bims-metlip 2025-06-08 papers

bims-metlip

Biomed News

on Methods and protocols in metabolomics and lipidomics

Issue of 2025–06–08
nine papers selected by
Sofia Costa, Matterworks

DuReS: An R Package for Denoising Experimental Tandem Mass Spectra and Metabolite Annotation.
Solid-Phase Extraction Coupled to Tandem Mass Spectrometry for Rapid Quantitation of Urinary Catecholamines and Total Metanephrines.
MALDI-TIMS-MS 2 Imaging and Annotation of Natural Products in Fungal-Bacterial Co-Culture.
MSI-Explorer: Napari-Powered Tool for Mass Spectrometry Imaging Data Analysis.
[Development and Performance Evaluation of an Analytical Method for Resorcylic Acid Lactones in Bovine Urine for Monitoring Japanese Beef Exports to the European Union].
Challenges of folate species analysis in food and biological matrices by liquid chromatography-tandem mass spectrometery.
An Evaluation of Actinide Reactivity with CO2, O2, and O2/He Gases using Inductively Coupled Plasma Tandem Mass Spectrometry: Application to Simultaneous Measurement of 241Am/241Pu Ratios in Unseparated Complex Matrices.
Development of a HILIC-MS/MS method for simultaneous quantification of lipophilic antitumor TriPPPro-prodrugs and their polar metabolites in HT29 cell extracts.
Comparative analysis of continuous similarity measures for compound identification in mass spectrometry-based metabolomics.

Anal Chem. 2025 Jun 06.

DuReS: An R Package for Denoising Experimental Tandem Mass Spectra and Metabolite Annotation.

Shayantan Banerjee, Prajval Nakrani, Aviral Singh, Pramod P Wangikar.

Mass spectrometry-based untargeted metabolomics is a powerful technique for profiling small molecules in biological samples, yet accurate metabolite identification remains challenging. The presence of random noise peaks in tandem mass spectra can lead to false annotations and necessitate time-consuming manual verification. A common method for removing noise from mass spectra is intensity thresholding, where low-intensity peaks are discarded by applying a user-defined cutoff. However, determining an optimal threshold is often data set-specific and may still retain many noisy peaks. We hypothesize that true signal peaks consistently recur across replicate tandem spectra generated from the same precursor ion, unlike random noise. Here, we present a freely available R package, Denoising Using Replicate Spectra (DuReS) (https://github.com/BiosystemEngineeringLab-IITB/dures), which accepts mzML files and feature lists and returns high-quality annotations and denoised mzML files, enabling users to integrate the denoising pipeline into their workflow seamlessly. This package is designed for data-dependent acquisition mode (DDA) data. It has (i) the main denoising module and (i) an optional tuning module to determine each data set's optimal recurrence frequency cutoff (Fthreshold), considering variations in the intrinsic noise characteristics. We tested the tool on eight representative data sets selected from those available in metabolomics repositories. Our approach minimizes signal loss while maximizing noise reduction, effectively preserving diagnostically significant low-intensity fragments that would otherwise be lost through conventional intensity thresholding. This improves spectral matching metrics, leading to more accurate annotations and fewer false positives.

DOI: https://doi.org/10.1021/acs.analchem.5c01726
Rapid Commun Mass Spectrom. 2025 Sep 15. 39(17): e10077

Solid-Phase Extraction Coupled to Tandem Mass Spectrometry for Rapid Quantitation of Urinary Catecholamines and Total Metanephrines.

Yuhan Li, Guangming Huang.

   RATIONALE: The measurement of urinary catecholamines and total metanephrines serves as one of the primary tests in the diagnosis of pheochromocytoma and paraganglioma (PPGL). The widely adopted liquid chromatography-tandem mass spectrometry (LC-MS/MS) method, however, typically necessitates sample pretreatments and chromatographic separation prior to MS, resulting in challenges for facile and rapid screening of targets from complex matrices. Therefore, it is crucial to develop an analytical method that can rapidly and efficiently detect urinary catecholamines and total metanephrines.
METHODS: A rapid and time-efficient procedure using solid-phase extraction (SPE) combined with pulsed direct current electrospray ionization tandem mass spectrometry (pulsed-dc-ESI-MS/MS) was validated for the specific and quantitative analysis of six urinary catecholamines and metanephrines. The SPE protocol was specifically optimized to enable direct analysis of the eluate obtained from SPE using MS/MS. All six compounds could be detected in a single complete operation.
RESULTS: The method was evaluated by the determination of catecholamines and metanephrines (dopamine, epinephrine, norepinephrine, normetanephrine, metanephrine, and 3-methoxytyramine) in artificial urine samples and raw urine samples. Under the optimized experimental conditions, the limits of detection for these six analytes were in the range of 0.02-68.37 nM L-1, using dopamine-d4 (DA-d4) and metanephrines-d3 (MN-d3) as internal standards, respectively, which achieved the detection requirements for the clinical diagnosis of PPGL.
CONCLUSIONS: SPE coupled with pulsed-dc-ESI-MS/MS demonstrated improved efficiency compared to existing methods, which successfully enabled the rapid screening of urinary catecholamines and total metanephrines. Therefore, we believe that this method could be potentially useful in the clinical screening of PPGL and suitable for the direct analysis of urine.

