bims-metlip 2023-06-18 papers

bims-metlip

Biomed News

on Methods and protocols in metabolomics and lipidomics

Issue of 2023‒06‒18
thirty-six papers selected by
Sofia Costa
Matterworks

IDSL.CSA: Composite Spectra Analysis for Chemical Annotation of Untargeted Metabolomics Datasets.
Comparison of Data-Dependent Acquisition, Data-Independent Acquisition, and Parallel Reaction Monitoring in Trapped Ion Mobility Spectrometry-Time-of-Flight Tandem Mass Spectrometry-Based Lipidomics.
Comprehensive Insight into Colorectal Cancer Metabolites and Lipids for Human Serum: A Proof-of-Concept Study.
mzapy: An Open-Source Python Library Enabling Efficient Extraction and Processing of Ion Mobility Spectrometry-Mass Spectrometry Data in the MZA File Format.
Measurement of vitamin K and its derivatives in human plasma through enzyme-assisted liquid chromatography-tandem mass spectrometry assay.
Identification of endogenous carbonyl steroids in human serum by chemical derivatization, hydrogen/deuterium exchange mass spectrometry and the quantitative structure-retention relationship.
Advantages of using biologically generated 13C-labelled multiple internal standards for stable isotope-assisted LC-MS-based lipidomics.
Automatic z-Axis Correction for IR-MALDESI Mass Spectrometry Imaging of Uneven Surfaces.
Development and Validation of a High-Performance Liquid Chromatography-Tandem Mass Spectrometry Method to Determine Promethazine and Its Metabolites in Edible Tissues of Swine.
Determination of Glycerol, Propylene Glycol, and Nicotine as the Main Components in Refill Liquids for Electronic Cigarettes.
Characterization of Oxidized Glycerophosphoethanolamines via Radical-Directed Dissociation Tandem Mass Spectrometry and the Paternò-Büchi Derivatization.
MCnebula: Critical Chemical Classes for the Classification and Boost Identification by Visualization for Untargeted LC-MS/MS Data Analysis.
Mass spectrometry imaging as an emerging tool for studying metabolism in human brain organoids.
A Dual-Gated Structures for Lossless Ion Manipulations-Ion Mobility Orbitrap Mass Spectrometry Platform for Combined Ultra-High-Resolution Molecular Analysis.
Statistical methods and resources for biomarker discovery using metabolomics.
Characterization of Bile Acid Isomers and the Implementation of High-Resolution Demultiplexing with Ion Mobility-Mass Spectrometry.
Formation and Tandem Mass Spectrometry of Doubly Charged Lipid-Metal Ion Complexes.
NOMspectra: An Open-Source Python Package for Processing High Resolution Mass Spectrometry Data on Natural Organic Matter.
The Impact of the Serum Extraction Protocol on Metabolomic Profiling Using UPLC-MS/MS and FTIR Spectroscopy.
Simultaneous quantitation of ketamine, norketamine and dehydronorketamine in human milk using a novel ultra high-performance liquid chromatography-mass spectrometry (UPLC-MS/MS) assay.
PeakDetective: A Semisupervised Deep Learning-Based Approach for Peak Curation in Untargeted Metabolomics.
Simplified Liquid Chromatography-Mass Spectrometry Methods for Gestagen Analysis in Animal Fat and Liver.
Development of an LC-MS/MS method for the determination of multiple mycotoxins in human urine.
Neonicotinoid insecticides and their metabolites: Specimens tested, analytical methods and exposure characteristics in humans.
High throughput and automated solid-phase microextraction and determination by liquid chromatography-mass spectrometry for the analysis of mycotoxins in beer.
Untargeted Metabolomics Identifies Biomarkers for MCADD Neonates in Dried Blood Spots.
Human scent characterization: A review.
A LC-MS/MS Method for Quantifying the Schisandrin B and Exploring Its Intracellular Exposure Correlating Antitumor Effect.
Spatiotemporal pharmacometabolomics based on ambient mass spectrometry imaging to evaluate the metabolism and hepatotoxicity of amiodarone in HepG2 spheroids.
Broad-range extraction of highly polar to non-polar organic contaminants for inclusive target analysis and suspect screening of environmental samples.
Progress of Mass Spectrometry-Based Lipidomics in the Dairy Field.
Development of High Throughput Microscope Mode Secondary Ion Mass Spectrometry Imaging.
Gas chromatography coupled-to Fourier transform orbitrap mass spectrometer for enantioselective amino acid analyses: Application to pre-cometary organic analog.
Recent advances in mass spectrometry-based spatially resolved molecular imaging of drug disposition and metabolomics.
Validation and Simultaneous Monitoring of 311 Pesticide Residues in Loamy Sand Agricultural Soils by LC-MS/MS and GC-MS/MS, Combined with QuEChERS-Based Extraction.
Development of a UPLC-MS/MS method for simultaneous therapeutic drug monitoring of anti-hepatocellular carcinoma drugs and analgesics in human plasma.

Anal Chem. 2023 Jun 13.

IDSL.CSA: Composite Spectra Analysis for Chemical Annotation of Untargeted Metabolomics Datasets.

Sadjad Fakouri Baygi, Yashwant Kumar, Dinesh Kumar Barupal.

Poor chemical annotation of high-resolution mass spectrometry data limits applications of untargeted metabolomics datasets. Our new software, the Integrated Data Science Laboratory for Metabolomics and Exposomics─Composite Spectra Analysis (IDSL.CSA) R package, generates composite mass spectra libraries from MS1-only data, enabling the chemical annotation of high-resolution mass spectrometry coupled with liquid chromatography peaks regardless of the availability of MS2 fragmentation spectra. We demonstrate comparable annotation rates for commonly detected endogenous metabolites in human blood samples using IDSL.CSA libraries versus MS/MS libraries in validation tests. IDSL.CSA can create and search composite spectra libraries from any untargeted metabolomics dataset generated using high-resolution mass spectrometry coupled to liquid or gas chromatography instruments. The cross-applicability of these libraries across independent studies may provide access to new biological insights that may be missed due to the lack of MS2 fragmentation data. The IDSL.CSA package is available in the R-CRAN repository at https://cran.r-project.org/package=IDSL.CSA. Detailed documentation and tutorials are provided at https://github.com/idslme/IDSL.CSA.

DOI: https://doi.org/10.1021/acs.analchem.3c00376
Anal Chem. 2023 Jun 12.

Comparison of Data-Dependent Acquisition, Data-Independent Acquisition, and Parallel Reaction Monitoring in Trapped Ion Mobility Spectrometry-Time-of-Flight Tandem Mass Spectrometry-Based Lipidomics.

E Rudt, M Feldhaus, C G Margraf, S Schlehuber, A Schubert, S Heuckeroth, U Karst, V Jeck, S W Meyer, A Korf, H Hayen.

The parallel accumulation-serial fragmentation (PASEF) approach based on trapped ion mobility spectrometry (TIMS) enables mobility-resolved fragmentation and a higher number of fragments in the same time period compared to conventional MS/MS experiments. Furthermore, the ion mobility dimension offers novel approaches for fragmentation. Using parallel reaction monitoring (prm), the ion mobility dimension allows a more accurate selection of precursor windows, while using data-independent aquisition (dia) spectral quality is improved through ion-mobility filtering. Owing to favorable implementation in proteomics, the transferability of these PASEF modes to lipidomics is of great interest, especially as a result of the high complexity of analytes with similar fragments. However, these novel PASEF modes have not yet been thoroughly evaluated for lipidomics applications. Therefore, data-dependent acquisition (dda)-, dia-, and prm-PASEF were compared using hydrophilic interaction liquid chromatography (HILIC) for phospholipid class separation in human plasma samples. Results show that all three PASEF modes are generally suitable for usage in lipidomics. Although dia-PASEF achieves a high sensitivity in generating MS/MS spectra, the fragment-to-precursor assignment for lipids with both, similar retention time as well as ion mobility, was difficult in HILIC-MS/MS. Therefore, dda-PASEF is the method of choice to investigate unknown samples. However, the best data quality was achieved by prm-PASEF, owing to the focus on fragmentation of specified targets. The high selectivity and sensitivity in generating MS/MS spectra of prm-PASEF could be a potential alternative for targeted lipidomics, e.g., in clinical applications.

