magnetic materials show great promise in simplifying sample handling and enhancing detection sensitivity. However, their complicated preparation and associated expense limit broader application. In this study, novel magnetic particles with abundant N-hydroxysuccinimide (NHS) esters on the surface are conveniently synthesized using a one-pot method without carbodiimide activation carboxylate molecules. Subsequently, multifunctional probes are synthesized by immobilizing high-density chemical probes on the surface of the magnetic materials through a postsynthetic modification strategy. This versatile probe facilitates the rapid capture of carboxylated compounds from complex matrices, with the labeled metabolites release from the magnetic materials subsequently analyzed using ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS). The advantages of this innovative chemical biological tool include the simplicity and low cost of the synthesis, as well as the capability to analyze polar and volatile carboxylated metabolites via LC-MS. This new strategy is successfully applied to analyze short-chain fatty acids (SCFAs) in rat cecal contents, demonstrating the reliability of the analytical method. This study presents a cost-effective and easy-to-implement approach for preparing NHS-activated magnetic particles and offers a versatile probe with chemoselective extraction and labeling capabilities, providing a practical tool for analyzing SCFAs in the gut.

Keywords:  SCFAs; functional materials; polymerization; versatile probes

DOI:  https://doi.org/10.1002/advs.202413830
J Am Soc Mass Spectrom. 2025 Feb 13.

Unveiling Readily Ionized and Robust Anionic Species: A Gateway to Enhanced Ionization Efficiency in ESI-MS Analysis.

Benjamin B Warnes, Jasmine Chihabi, Jeffrey M Manthorpe.

  Electrospray ionization mass spectrometry has long been a prevalent ionization method in the analysis of low volatility molecules with biological, environmental, and industrial relevance. To address analytical challenges associated with molecules suffering from low ionization efficiencies (IEs), chemical derivatization (CD) strategies have been developed and are frequently adopted into workflows. However, only a minute number of CD techniques have been developed for negative polarity. To address this disparity, we evaluated 27 anions based on three criteria: (1) IE relative to a sodium dodecyl sulfate (11 + Na+) internal standard; (2) stability to collision induced dissociation; (3) diagnostic tandem mass spectrometry behavior. Highly fluorous ions exhibiting weakly coordinating and hydrophobic properties displayed enhanced IE. Trifluoromethanesulfonyl-containing ions proved to be unexpectedly labile, while tetrakis[3,5-bis(trifluoromethyl)phenyl]borate (23) and bis(nonafluoro-1-butane)sulfonimidate (25) were determined to be of optimal IE of 332% ± 25% and 939% ± 92%, respectively, and in tandem MS exhibited survival yields of 100% ± 0% and 72.6% ± 0.8% at -50 eV. 23 and 25 were also comparable in IE across several solvents, and combinations thereof, that are ubiquitous in liquid chromatography. Various salts of 25 were evaluated for cation effects, where the IE of 25 ranged from 939% ± 92% to 3195% ± 145% across K+, NH4+, Na+, and H+. Compared to tetra-n-butylammonium, tetra-n-butylphosphonium, and (4-methylphenyl)diphenylsulfonium cations, 25 displayed signal enhancements ranging from 136% ± 6% to 181% ± 14%, thereby making it an optimal candidate for CD development.

Keywords:  anions; electrospray ionization; ionization efficiency; negative polarity; survival yield; tandem mass spectrometry

DOI:  https://doi.org/10.1021/jasms.4c00400
J Anal Toxicol. 2025 Feb 08. pii: bkaf003. [Epub ahead of print]

Validation of a Novel LC-MS-MS Method for the Separation and Differentiation of Δ8- and Δ9-Tetrahydrocannabinol Isomers and their Major Metabolites in Antemortem Whole Blood.

Petronela Mikhaltsevich.