Keywords:  catecholamines; metanephrines; solid‐phase extraction; tandem mass spectrometry

DOI:  https://doi.org/10.1002/rcm.10077
bioRxiv. 2025 May 13. pii: 2025.05.11.653367. [Epub ahead of print]

MALDI-TIMS-MS 2 Imaging and Annotation of Natural Products in Fungal-Bacterial Co-Culture.

Robert A Shepherd, Gordon T Luu, Laura M Sanchez.

Mass spectrometry imaging (MSI) is a powerful tool for monitoring the spatial distributions of microbial metabolites directly from culture. MSI can identify secretion and retention patterns for microbial metabolites, allowing for the assessment of chemical communication within complex microbial communities. Microbial imaging via matrix-assisted laser desorption/ionization (MALDI) MSI remains challenging due to high sample complexity and heterogeneity associated with the required sample preparation, making annotation of molecules by MS 1 alone challenging. The implementation of trapped ion mobility spectrometry (TIMS) has increased the dimensionality of MALDI-MSI experiments, allowing for the resolution of isomers and isobars, and can increase sensitivity of metabolite detection within complex samples. Parallel reaction monitoring - parallel accumulation serial fragmentation (prm-PASEF) leverages TIMS to enhance the targeted acquisition of MS 2 data by increasing the number of precursors that can be fragmented in a single acquisition. Recently, imaging prm-PASEF (iprm-PASEF) has been developed to provide more accurate annotation from MALDI-TIMS-MSI datasets through the inclusion of MS 2 . Here, we showcase the use of MALDI iprm-PASEF to provide rapid and accurate annotation coproporphyrin III directly from a bacterial-fungal co-culture between Glutamicibacter arilaitensis (strain JB182) and Penicillium solitum (strain #12). Additionally, we present a workflow for untargeted iprm-PASEF precursor selection directly in SCiLS Lab, followed by direct export for iprm-PASEF acquisition.
Abstract Figure:

DOI: https://doi.org/10.1101/2025.05.11.653367
Anal Chem. 2025 Jun 06.

MSI-Explorer: Napari-Powered Tool for Mass Spectrometry Imaging Data Analysis.

Nay Min Min Thaw Saw, Lennart Kowitz, Peter Lampen, Siva Swapna Kasarla, Antonia Fecke, Jianxu Chen, Prasad Phapale.

Mass spectrometry imaging (MSI) enables label-free spatial localization of biomolecules from single cells to whole tissues, making it a key technology in the growing fields of spatial omics. However, a lack of comprehensive open-source tools for MSI data analysis, visualization, and quantification has hindered its broader adoption. Napari, a widely used interactive Python-based image analysis platform, currently lacks native support for MSI data, limiting its applications in MSI research. To address this gap, we present MSI-Explorer, the first napari plugin that provides an interactive and user-friendly interface for MSI data processing, spectral analysis, molecular annotation, and quantification. By integrating napari's advanced visualization capabilities with MSI-specific functionalities, MSI-Explorer provides image curation, multimodal, and efficient analysis of MSI data sets. As the first dedicated MSI plugin for napari, MSI-Explorer bridges the gap between spatial metabolomics and the broader bioimaging research community, promoting open, accessible, and integrated MSI data analysis.

DOI: https://doi.org/10.1021/acs.analchem.5c01513
Shokuhin Eiseigaku Zasshi. 2025 ;66(2): 32-38

[Development and Performance Evaluation of an Analytical Method for Resorcylic Acid Lactones in Bovine Urine for Monitoring Japanese Beef Exports to the European Union].

Chiharu Takagi, Ayumu Nakamura, Youichi Kouno, Rie Ito, Tomoaki Tsutsumi, Hiroshi Akiyama, Shizuka Saito-Shida.