DOI: https://doi.org/10.1021/acs.analchem.3c00440
Int J Mol Sci. 2023 Jun 01. pii: 9614. [Epub ahead of print]24(11):

Comprehensive Insight into Colorectal Cancer Metabolites and Lipids for Human Serum: A Proof-of-Concept Study.

Kinjal Bhatt, Titziana Orlando, Marie-Alice Meuwis, Edouard Louis, Pierre-Hugues Stefanuto, Jean-François Focant.

  Colorectal cancer (CRC) ranks as the third most frequently diagnosed cancer and the second leading cause of cancer-related deaths. The current endoscopic-based or stool-based diagnostic techniques are either highly invasive or lack sufficient sensitivity. Thus, there is a need for less invasive and more sensitive screening approaches. We, therefore, conducted a study on 64 human serum samples representing three different groups (adenocarcinoma, adenoma, and control) using cutting-edge GC×GC-LR/HR-TOFMS (comprehensive two-dimensional gas chromatography coupled with low/high-resolution time-of-flight mass spectrometry). We analyzed samples with two different specifically tailored sample preparation approaches for lipidomics (fatty acids) (25 μL serum) and metabolomics (50 μL serum). In-depth chemometric screening with supervised and unsupervised approaches and metabolic pathway analysis were applied to both datasets. A lipidomics study revealed that specific PUFA (ω-3) molecules are inversely associated with increased odds of CRC, while some PUFA (ω-6) analytes show a positive correlation. The metabolomics approach revealed downregulation of amino acids (alanine, glutamate, methionine, threonine, tyrosine, and valine) and myo-inositol in CRC, while 3-hydroxybutyrate levels were increased. This unique study provides comprehensive insight into molecular-level changes associated with CRC and allows for a comparison of the efficiency of two different analytical approaches for CRC screening using same serum samples and single instrumentation.

Keywords:  GC×GC–TOFMS; blood; chemometrics; colorectal cancer; comprehensive gas chromatography; lipidomics; mass spectrometry; metabolomics; sample preparation; separation science; serum

DOI:  https://doi.org/10.3390/ijms24119614
Anal Chem. 2023 Jun 12.

mzapy: An Open-Source Python Library Enabling Efficient Extraction and Processing of Ion Mobility Spectrometry-Mass Spectrometry Data in the MZA File Format.

Dylan Ross, Aivett Bilbao, Joon-Yong Lee, Xueyun Zheng.

Analysis of ion mobility spectrometry (IMS) data has been challenging and limited the full utility of these measurements. Unlike liquid chromatography-mass spectrometry, where a plethora of tools with well-established algorithms exist, the incorporation of the additional IMS dimension requires upgrading existing computational pipelines and developing new algorithms to fully exploit the advantages of the technology. We have recently reported MZA, a new and simple mass spectrometry data structure based on the broadly supported HDF5 format and created to facilitate software development. While this format is inherently supportive of application development, the availability of core libraries in popular programming languages with standard mass spectrometry utilities will facilitate fast software development and broader adoption of the format. To this end, we present a Python package, mzapy, for efficient extraction and processing of mass spectrometry data in the MZA format, especially for complex data containing ion mobility spectrometry dimension. In addition to raw data extraction, mzapy contains supporting utilities enabling tasks including calibration, signal processing, peak finding, and generating plots. Being implemented in pure Python and having minimal and largely standardized dependencies makes mzapy uniquely suited to application development in the multiomics domain. The mzapy package is free and open-source, includes comprehensive documentation, and is structured to support future extension to meet the evolving needs of the MS community. The software source code is freely available at https://github.com/PNNL-m-q/mzapy.

DOI: https://doi.org/10.1021/acs.analchem.3c01653
Eur J Mass Spectrom (Chichester). 2023 Jun 12. 14690667231183046

Measurement of vitamin K and its derivatives in human plasma through enzyme-assisted liquid chromatography-tandem mass spectrometry assay.

Metin Demirel, Sahabettin Selek.

  Vitamin K is an essential lipophilic vitamin that acts as a coenzyme in several metabolic pathways. Accurate measurement of apolar metabolites transported by lipoproteins in serum matrices requires high-recovery extractions of vitamin K and its derivatives following standardized protocols. Conventionally developed methods in this field have predominantly employed solid-phase extraction for the measurement of vitamin K and its derivatives. In this study, our objective was to develop an enzyme-assisted extraction method for the precise measurement of vitamin K and its derivatives. Our methodology involved mixing 450 µL of serum samples with 50 µL of an internal standard and 50 µL of a lipase enzyme solution. Following vortexing, the mixture was incubated at 37°C for 15 min to activate the enzymes. The enzyme reaction was subsequently quenched with a mixture of 250 µL of methanol and 1 mL of hexane, followed by centrifugation at 12,000 g for 5 min. The upper phase was collected, concentrated using a concentrator device, and dissolved in a 100 µL solution of methanol/acetone/isopropanol (7:1:1, v/v/v) for analysis. Spectrum analysis was performed using the open-source MZmine 3 software, and a reference interval was established using the Python programming language on the Google Colab platform. The developed method for measuring vitamin K and its derivatives exhibited limit of detection and limit of quantitation values of 0.005 and 0.01 ng/mL, respectively. In conclusion, our study presents a precise and reliable method for the measurement of vitamin K and its derivatives using enzyme-assisted extraction.

Keywords:  Method; enzyme-assisted; mass spectrometry; menaquinone; phylloquinone; vitamin K1

DOI:  https://doi.org/10.1177/14690667231183046
J Chromatogr B Analyt Technol Biomed Life Sci. 2023 Jun 08. pii: S1570-0232(23)00186-1. [Epub ahead of print]1226 123776

Identification of endogenous carbonyl steroids in human serum by chemical derivatization, hydrogen/deuterium exchange mass spectrometry and the quantitative structure-retention relationship.

Yinyu Wei, Yi Sun, Shuailong Jia, Pan Yan, Chaomei Xiong, Meiling Qi, Chenxi Wang, Zhifeng Du, Hongliang Jiang.

  Steroids are tetracyclic aliphatic compounds, and most of them contain carbonyl groups. The disordered homeostasis of steroids is closely related to the occurrence and progression of various diseases. Due to high structural similarity, low concentrations in vivo, poor ionization efficiency, and interference from endogenous substances, it is very challenging to comprehensively and unambiguously identify endogenous steroids in biological matrix. Herein, an integrated strategy was developed for the characterization of endogenous steroids in serum based on chemical derivatization, ultra-performance liquid chromatography quadrupole Exactive mass spectrometry (UPLC-Q-Exactive-MS/MS), hydrogen/deuterium (H/D) exchange, and a quantitative structure-retention relationship (QSRR) model. To enhance the mass spectrometry (MS) response of carbonyl steroids, the ketonic carbonyl group was derivatized by Girard T (GT). Firstly, the fragmentation rules of derivatized carbonyl steroid standards by GT were summarized. Then, carbonyl steroids in serum were derivatized by GT and identified based on the fragmentation rules or by comparing retention time and MS/MS spectra with those of standards. H/D exchange MS was utilized to distinguish derivatized steroid isomers for the first time. Finally, a QSRR model was constructed to predict the retention time of the unknown steroid derivatives. With this strategy, 93 carbonyl steroids were identified from human serum, and 30 of them were determined to be dicarbonyl steroids by the charge number of characteristic ions and the number of exchangeable hrdrogen or comparing with standards. The QSRR model built by the machine learning algorithms has an excellent regression correlation, thus the accurate structures of 14 carbonyl steroids were determined, among which three steroids were reported for the first time in human serum. This study provides a new analytical method for the comprehensive and reliable identification of carbonyl steroids in biological matrix.