The 2018 Farm Bill legalized hemp and defined it as cannabis plant material having not more than 0.3% ∆9-tetrahydrocannabinol (∆9-THC) by dry weight. This has opened the door for the sale of hemp-derived ∆8-tetrahydrocannabinol (∆8-THC), a psychoactive isomer of ∆9-THC. Hemp has minimal amounts of naturally occurring ∆8-THC; however, the cannabidiol (CBD) found in hemp can be chemically converted into ∆8-THC. Unfortunately, depending on the method of conversion, the amount of ∆8-THC, ∆9-THC and other by-products can vary widely. For many laboratories, the emergence of ∆8-THC products resulted in analytical challenges because of the structural similarity of the isomers resulting in coelution. In response, a novel liquid chromatography-tandem mass spectrometry method was developed to separate the two isomers, with improved limit of detection (LOD) and lower limit of quantification (LLOQ). With this method, clear separation was achieved between ∆9-THC and ∆8-THC, 11-nor-9-carboxy-∆9-tetrahydrocannabinol (∆9-THC-COOH) and 11-nor-9-carboxy-∆8-tetrahydrocannabinol (∆8-THC-COOH) and partial separation of 11-hydroxy-∆9-tetrahydrocannabinol (∆9-THC-OH) and 11-hydroxy-∆8-tetrahydrocannabinol (∆8-THC-OH). While ∆9-THC-OH and ∆8-THC-OH did not achieve baseline separation, sufficient separation was achieved to confidently identify and differentiate the two compounds. LOD and LLOQ were the same for quantitative compounds. Quantitative range of 0.5 ng/mL to 100 ng/mL was achieved for ∆9-THC, ∆8-THC and ∆9-THC-OH and 2.5 ng/mL to 250 ng/mL for ∆9-THC-COOH. Qualitative analysis with LOD of 0.5 ng/mL was achieved for ∆8-THC-OH and 2.5 ng/mL for ∆8-THC-COOH. To achieve the desired LODs and LLOQs, alternate multiple reaction monitoring (MRM) transitions were also explored in addition to those utilized in the laboratory's prior method and other published methods. The method was validated following the American National Standards Institute/Academy Standards Board (ANSI/ASB) Standard 036, Standard Practices for Method Validation in Forensic Toxicology with minor exceptions, and was proven to be reliable and robust.

DOI: https://doi.org/10.1093/jat/bkaf003
Rapid Commun Mass Spectrom. 2025 Feb 10. e10000

Molecular Structure and Mass Spectral Data Quality-Driven Processing of High-Resolution Mass Spectrometry for Quantitative Analysis.

Fabien Fontaine, Luca Morettoni, Ken Anderson, Bernard Choi, Ismael Zamora, Kevin P Bateman.

   RATIONALE: LC-MS-based quantification is traditionally performed using selected or multiple reaction monitoring (SRM/MRM) acquisition functions on triple quadrupole (QQQ) instruments resulting in both high sensitivity and selectivity. This workflow requires a previously identified reaction or transition from a precursor ion to a fragment ion to be monitored to obtain the needed selectivity for the compound of interest. High-resolution mass spectrometry (HRMS) has long sought to be a viable alternative for quantitatipve workflows but has been unable to broadly compete, mainly due to the lack of suitable data processing software.
METHODS: The approach we developed agnostically and automatically identifies all ions related to the compound being analyzed in both the MS and MSMS data, acquired with data-dependent or data-independent methods. The algorithm automatically selects optimal parameters (ion extraction window, ions to sum, etc.) to provide the best overall method to meet the acceptance criteria defined by the user (accuracy/precision).
RESULTS: The results obtained are directly compared to QQQ data collected from the same set of samples and show that the automated HRMS approach is as good as and, in some cases, better than the traditional QQQ approach in terms of selectivity, sensitivity, and dynamic range.
CONCLUSIONS: This new methodology enables the use of generic methods for data collection for quantitative analysis using high-resolution mass spectrometry. With this approach, data collection is faster, and the processing algorithm provides quality equal to or better than the current QQQ methodology. This enables an overall reduction in cycle time and improved assay performance versus current HRMS-based quantitative analysis as well as traditional QQQ workflows.

Keywords:  HRMS; automated; quantitation; structure based

DOI:  https://doi.org/10.1002/rcm.10000
Anal Bioanal Chem. 2025 Feb 13.

Recent advances in analytical methods and bioinformatic tools for quantitative glycomics.

Jihong Lu, Shuhong Guo, Qiannan Liu, Nafisa Tursumamat, Shengyang Liu, Shuye Wu, Heming Li, Juan Wei.