  A quantitative method for determining resorcylic acid lactones (zeranol, taleranol, zearalanone, and zearalenone) in bovine urine using liquid chromatography-tandem mass spectrometry (LC-MS/MS) was developed and evaluated for use in the monitoring of Japanese beef exports to the European Union. This method involves the hydrolysis of conjugates by ß-glucuronidase/aryl sulfatase, clean-up with an immunoaffinity cartridge, and analysis using LC-MS/MS. The developed method was evaluated for zeranol, taleranol, zearalanone, and zearalenone in bovine urine at concentrations of 1 and 2 μg/L. The trueness ranged from 92 to 101%, with intra-day precision of <9% and inter-day precision of <13%. No interfering peaks were observed in the chromatogram near the analyte retention times. This analytical method is valuable for monitoring taleranol, zearalanone, and zearalenone in beef exports to the European Union. The proposed method is also applicable for screening whether zeranol was illegally administered or ingested via feed contaminated with Fusarium toxins, particularly in cases in which taleranol was detected.

Keywords:  bovine urine; resorcylic acid lactone; taleranol; zearalanone; zearalenone; zeranol

DOI:  https://doi.org/10.3358/shokueishi.66.32
Bioanalysis. 2025 Jun 05. 1-20

Challenges of folate species analysis in food and biological matrices by liquid chromatography-tandem mass spectrometery.

Nigatu Tadesse Gebrehiwot, Man-Ni He, Juan Li, Hong-Min Liu.

  Folates are group of water-soluble B-vitamins indispensable to one carbon metabolism as acceptor and donor of methyl group during purine and pyrimidine biosynthesis, DNA and histone methylations, and in mitochondrial protein translation. The deficiencies associated with risk of neural tube defect, cancer, cardiac and psychiatric disorders. Thus, detecting and quantifying folate species accurately become a crucial step in food omics, disease metabolomics, proteomics, genomics, toxicology, and pharmacokinetics, and regulatory sciences. However, the detection and quantitative determination of folate species yet subjected to analytical challenges due to physio-chemical instability, structural similarity, ultra-trace availability. Advances in liquid chromatography tandem mass spectrometry (LC-MS/MS) method enabled the detection and quantification of folate species in short span of time using low sample volume. However, risk of inter conversion, degradation or loss during sample preparation, coupled with folate isomers and isobars challenged the selectivity, specificity and sensitivity for quantification by LC-MS/MS at trace level. Systematic literature search was conducted through major indexing databases such as Pub med, Embase, and Google Scholar to include the most relevant articles published 2010-2025 in preparing the review highlighting the challenges of folate species analysis in food and biological matrices from sample preparation to mass spectrometry detection with a future perspective on innovative optimization methods.

Keywords:  Folate species; LC-MS/MS; analytical challenges; biological matrices; food; innovative methods; sample preparation

DOI:  https://doi.org/10.1080/17576180.2025.2515009
Anal Chem. 2025 Jun 04.

An Evaluation of Actinide Reactivity with CO2, O2, and O2/He Gases using Inductively Coupled Plasma Tandem Mass Spectrometry: Application to Simultaneous Measurement of 241Am/241Pu Ratios in Unseparated Complex Matrices.

Tyler D Schlieder, Kirby P Hobbs, Amanda D French, Lee H Hughes, Isaac J Arnquist, Chelsie Beck.

Accurate actinide measurements are critical within the field of nuclear science. Traditional methods for actinide quantification require time-consuming sample processing prior to analysis. There is a need for rapid analytical techniques that still maintain a high degree of accuracy. In this work, actinide reactivity was assessed for multiple oxygen-containing reaction gases using quadrupole inductively coupled plasma tandem mass spectrometry (Q-ICP-MS/MS) to evaluate actinide analysis in complex sample matrices without analyte-matrix separation. A novel method was developed to measure 241Am/241Pu in complex sample matrices using an O2/He reaction gas with no matrix removal or analyte preconcentration. This inline method reduces matrix-derived polyatomic interferences that complicate traditional ICP-MS analyses by mass-shifting to 241Am16O+ and 241Pu16O2+, allowing Am and Pu to be mass separated for simultaneous analysis. While mass shifting is efficient, a small portion of Am+ (<1.3%) and Pu+ (<1.4%) react to form AmO2+ and PuO+, respectively. Therefore, a mass balance approach was used, in combination with reactivity determined from 242Pu and 243Am standard solutions, to correct for residual 241PuO+ and 241AmO2+. The method was validated by measuring 241Am/241Pu in Pu isotope standards CRM-136 and CRM-137 (separated in March/April 1970 and February 2022, respectively) in both neat solutions and complex matrices containing diluted soil (NIST SRM 2711a, > 1000 μg·g-1). Method detection limits of 15.9 and 9.6 fg·g-1 were determined for 241Am and 241Pu, respectively, and 241Am/241Pu ratios were measured with accuracies within <3.5%. This work presents the first direct analysis of 241Am/241Pu in unseparated complex matrices, advancing the capabilities for rapid actinide measurements.