Keywords:  Carbonyl steroids; Derivatization; H/D exchange; Quantitative structure-retention relationship; UPLC-Q-exactive-MS/MS

DOI:  https://doi.org/10.1016/j.jchromb.2023.123776
Anal Methods. 2023 Jun 13.

Advantages of using biologically generated 13C-labelled multiple internal standards for stable isotope-assisted LC-MS-based lipidomics.

Malak A Jaber, Bruna de Falco, Salah Abdelrazig, Catharine A Ortori, David A Barrett, Dong-Hyun Kim.

In comprehensive lipidomics studies, accurate quantification is essential but biological and/or clinical relevance is often hindered due to unwanted variations such as lipid degradation during sample preparation, matrix effects and non-linear responses of analytical instruments. In addition, the wide chemical diversity of lipids can complicate the accurate identification of individual lipids. These analytical limitations can potentially be corrected efficiently by the use of lipid-specific isotopically labelled internal standards (IS) but currently such IS mixtures have limited coverage of the mammalian lipidome. In this study, an in vivo13C labelling strategy was employed to explore four species (Escherichia coli, Arthrospira platensis, Saccharomyces cerevisiae and Pichia pastoris) as a source of 13C-labelled internal standards (13C-ISs) for more accurate and quantitative liquid chromatography (LC)-mass spectrometry (MS)-based lipidomics. Results showed that extracts from 13C-labelled P. pastoris and S. cerevisiae contain the highest percentage of uniformly labelled lipids (both 83% compared to 67% and 69% in A. platensis and E. coli, respectively) and 13C-labelled P. pastoris extract was identified as the optimum source of 13C-ISs for comprehensive data normalisation to correct unwanted variations during sample preparation and LC-MS analysis. Overall, use of a biologically generated 13C-IS lipid mixture of 357 identified lipid ions resulted in significant reduction in the lipid CV% of normalisation compared with other normalisation methods using total ion counts or a commercially available deuterated internal standard mixture. This improved normalisation using 13C-IS was confirmed in a typical lipidomics analysis using a large number of samples (>100+) and long analysis time (>70 h). This study highlights the benefit of an in vivo labelling strategy for reducing technical and analytical variations introduced during sample preparation and analysis in lipidomics studies.

DOI: https://doi.org/10.1039/d3ay00460k
J Am Soc Mass Spectrom. 2023 Jun 12.

Automatic z-Axis Correction for IR-MALDESI Mass Spectrometry Imaging of Uneven Surfaces.

Ying Xi, Kevan T Knizner, Kenneth P Garrard, David C Muddiman.

  Two-dimensional mass spectrometry imaging (2D MSI) experiments mainly involve samples with a flat surface and constant thickness, but some samples are challenging to section due to the texture and topography. Herein, we present an MSI method that automatically corrects for discernible height differences across surfaces during imaging experiments. A chromatic confocal sensor was incorporated into the infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) system to measure the sample surface height at the location of each analytical scan. The height profile is subsequently used for adjusting the z-axis position of the sample during MSI data acquisition. We evaluated this method using a tilted mouse liver section and an unsectioned Prilosec tablet due to their exterior quasi-homogeneity and height differences of approximately ∼250 μm. MSI with automatic z-axis correction showed consistent ablated spot sizes and shapes, revealing the measured ion spatial distribution across a mouse liver section and a Prilosec tablet. Conversely, irregular spots and reduced signals with large variability were observed when no z-axis correction was applied.

Keywords:  IR-MALDESI; automatic z-axis correction; mass spectrometry imaging; nonflat surfaces

DOI:  https://doi.org/10.1021/jasms.3c00151
Foods. 2023 May 29. pii: 2180. [Epub ahead of print]12(11):

Development and Validation of a High-Performance Liquid Chromatography-Tandem Mass Spectrometry Method to Determine Promethazine and Its Metabolites in Edible Tissues of Swine.

Dehui Wen, Rong Shi, Haiming He, Rundong Chen, Yingzi Zhang, Rong Liu, Hong Chen.

  This study aimed to determine promethazine (PMZ) and its metabolites, promethazine sulfoxide (PMZSO) and monodesmethyl-promethazine (Nor1PMZ), in swine muscle, liver, kidney, and fat. A sample preparation method and high-performance liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis were established and validated. The samples were extracted using 0.1% formic acid-acetonitrile and purified with acetonitrile-saturated n-hexane. After concentration by rotary evaporation, the extract was re-dissolved in a mixture of 0.1% formic acid-water and acetonitrile (80:20, v/v). Analysis was performed using a Waters Symmetry C18 column (100 mm × 2.1 mm i.d., 3.5 μm) with 0.1% formic acid-water and acetonitrile as the mobile phase. The target compounds were determined using positive ion scan and multiple reaction monitoring. PMZ and Nor1PMZ were quantified with deuterated promethazine (PMZ-d6) as the internal standard, while PMZSO was quantified using the external standard method. In spiked muscle, liver, and kidney samples, the limits of detection (LOD) and limits of quantification (LOQ) for PMZ and PMZSO were 0.05 μg/kg and 0.1 μg/kg, respectively, while for Nor1PMZ, these values were 0.1 μg/kg and 0.5 μg/kg, respectively. For spiked fat samples, the LOD and LOQ for all three analytes were found to be 0.05 μg/kg and 0.1 μg/kg, respectively. The sensitivity of this proposed method reaches or exceeds that presented in previous reports. The analytes PMZ and PMZSO exhibited good linearity within the range of 0.1 μg/kg to 50 μg/kg, while Nor1PMZ showed good linearity within the range of 0.5 μg/kg to 50 μg/kg, with correlation coefficients (r) greater than 0.99. The average recoveries of the target analytes in the samples varied from 77% to 111%, with the precision fluctuating between 1.8% and 11%. This study developed, for the first time, an HPLC-MS/MS method for the determination of PMZ, PMZSO, and Nor1PMZ in four swine edible tissues, comprehensively covering the target tissues of monitoring object. The method is applicable for monitoring veterinary drug residues in animal-derived foods, ensuring food safety.

Keywords:  high-performance liquid chromatography–tandem mass spectrometry; monodesmethyl-promethazine; promethazine; promethazine sulfoxide; swine edible tissues

DOI:  https://doi.org/10.3390/foods12112180
Molecules. 2023 May 29. pii: 4425. [Epub ahead of print]28(11):

Determination of Glycerol, Propylene Glycol, and Nicotine as the Main Components in Refill Liquids for Electronic Cigarettes.

Paweł Kubica.

  Refill liquids for electronic cigarettes are an important area of research due to the health safety and quality control of such products. A method was developed for the determination of glycerol, propylene glycol, and nicotine in refill liquids using liquid chromatography, coupled with tandem mass spectrometry (LC-MS/MS) in multiple reaction monitoring (MRM) mode with electrospray ionisation (ESI). Sample preparation was based on a simple dilute-and-shoot approach, with recoveries ranging from 96 to 112% with coefficients of variation < 6.4%. Linearity, limits of detection and quantification (LOD, LOQ), repeatability, and accuracy were determined for the proposed method. The proposed sample preparation and the developed chromatographic method using hydrophilic interaction liquid chromatography (HILIC) were successfully applied for the determination of glycerol, propylene glycol, and nicotine in refill liquid samples. For the first time, the developed method using HILIC-MS/MS has been applied for the determination of the main components of refill liquids in a single analysis. The proposed procedure is rapid and straightforward and is suitable for quick determination of glycerol, propylene glycol, and nicotine. The nicotine concentrations corresponded to the labelling of samples (it varied from <LOD-11.24 mg/mL), and the ratios of propylene glycol to glycerol were also determined.