  The significance of glycans in various biological processes has been widely acknowledged. Quantitative glycomics is emerging as an important addition to clinical biomarker discovery, as it helps uncover disease-associated glycosylation patterns that are valuable for diagnosis, prognosis, and treatment evaluation. Compared to glycoproteomics and other established omics approaches, quantitative glycomics exhibits greater methodological diversity and it encounters various challenges in automation and standardization. Nonetheless, numerous advancements have been made in this field over the past 5 years. Here, we have reviewed recent progress in analytical methods and software to improve mass spectrometry-based quantitative glycomics primarily on N- and O-glycosylation. The discussion is organized into four sections: stable isotopic labeling, isobaric labeling, label-free, and fluorescence labeling strategies, with a particular emphasis on quantitative data interpretation. Novel derivatization methods and advanced techniques have been developed for high-throughput and highly sensitive glycan quantification with high accuracy. However, due to variations in glycan derivatization and difficulties in structural identification, most glycomic quantification methods are tailored to specific applications, and manual inspection is frequently necessary for precise data interpretation. Therefore, further advancements in glycan sample preparation, structural characterization, and automated data interpretation are essential to facilitate comprehensive and accurate quantification across a wide array of glycans.

Keywords:  Bioinformatic tools; Glycosylation; Mass spectrometry; Quantitative glycomics

DOI:  https://doi.org/10.1007/s00216-025-05778-3
Molecules. 2025 Feb 06. pii: 726. [Epub ahead of print]30(3):

Groomed Fingerprint Sebum Sampling: Reproducibility and Variability According to Anatomical Collection Region and Biological Sex.

Madeline Isom, Eden P Go, Heather Desaire.

  Sebum lipids, accessible via groomed latent fingerprints, may be a valuable, underappreciated sample source for future biomarker research. Sampling sebum lipids from the skin is painless for patients, efficient for researchers, and has already demonstrated the potential to contain disease biomarkers. However, before sebum sampling can be implemented in routine studies, more information is needed regarding sampling reproducibility and variability. This information will enable researchers to choose the best practices for sebum-based studies. Herein, we use our recently established workflow for the collection and analysis of groomed fingerprints to assess the reproducibility of lipid profiles obtained via mass spectrometry. Using 180 fingerprint samples collected from 30 participants, we also assess lipid changes according to biological sex and anatomical grooming region (cheek, neck, and forehead) via supervised and unsupervised classification. The results demonstrate that this sampling protocol achieves satisfactory reproducibility, and negligible differences exist between male and female groomed fingerprint lipids. Moreover, the anatomical grooming region can impact the fingerprint lipid profile: cheek- and forehead-groomed fingerprints are more similar to one another than either collection site is to neck-groomed fingerprints. This information will inform future sebum-based biomarker investigations, enabling researchers to collect meaningful lipidomic datasets from groomed fingerprint samples.

Keywords:  biomarkers; fingerprint; lipidomics; lipids; machine learning; mass spectrometry; noninvasive sampling; sebum; skin

DOI:  https://doi.org/10.3390/molecules30030726
Sci Data. 2025 Feb 12. 12(1): 244

An expanded database of high-resolution MS/MS spectra for lichen-derived natural products.

Joe Bracegirdle, John A Elix, Udayangani Mawalagedera, Yit-Heng Chooi, Cécile Gueidan.

The history of lichen compound identification has long relied on techniques such as spot tests and TLC, which have been surpassed in sensitivity and accuracy by modern metabolomic techniques such as high-resolution MS/MS. In 2019, Olivier-Jimenez et al. released the Lichen DataBase (LDB), a library containing the Q-TOF MS/MS spectra of 251 metabolites on the MetaboLights and GNPS platforms, that has been widely used for the identification of lichen-derived unknowns. To increase the compound coverage, we have generated the Orbitrap MS/MS spectra of a further 534 lichen-derived compounds from the metabolite library of Jack Elix, housed at the CANB herbarium (Canberra, Australia). This included 399 unique metabolites that are not in the LDB, bringing the total number combined to 650. Technical validation was achieved by investigating the compounds in three Australian lichen extracts using the Library Search and Molecular Networking tools on the GNPS platform. This update provides a much larger database for lichen compound identification, which we envisage will allow refining the lichen chemotaxonomy framework and contribute to compound discovery.

DOI: https://doi.org/10.1038/s41597-025-04488-w