DOI: https://doi.org/10.1021/acs.analchem.5c01397
J Chromatogr B Analyt Technol Biomed Life Sci. 2025 May 28. pii: S1570-0232(25)00227-2. [Epub ahead of print]1263 124673

Development of a HILIC-MS/MS method for simultaneous quantification of lipophilic antitumor TriPPPro-prodrugs and their polar metabolites in HT29 cell extracts.

Michelle Vogts, Julian Witt, Maria Riedner, Chris Meier.

  Nucleoside analogues are among the most widely used antiviral and also antitumoral agents. The nucleoside analogues require intracellular metabolic activation through stepwise phosphorylation resulting in the bioactive nucleoside triphosphates. To directly deliver the active metabolite, our group developed a prodrug system where the nucleoside triphosphate (NTP) is masked by two lipophilic moieties which are enzymatically cleaved off after successful cellular uptake. To date, no data are available on the intracellular concentrations of the active metabolites responsible for the determined antiviral or antitumor activity. In this paper, we describe the development of a HILIC-MS/MS method for the quantification of TriPPPro-prodrugs, derived from the anticancer drug fluorouracil (5-FU) and all resulting metabolites, FdU, FdU-monophosphate (MP), FdU-diphosphate (DP), and FdU-triphosphate (TP), in cancer cell lysate. Because of the different chemical properties of the lipophilic prodrugs and the hydrophilic metabolites, sample preparation as well as liquid chromatography method development were challenging factors. A liquid-liquid extraction protocol was employed and with use of hydrophilic liquid chromatography, the simultaneous retention of all analytes was guaranteed. The method was validated for the following concentration ranges in cancer cell lysate and the associated supernatant: 2.0-1000 ng/mL. The method was successfully applied to quantify prodrugs and metabolites in HT29 cancer cell lysate and supernatant samples after cellular uptake studies with two different TriPPPro-prodrugs. The method can also be employed for the quantification of other lipophilic prodrugs, as well as nucleotides and nucleosides (derivatives).

Keywords:  5-Fluorodeoxyuridine diphosphate (FdU-DP); 5-Fluorodeoxyuridine monophosphate (FdU-MP); 5-Fluorodeoxyuridine triphosphate (FdU-TP); HILIC; MRM; Prodrugs; cancer cell lysate

DOI:  https://doi.org/10.1016/j.jchromb.2025.124673
Chemometr Intell Lab Syst. 2025 Aug 15. pii: 105417. [Epub ahead of print]263

Comparative analysis of continuous similarity measures for compound identification in mass spectrometry-based metabolomics.

Hunter Dlugas, Xiang Zhang, Seongho Kim.

  In mass spectrometry (MS)-based metabolomics, the most straightforward and efficient approach for compound identification is the comparison of similarity scores between experimental spectra and reference spectra. Among various single and composite similarity measures, the Cosine Correlation is favored due to its simplicity, efficiency, and effectiveness. Recently, the Shannon Entropy Correlation has shown superior performance over several other measures, including the Cosine Correlation, in LC-MS-based metabolomics, particularly concerning receiver operating characteristic (ROC) curves and false discovery rates. However, previous comparisons did not consider the weight factor transformation, which is critical for achieving higher accuracy with the cosine correlation. This study conducted a comparative analysis of the Cosine Correlation and Shannon Entropy Correlation, incorporating the weight factor transformation during preprocessing. Additionally, we developed a novel entropy correlation measure, the Tsallis Entropy Correlation, which offers greater versatility than the Shannon Entropy Correlation. Our accuracy-based results indicate that the weight factor transformation is essential for achieving higher identification performance in both LC-MS and GC-MS-based compound identification. Although the Tsallis Entropy Correlation outperforms the Shannon Entropy Correlation in terms of accuracy, it comes with higher computational expense. In contrast, the Cosine Correlation, when combined with the weight factor transformation, achieves the highest accuracy and the lowest computational expense, demonstrating both robustness and efficiency in MS-based compound identification.

Keywords:  Compound identification; Cosine correlation; Entropy correlation; GC-MS; LC-MS

DOI:  https://doi.org/10.1016/j.chemolab.2025.105417