Keywords:  electronic cigarettes; liquid chromatography; mass spectrometry; nicotine; refill liquids

DOI:  https://doi.org/10.3390/molecules28114425
Anal Chem. 2023 Jun 12.

Characterization of Oxidized Glycerophosphoethanolamines via Radical-Directed Dissociation Tandem Mass Spectrometry and the Paternò-Büchi Derivatization.

Qiaohong Lin, Ruijun Jian, Shengzhuo Wang, Yu Xia.

Oxidized glycerophosphoethanolamines (oxPEs) represent a subclass of bioactive lipids that have intricate roles in various physiological and pathological events. Conventional mass spectrometric methods cannot provide unambiguous information to locate the OH group and the sites of unsaturation. Herein, we report a combined strategy for in-depth structural characterization of oxPEs, including radical-directed dissociation tandem mass spectrometry (RDD-MS/MS) for localizing the OH group and the Paternò-Büchi derivatization coupled with tandem mass spectrometry for pinpointing carbon-carbon double-bond locations. The RDD-MS/MS method has been integrated on a reversed-phase liquid chromatography-mass spectrometry workflow. It enables the profiling of 24 distinct oxPE molecules with unequivocal assignment of the OH sites at nM sensitivity in bovine liver lipid extract treated by soybean 15-lipoxygenase. These findings showcase that the developed method has a good potential in analyzing biological systems where oxPEs may play important roles.

DOI: https://doi.org/10.1021/acs.analchem.3c00792
Anal Chem. 2023 Jun 14.

MCnebula: Critical Chemical Classes for the Classification and Boost Identification by Visualization for Untargeted LC-MS/MS Data Analysis.

Lichuang Huang, Qiyuan Shan, Qiang Lyu, Shuosheng Zhang, Lu Wang, Gang Cao.

Untargeted mass spectrometry is a robust tool for biology, but it usually requires a large amount of time on data analysis, especially for system biology. A framework called Multiple-Chemical nebula (MCnebula) was developed herein to facilitate the LC-MS data analysis process by focusing on critical chemical classes and visualization in multiple dimensions. This framework consists of three vital steps as follows: (1) abundance-based classes (ABC) selection algorithm, (2) critical chemical classes to classify "features" (corresponding to compounds), and (3) visualization as multiple Child-Nebulae (network graph) with annotation, chemical classification, and structure. Notably, MCnebula can be used to explore the classification and structural characteristic of unknown compounds beyond the limit of the spectral library. Moreover, it is intuitive and convenient for pathway analysis and biomarker discovery because of its function of ABC selection and visualization. MCnebula was implemented in the R language. A series of tools in R packages were provided to facilitate downstream analysis in an MCnebula-featured way, including feature selection, homology tracing of top features, pathway enrichment analysis, heat map clustering analysis, spectral visualization analysis, chemical information query, and output analysis reports. The broad utility of MCnebula was illustrated by a human-derived serum data set for metabolomics analysis. The results indicated that "Acyl carnitines" were screened out by tracing structural classes of biomarkers, which was consistent with the reference. A plant-derived data set was investigated to achieve a rapid annotation and discovery of compounds in E. ulmoides.

DOI: https://doi.org/10.1021/acs.analchem.3c01072
Front Mol Biosci. 2023 ;10 1181965

Mass spectrometry imaging as an emerging tool for studying metabolism in human brain organoids.

Gerarda Cappuccio, Saleh M Khalil, Sivan Osenberg, Feng Li, Mirjana Maletic-Savatic.

  Human brain organoids are emerging models to study human brain development and pathology as they recapitulate the development and characteristics of major neural cell types, and enable manipulation through an in vitro system. Over the past decade, with the advent of spatial technologies, mass spectrometry imaging (MSI) has become a prominent tool for metabolic microscopy, providing label-free, non-targeted molecular and spatial distribution information of the metabolites within tissue, including lipids. This technology has never been used for studies of brain organoids and here, we set out to develop a standardized protocol for preparation and mass spectrometry imaging of human brain organoids. We present an optimized and validated sample preparation protocol, including sample fixation, optimal embedding solution, homogenous deposition of matrices, data acquisition and processing to maximize the molecular information derived from mass spectrometry imaging. We focus on lipids in organoids, as they play critical roles during cellular and brain development. Using high spatial and mass resolution in positive- and negative-ion modes, we detected 260 lipids in the organoids. Seven of them were uniquely localized within the neurogenic niches or rosettes as confirmed by histology, suggesting their importance for neuroprogenitor proliferation. We observed a particularly striking distribution of ceramide-phosphoethanolamine CerPE 36:1; O2 which was restricted within rosettes and of phosphatidyl-ethanolamine PE 38:3, which was distributed throughout the organoid tissue but not in rosettes. This suggests that ceramide in this particular lipid species might be important for neuroprogenitor biology, while its removal may be important for terminal differentiation of their progeny. Overall, our study establishes the first optimized experimental pipeline and data processing strategy for mass spectrometry imaging of human brain organoids, allowing direct comparison of lipid signal intensities and distributions in these tissues. Further, our data shed new light on the complex processes that govern brain development by identifying specific lipid signatures that may play a role in cell fate trajectories. Mass spectrometry imaging thus has great potential in advancing our understanding of early brain development as well as disease modeling and drug discovery.

Keywords:  brain organoids; mass spectrometry imaging method; metabolome; neurons; neuroprogenitors

DOI:  https://doi.org/10.3389/fmolb.2023.1181965
Anal Chem. 2023 Jun 12.

A Dual-Gated Structures for Lossless Ion Manipulations-Ion Mobility Orbitrap Mass Spectrometry Platform for Combined Ultra-High-Resolution Molecular Analysis.

Adam L Hollerbach, Yehia M Ibrahim, Vanessa Meras, Randolph V Norheim, Adam P Huntley, Gordon A Anderson, Thomas O Metz, Robert G Ewing, Richard D Smith.

High-resolution ion mobility spectrometry-mass spectrometry (HR-IMS-MS) instruments have enormously advanced the ability to characterize complex biological mixtures. Unfortunately, HR-IMS and HR-MS measurements are typically performed independently due to mismatches in analysis time scales. Here, we overcome this limitation by using a dual-gated ion injection approach to couple an 11 m path length structures for lossless ion manipulations (SLIM) module to a Q-Exactive Plus Orbitrap MS platform. The dual-gate setup was implemented by placing one ion gate before the SLIM module and a second ion gate after the module. The dual-gated ion injection approach allowed the new SLIM-Orbitrap platform to simultaneously perform an 11 m SLIM separation, Orbitrap mass analysis using the highest selectable mass resolution setting (up to 140 k), and high-energy collision-induced dissociation (HCD) in ∼25 min over an m/z range of ∼1500 amu. The SLIM-Orbitrap platform was initially characterized using a mixture of standard phosphazene cations and demonstrated an average SLIM CCS resolving power (RpCCS) of ∼218 and an SLIM peak capacity of ∼156, while simultaneously obtaining high mass resolutions. SLIM-Orbitrap analysis with fragmentation was then performed on mixtures of standard peptides and two reverse peptides (SDGRG1+, GRGDS1+, and RpCCS = 305) to demonstrate the utility of combined HR-IMS-MS/MS measurements for peptide identification. Our new HR-IMS-MS/MS capability was further demonstrated by analyzing a complex lipid mixture and showcasing SLIM separations on isobaric lipids. This new SLIM-Orbitrap platform demonstrates a critical new capability for proteomics and lipidomics applications, and the high-resolution multimodal data obtained using this system establish the foundation for reference-free identification of unknown ion structures.

DOI: https://doi.org/10.1021/acs.analchem.3c00881
BMC Bioinformatics. 2023 Jun 15. 24(1): 250

Statistical methods and resources for biomarker discovery using metabolomics.

Najeha R Anwardeen, Ilhame Diboun, Younes Mokrab, Asma A Althani, Mohamed A Elrayess.

  Metabolomics is a dynamic tool for elucidating biochemical changes in human health and disease. Metabolic profiles provide a close insight into physiological states and are highly volatile to genetic and environmental perturbations. Variation in metabolic profiles can inform mechanisms of pathology, providing potential biomarkers for diagnosis and assessment of the risk of contracting a disease. With the advancement of high-throughput technologies, large-scale metabolomics data sources have become abundant. As such, careful statistical analysis of intricate metabolomics data is essential for deriving relevant and robust results that can be deployed in real-life clinical settings. Multiple tools have been developed for both data analysis and interpretations. In this review, we survey statistical approaches and corresponding statistical tools that are available for discovery of biomarkers using metabolomics.

Keywords:  Analytical workflow; Metabolomics; Metabolomics tools; Multivariate; Statistical methods; Univariate

DOI:  https://doi.org/10.1186/s12859-023-05383-0
J Am Soc Mass Spectrom. 2023 Jun 15.

Characterization of Bile Acid Isomers and the Implementation of High-Resolution Demultiplexing with Ion Mobility-Mass Spectrometry.

Robin H J Kemperman, Christopher D Chouinard, Richard A Yost.

Bile acids (BAs) are a complex suite of clinically relevant metabolites that include many isomers. Liquid chromatography coupled to mass spectrometry (LC-MS) is an increasingly popular technique due to its high specificity and sensitivity; nonetheless, acquisition times are generally 10-20 min, and isomers are not always resolved. In this study, the application of ion mobility (IM) spectrometry coupled to MS was investigated to separate, characterize, and measure BAs. A subset of 16 BAs was studied, including three groups of isomers belonging to unconjugated, glycine-conjugated, and taurine-conjugated BA classes. A variety of strategies were explored to increase BA isomer separation such as changing the drift gas, measuring different ionic species (i.e., multimers and cationized species), and enhancing the instrumental resolving power. In general, Ar, N2, and CO2 provided the best peak shape, resolving power (Rp), and separation, especially CO2; He and SF6 were less preferable. Furthermore, measuring dimers versus monomers improved isomer separation due to enhanced gas-phase structural differences. A variety of cation adducts other than sodium were characterized. Mobility arrival times and isomer separation were affected by the choice of adduct, which was shown to be used to target certain BAs. Finally, a novel workflow that involves high-resolution demultiplexing in combination with dipivaloylmethane ion-neutral clusters was implemented to improve Rp dramatically. A maximum Rp increase was observed with lower IM field strengths to obtain longer drift times, increasing Rp from 52 to 187. A combination of these separation enhancement strategies demonstrates great potential for rapid BA analysis.

DOI: https://doi.org/10.1021/jasms.3c00143
J Am Soc Mass Spectrom. 2023 Jun 14.

Formation and Tandem Mass Spectrometry of Doubly Charged Lipid-Metal Ion Complexes.

Felix-Levin Hormann, Simon Sommer, Sven Heiles.

  Phospholipids are major components of most eukaryotic cell membranes. Changes in metabolic states are often accompanied by phospholipid structure variations. The structural changes of phospholipids are the hallmark of disease states, or specific lipid structures have been associated with distinct organisms. Prime examples are microorganisms that synthesize phospholipids with, for example, different branched chain fatty acids. Assignment and relative quantitation of structural isomers of phospholipids that arise from attachment of different fatty acids to the glycerophospholipid backbone are difficult with routine tandem mass spectrometry or with liquid chromatography without authentic standards. In this work, we report on the observation that all investigated phospholipid classes form doubly charged lipid-metal ion complexes during electrospray ionization (ESI) and show that these complexes can be used to assign lipid classes and fatty acid moieties, distinguish isomers of branched chain fatty acids, and relatively quantify these isomers in positive-ion mode. Use of water free methanol and addition of divalent metal salts (100 mol %) to ESI spray solutions afford highly abundant doubly charged lipid-metal ion complexes (up to 70 times of protonated compounds). Higher-energy collisional dissociation and collision-induced dissociation of doubly charged complexes yield a diverse set of lipid class-dependent fragment ions. In common for all lipid classes is the liberation of fatty acid-metal adducts that yield fragment ions from the fatty acid hydrocarbon chain upon activation. This ability is used to pinpoint sites of branching in saturated fatty acids and is showcased for free fatty acids as well as glycerophospholipids. The analytical utility of doubly charged phospholipid-metal ion complexes is demonstrated by distinguishing fatty acid branching-site isomers in phospholipid mixtures and relatively quantifying the corresponding isomeric compounds.

Keywords:  Branched chain fatty acids; Electrospray ionization; Hydrocarbons; Ions; Lipids; Tandem mass spectrometry

DOI:  https://doi.org/10.1021/jasms.3c00126
J Am Soc Mass Spectrom. 2023 Jun 14.

NOMspectra: An Open-Source Python Package for Processing High Resolution Mass Spectrometry Data on Natural Organic Matter.

Alexander Volikov, Gleb Rukhovich, Irina V Perminova.

The present study introduces NOMspectra, a Python package for processing high resolution mass spectrometry data on complex systems of natural organic matter (NOM). NOM is characterized by multicomponent composition reflected as thousands of signals producing very complex patterns in high resolution mass spectra. This complexity sets special demands on the methods of data processing used for analysis. The developed NOMspectra package offers a comprehensive workflow for processing, analyzing, and visualizing information-rich mass spectra of NOM and HS including algorithms for filtering spectra, recalibrating, and assigning elemental compositions to molecular ions. Additionally, the package includes functions for calculating various molecular descriptors and methods for data visualization. A graphical user interface (GUI) has been developed to make a user-friendly interface for the proposed package.

DOI: https://doi.org/10.1021/jasms.3c00003
ACS Omega. 2023 Jun 13. 8(23): 20755-20766

The Impact of the Serum Extraction Protocol on Metabolomic Profiling Using UPLC-MS/MS and FTIR Spectroscopy.

Tiago A H Fonseca, Cristiana P Von Rekowski, Rúben Araújo, M Conceição Oliveira, Gonçalo C Justino, Luís Bento, Cecília R C Calado.

Biofluid metabolomics is a very appealing tool to increase the knowledge associated with pathophysiological mechanisms leading to better and new therapies and biomarkers for disease diagnosis and prognosis. However, due to the complex process of metabolome analysis, including the metabolome isolation method and the platform used to analyze it, there are diverse factors that affect metabolomics output. In the present work, the impact of two protocols to extract the serum metabolome, one using methanol and another using a mixture of methanol, acetonitrile, and water, was evaluated. The metabolome was analyzed by ultraperformance liquid chromatography associated with tandem mass spectrometry (UPLC-MS/MS), based on reverse-phase and hydrophobic chromatographic separations, and Fourier transform infrared (FTIR) spectroscopy. The two extraction protocols of the metabolome were compared over the analytical platforms (UPLC-MS/MS and FTIR spectroscopy) concerning the number of features, the type of features, common features, and the reproducibility of extraction replicas and analytical replicas. The ability of the extraction protocols to predict the survivability of critically ill patients hospitalized at an intensive care unit was also evaluated. The FTIR spectroscopy platform was compared to the UPLC-MS/MS platform and, despite not identifying metabolites and consequently not contributing as much as UPLC-MS/MS in terms of information concerning metabolic information, it enabled the comparison of the two extraction protocols as well as the development of very good predictive models of patient's survivability, such as the UPLC-MS/MS platform. Furthermore, FTIR spectroscopy is based on much simpler procedures and is rapid, economic, and applicable in the high-throughput mode, i.e., enabling the simultaneous analysis of hundreds of samples in the microliter range in a couple of hours. Therefore, FTIR spectroscopy represents a very interesting complementary technique not only to optimize processes as the metabolome isolation but also for obtaining biomarkers such as those for disease prognosis.

DOI: https://doi.org/10.1021/acsomega.3c01370
J Pharm Biomed Anal. 2023 Jun 01. pii: S0731-7085(23)00271-6. [Epub ahead of print]234 115502

Simultaneous quantitation of ketamine, norketamine and dehydronorketamine in human milk using a novel ultra high-performance liquid chromatography-mass spectrometry (UPLC-MS/MS) assay.

Aditi Shahane, Wenchen Zhao, Naren Pakalapati, Osama Y Alshogran, Steve N Caritis, Grace Lim, Imam H Shaik, Raman Venkataramanan.

  There is a paucity of data on the transfer of ketamine from maternal blood into human milk. Quantification of ketamine in human milk provides information about the potential exposure of the infant to ketamine and its metabolites from the mother during lactation. A highly specific, reproducible, and sensitive UPLC-MS/MS based analytical method was developed and validated for the quantitation of ketamine and its metabolites (norketamine and dehydronorketamine) in human milk. Samples were subjected to a simple protein precipitation and ketamine-d4 and norketamine-d4 were used as internal standards. Separation of the analytes was achieved using an Acquity UPLC equipped with BEH RP18 1.7 µm, 2.1 × 100 mm column. Mass spectrometric analysis of the analyte ions was carried out using electrospray with positive ionization and multiple reaction monitoring mode. The assay was linear over a concentration range of 1-100 ng/mL for ketamine and norketamine, and 0.1-10 ng/mL for dehydronorketamine. Acceptable intra-day and inter-day accuracy and precision were observed for all the analytes. High recovery of the analytes and minimal matrix effect were observed. Stability of analytes was confirmed at the tested conditions. This assay was successfully used to measure analytes in human milk samples collected from lactating women enrolled in a clinical research study. This is the first validated method that simultaneously quantified ketamine and its metabolites in human milk.

Keywords:  Human milk; Ketamine; Lactation; UPLC-MS/MS

DOI:  https://doi.org/10.1016/j.jpba.2023.115502
Anal Chem. 2023 Jun 14.

PeakDetective: A Semisupervised Deep Learning-Based Approach for Peak Curation in Untargeted Metabolomics.

Ethan Stancliffe, Gary J Patti.

Peak-detection algorithms currently used to process untargeted metabolomics data were designed to maximize sensitivity at the sacrifice of selectively. Peak lists returned by conventional software tools therefore contain a high density of artifacts that do not represent real chemical analytes, which, in turn, hinder downstream analyses. Although some innovative approaches to remove artifacts have recently been introduced, they involve extensive user intervention due to the diversity of peak shapes present within and across metabolomics data sets. To address this bottleneck in metabolomics data processing, we developed a semisupervised deep learning-based approach, PeakDetective, for classification of detected peaks as artifacts or true peaks. Our approach utilizes two techniques for artifact removal. First, an unsupervised autoencoder is used to extract a low-dimensional, latent representation of each peak. Second, a classifier is trained with active learning to discriminate between artifacts and true peaks. Through active learning, the classifier is trained with less than 100 user-labeled peaks in a matter of minutes. Given the speed of its training, PeakDetective can be rapidly tailored to specific LC/MS methods and sample types to maximize performance on each type of data set. In addition to curation, the trained models can also be utilized for peak detection to immediately detect peaks with both high sensitivity and selectivity. We validated PeakDetective on five diverse LC/MS data sets, where PeakDetective showed greater accuracy compared to current approaches. When applied to a SARS-CoV-2 data set, PeakDetective enabled more statistically significant metabolites to be detected. PeakDetective is open source and available as a Python package at https://github.com/pattilab/PeakDetective.

DOI: https://doi.org/10.1021/acs.analchem.3c00764
J Agric Food Chem. 2023 Jun 15.

Simplified Liquid Chromatography-Mass Spectrometry Methods for Gestagen Analysis in Animal Fat and Liver.

Randy W Purves, Michelle West, Ratnadipsinh Vaghela, Jana Kinar, Yash Patel, Michael W Belford, Bryn O Shurmer.

  Gestagens, a class of veterinary drugs also called progestogens, are synthetic hormones used to increase feed efficiency and rate of gain in heifers. The Canadian Food Inspection Agency analyzes progestogens melengestrol acetate (MGA), megestrol acetate, and chlormadinone acetate using liquid chromatography-mass spectrometry (LC-MS). Our conventional gestagen method for kidney fat has many time-consuming steps, including solid-phase extraction. A sample preparation procedure having fewer clean-up steps was developed for routine diagnostic analysis of kidney fat and provided similar results faster, and at lower cost. A confirmatory liver method for gestagens, developed using salt-assisted extraction, employed minimal clean-up steps that resulted in high chemical background at the desired lower limit of quantification (LLOQ). Differential ion mobility spectrometry, specifically high-field asymmetric waveform ion mobility spectrometry (FAIMS), was used to filter chemical background in the gas phase. The effect of the ionization probe position on FAIMS parameters, including sensitivity, is described. With LC-FAIMS-MS, chemical background for each gestagen was virtually eliminated, resulting in a quantitative liver method having the desired 0.6 ng/g LLOQ and estimated limits of detection (LODs) up to 140 times lower than LC-MS. Incurred MGA samples, analyzed using kidney fat and liver methods from the same animal, show levels within the quantitative ranges of both methods.

Keywords:  LC−MS; MGA; MRL; food safety; mass spectrometry; melengestrol acetate; progestogens

DOI:  https://doi.org/10.1021/acs.jafc.3c01200
Food Addit Contam Part A Chem Anal Control Expo Risk Assess. 2023 Jun 14. 1-11

Development of an LC-MS/MS method for the determination of multiple mycotoxins in human urine.

Mobing Chen, Wei Liu, Ping Xiang, Linhao Xu, Yiling Tang, Ran Kong, Shuo Yang, Hui Yan, Bin Di.

  A sensitive liquid chromatography-tandem mass spectrometry method was developed for the determination of 17 mycotoxins in human urine. The method incorporates a two-step liquid-liquid extraction with ethyl acetate:acetonitrile (7:1), which had good extraction recovery. The LOQs of all mycotoxins ranged from 0.1 to 1 ng/mL. Intra-day accuracy ranged from 94 to 106%, and intra-day precision ranged from 1 to 12% for all mycotoxins. Inter-day accuracy and precision were 95-105% and 2-8%, respectively. The method was successfully applied to investigate the urine levels of 17 mycotoxins from 42 volunteers. Deoxynivalenol (DON, 0.97-9.88 ng/mL) was detected in 10 (24%) urine samples and zearalenone (ZEN, 0.13-1.11 ng/mL) in 2 (5%) urine samples.

Keywords:  LC-MS/MS; aflatoxin B1; deoxynivalenol; mycotoxin; urine; zearalenone

DOI:  https://doi.org/10.1080/19440049.2023.2222842
J Hazard Mater. 2023 May 27. pii: S0304-3894(23)01011-7. [Epub ahead of print]457 131728

Neonicotinoid insecticides and their metabolites: Specimens tested, analytical methods and exposure characteristics in humans.

Haixin Tu, Xin Wei, Yanan Pan, Zixiong Tang, Renli Yin, Junhao Qin, Huashou Li, Adela Jing Li, Rongliang Qiu.

  The use of neonicotinoid insecticides (NEOs) has been rising globally due to their broad-spectrum insecticidal activity, unique mode of neurotoxic action and presumed low mammalian toxicity. Given their growing ubiquity in the environment and neurological toxicity to non-target mammals, human exposure to NEOs is flourishing and now becomes a big issue. In the present work, we demonstrated that 20 NEOs and their metabolites have been reported in different human specimens with urine, blood and hair as the dominance. Sample pretreatment techniques of solid-phase and liquid-liquid extractions coupled with high performance liquid chromatography-tandem mass spectrometry have successfully achieved matrix elimination and accurate analysis. We also discussed and compared exposure characteristics of these compounds among types of specimens and different regions. A number of important knowledge gaps were also identified in order to further facilitate the understanding of health effects of NEO insecticides, which include, but are not limited to, identification and use of neuro-related human biological samples for better elucidating neurotoxic action of NEO insecticides, adoption of advanced non-target screening analysis for a whole picture in human exposure, and expanding investigations to cover non-explored but NEO-used regions and vulnerable populations.

Keywords:  Exposure profile; Human specimen; Metabolites; Neonicotinoid insecticides; Sample analysis

DOI:  https://doi.org/10.1016/j.jhazmat.2023.131728
Food Chem. 2023 Jun 07. pii: S0308-8146(23)01175-5. [Epub ahead of print]426 136557

High throughput and automated solid-phase microextraction and determination by liquid chromatography-mass spectrometry for the analysis of mycotoxins in beer.

Wei Zhou, Martyna N Wieczorek, Janusz Pawliszyn.

  There is high demand for rapid screening of toxics in food analysis. In this study, a new high-throughput and automated solid-phase microextraction (SPME) system was employed for the sample preparation of mycotoxins in beers. Matrix compatible SPME blades with thin coating layer were used, which significantly decreased the matrix effects in beer samples (≤ 12%). This SPME system allows 96 samples to be processed automatically and simultaneously with average preparation time of 57 s per sample. After sample preparation, the 96-well plate with desorption solution was sealed with a thin film and put into the LC-MS sampler for analysis via positive/negative ESI switching mode. The results also showed good sensitivity (limits of detection between 0.02 and 3 ng/mL) with R2≥ 0.9971, reproducibility (intra- and inter-day ≤ 8% and ≤ 13%, respectively), and accuracy (recoveries between 79% and 121%).

Keywords:  Automation; High-throughput; LC-MS; Mycotoxin; Solid-phase microextraction

DOI:  https://doi.org/10.1016/j.foodchem.2023.136557
Int J Mol Sci. 2023 Jun 02. pii: 9657. [Epub ahead of print]24(11):

Untargeted Metabolomics Identifies Biomarkers for MCADD Neonates in Dried Blood Spots.

Rajaa Sebaa, Maha AlMogren, Wafaa Alseraty, Anas M Abdel Rahman.

  Medium-chain acyl-CoA dehydrogenase deficiency (MCADD) is the most common inherited mitochondrial metabolic disease of fatty acid β-oxidation, especially in newborns. MCADD is clinically diagnosed using Newborn Bloodspot Screening (NBS) and genetic testing. Still, these methods have limitations, such as false negatives or positives in NBS and the variants of uncertain significance in genetic testing. Thus, complementary diagnostic approaches for MCADD are needed. Recently, untargeted metabolomics has been proposed as a diagnostic approach for inherited metabolic diseases (IMDs) due to its ability to detect a wide range of metabolic alterations. We performed an untargeted metabolic profiling of dried blood spots (DBS) from MCADD newborns (n = 14) and healthy controls (n = 14) to discover potential metabolic biomarkers/pathways associated with MCADD. Extracted metabolites from DBS samples were analyzed using UPLC-QToF-MS for untargeted metabolomics analyses. Multivariate and univariate analyses were used to analyze the metabolomics data, and pathway and biomarker analyses were also performed on the significantly identified endogenous metabolites. The MCADD newborns had 1034 significantly dysregulated metabolites compared to healthy newborns (moderated t-test, no correction, p-value ≤ 0.05, FC 1.5). A total of 23 endogenous metabolites were up-regulated, while 84 endogenous metabolites were down-regulated. Pathway analyses showed phenylalanine, tyrosine, and tryptophan biosynthesis as the most affected pathways. Potential metabolic biomarkers for MCADD were PGP (a21:0/PG/F1alpha) and glutathione, with an area under the curve (AUC) of 0.949 and 0.898, respectively. PGP (a21:0/PG/F1alpha) was the first oxidized lipid in the top 15 biomarker list affected by MCADD. Additionally, glutathione was chosen to indicate oxidative stress events that could happen during fatty acid oxidation defects. Our findings suggest that MCADD newborns may have oxidative stress events as signs of the disease. However, further validations of these biomarkers are needed in future studies to ensure their accuracy and reliability as complementary markers with established MCADD markers for clinical diagnosis.

Keywords:  DBS; MCADD; glutathione; mass-spectrometry; metabolic biomarkers; newborns; oxidized lipids; untargeted metabolomics

DOI:  https://doi.org/10.3390/ijms24119657
Forensic Sci Int. 2023 Jun 01. pii: S0379-0738(23)00193-7. [Epub ahead of print]349 111743

Human scent characterization: A review.

Ruud Peters, Rick Veenstra, Karin Heutinck, Albert Baas, Sandra Munniks, Jaap Knotter.

  Human scent has long been cited as a probable parameter that can be exploited as a biometric measure. Identifying the scent of individual persons using specially trained canines is a well-known forensic method which is frequently used in criminal investigations. To date there has been limited research on the chemical components present in human scent and their usefulness in distinguishing between people. This review delivers insight into studies which have dealt with human scent in forensics. Sample collection methods, sample preparation, instrumental analysis, compounds identified in human scent and data analysis techniques are discussed. Methods for sample collection and preparation are presented, but to date, there is no available validated method. Instrumental methods are presented and from the overview it is clear that gas chromatography combined with mass spectrometry is the method of choice. New developments such as two-dimensional gas chromatography offer exiting possibilities to collect more information. Given the amount and complexity of data, data processing is used to extract the relevant information to discriminate people. Finally, sensors offer new opportunities for the characterization of human scent.

Keywords:  Forensic science; Gas chromatography; Human odor; Human scent; Mass spectrometry; Sensors; VOCs

DOI:  https://doi.org/10.1016/j.forsciint.2023.111743
J Anal Methods Chem. 2023 ;2023 8898426

A LC-MS/MS Method for Quantifying the Schisandrin B and Exploring Its Intracellular Exposure Correlating Antitumor Effect.

Bosu Meng, Shouhong Gao, Jihui Chen, Bin Wang, Yuhui Mu, Yan Liu, Zhipeng Wang, Wansheng Chen.

Schisandrin B (Sch.B) shows antineoplastic activity in colorectal cancer, but the mechanism is still obscure. The intracellular spatial distribution may be helpful in elucidating the mechanism. To investigate the intracellular drug distribution of Sch.B in cancer cells, a simple, rapid, and sensitive ultra-highperformance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) method was established for the determination of Sch.B in colorectal cancer cells. Warfarin was utilized as an internal standard. The sample pretreatment was carried out with protein precipitation using methanol. The analyte was separated on an Atlantis T3-C18 column (3 μm, 2.1∗100 mm) using gradient elution with a mobile phase comprised of methanol and 0.2% formic acid in water. The flow rate was 0.4 mL/min. The linear range of Sch.B was 20.0-1000.0 ng/mL with a correlation coefficient (R) more than 0.99. The matrix effect and recovery ranged from 88.01% to 94.59% and from 85.25% to 91.71%; the interday and intraday precision and accuracy, stability, specificity, carryover, matrix effect, and recovery all conformed to the requirements of pharmacopoeia. Cell viability and apoptosis assays demonstrated that Sch.B has an inhibitory effect in a dose-dependent way on HCT116 proliferation and achieved significant suppression at 75 μM (IC50). It was found that in HCT116 cell, nucleus, and mitochondria, exposure levels of Sch.B peaked at 36 h and then decreased, and mitochondria possessed more Sch.B than nucleus. These results may help to elucidate the antitumor effect of Sch.B.

DOI: https://doi.org/10.1155/2023/8898426
J Pharm Anal. 2023 May;13(5): 483-493

Spatiotemporal pharmacometabolomics based on ambient mass spectrometry imaging to evaluate the metabolism and hepatotoxicity of amiodarone in HepG2 spheroids.

Limei Li, Qingce Zang, Xinzhu Li, Ying Zhu, Shanjing Wen, Jiuming He, Ruiping Zhang, Zeper Abliz.

  Three-dimensional (3D) cell spheroid models combined with mass spectrometry imaging (MSI) enables innovative investigation of in vivo-like biological processes under different physiological and pathological conditions. Herein, airflow-assisted desorption electrospray ionization-MSI (AFADESI-MSI) was coupled with 3D HepG2 spheroids to assess the metabolism and hepatotoxicity of amiodarone (AMI). High-coverage imaging of >1100 endogenous metabolites in hepatocyte spheroids was achieved using AFADESI-MSI. Following AMI treatment at different times, 15 metabolites of AMI involved in N-desethylation, hydroxylation, deiodination, and desaturation metabolic reactions were identified, and according to their spatiotemporal dynamics features, the metabolic pathways of AMI were proposed. Subsequently, the temporal and spatial changes in metabolic disturbance within spheroids caused by drug exposure were obtained via metabolomic analysis. The main dysregulated metabolic pathways included arachidonic acid and glycerophospholipid metabolism, providing considerable evidence for the mechanism of AMI hepatotoxicity. In addition, a biomarker group of eight fatty acids was selected that provided improved indication of cell viability and could characterize the hepatotoxicity of AMI. The combination of AFADESI-MSI and HepG2 spheroids can simultaneously obtain spatiotemporal information for drugs, drug metabolites, and endogenous metabolites after AMI treatment, providing an effective tool for in vitro drug hepatotoxicity evaluation.

Keywords:  Amiodarone; Drug metabolism; HepG2 spheroids; Hepatotoxicity; Mass spectrometry imaging

DOI:  https://doi.org/10.1016/j.jpha.2023.04.007
Sci Total Environ. 2023 Jun 08. pii: S0048-9697(23)03330-2. [Epub ahead of print] 164707

Broad-range extraction of highly polar to non-polar organic contaminants for inclusive target analysis and suspect screening of environmental samples.

Lahiruni M Halwatura, Diana S Aga.

  The lack of carefully optimized extraction techniques for the analysis of compounds with diverse polarities limits the identification of toxic pollutants in aqueous environmental matrices, particularly those that are considered persistent and mobile organic compounds (PMOCs). Tailored extraction techniques for specific classes of chemicals often result in very low to no extraction of either very polar or relatively non-polar chemicals, depending on the sorbent used. Hence, it is crucial to develop a balanced extraction for a wider range of polarity, especially for non-target analysis of chemical residues, in order to capture the occurrence of the full profile of micropollutants. Herein, a tandem solid-phase extraction (SPE) technique incorporating both hydrophilic-lipophilic balance (HLB) and mixed-mode cation exchange (MCX) sorbents was developed to extract and analyze 60 model compounds with a wide range of polarities (log Kow - 1.9 to 5.5) from untreated sewage matrices. Extraction efficiencies were assessed in NanoPure™ water and untreated sewage samples; 51 compounds in NanoPure™ water and 44 compounds in untreated sewage had ≥60 % extraction recoveries using the developed tandem SPE method. The method limits of detection ranged from 0.25 to 88 ng/L in untreated sewage matrix. The applicability of the extraction method was demonstrated in untreated wastewater samples; using the tandem SPE for suspect screening analysis captured an additional 22 compounds that were not extracted when using the HLB sorbent only. The optimized SPE method was also evaluated for the extraction of per- and polyfluoroalkyl substances (PFASs) by analyzing the same sample extracts under negative electrospray ionization liquid chromatography-tandem mass spectrometry (LC-MS/MS). The wastewater samples revealed the presence of sulfonamide-, sulfonic-, carboxylic-, and fluorotelomer sulfonic- PFASs with chain lengths 8, 4-8, 4-9, and 8, respectively, indicating that the tandem SPE procedure provides an efficient one-step extraction for the analysis of PMOCs that include pharmaceuticals, pesticides, and PFASs.

Keywords:  Emerging contaminants; Non-target analysis; Persistent and mobile organic compounds; Raw sewage; Tandem solid-phase extraction

DOI:  https://doi.org/10.1016/j.scitotenv.2023.164707
Foods. 2023 May 23. pii: 2098. [Epub ahead of print]12(11):

Progress of Mass Spectrometry-Based Lipidomics in the Dairy Field.

Wei Ren, Mengqi Sun, Xiaoyuan Shi, Tianqi Wang, Yonghui Wang, Changfa Wang, Mengmeng Li.

  Lipids play important biological roles, such as providing essential fatty acids and signaling. The wide variety and structural diversity of lipids, and the limited technical means to study them, have seriously hampered the resolution of the mechanisms of action of lipids. With advances in mass spectrometry (MS) and bioinformatic technologies, large amounts of lipids have been detected and analyzed quickly using MS-based lipidomic techniques. Milk lipids, as complex structural metabolites, play a crucial role in human health. In this review, the lipidomic techniques and their applications to dairy products, including compositional analysis, quality identification, authenticity identification, and origin identification, are discussed, with the aim of providing technical support for the development of dairy products.

Keywords:  application; dairy products; lipidomics; lipids; mass spectrometry

DOI:  https://doi.org/10.3390/foods12112098
J Am Soc Mass Spectrom. 2023 Jun 15.

Development of High Throughput Microscope Mode Secondary Ion Mass Spectrometry Imaging.

Felicia M Green, Maria Elena Castellani, Yifeng Jia, Anya Eyres, Natasha Smith, Steve Thompson, Paul Blenkinsopp, Michael Burt, Claire Vallance, Josephine Bunch, Zoltan Takats, Mark Brouard.

This paper describes the development and initial results from a secondary ion mass spectrometer coupled with microscope mode detection. Stigmatic ion microscope imaging enables us to decouple the primary ion (PI) beam focus from spatial resolution and is a promising route to attaining higher throughput for mass spectrometry imaging (MSI). Using a commercial C60+ PI beam source, we can defocus the PI beam to give uniform intensity across a 2.5 mm2 area. By coupling the beam with a position-sensitive spatial detector, we can achieve mass spectral imaging of positive and negative secondary ions (SIs), which we demonstrate using samples comprising metals and dyes. Our approach involves simultaneous desorption of ions across a large field of view, enabling mass spectral images to be recorded over an area of 2.5 mm2 in a matter of seconds. Our instrument can distinguish spatial features with a resolution of better than 20 μm, and has a mass resolution of >500 at 500 u. There is considerable scope to improve this, and through simulations we estimate the future performance of the instrument.

DOI: https://doi.org/10.1021/jasms.2c00371
J Chromatogr A. 2023 Jun 03. pii: S0021-9673(23)00344-8. [Epub ahead of print]1704 464118

Gas chromatography coupled-to Fourier transform orbitrap mass spectrometer for enantioselective amino acid analyses: Application to pre-cometary organic analog.

A Garcia, C Serra, Q Blancart Remaury, A D Garcia, M Righezza, C Meinert, P Poinot, G Danger.

  Gas chromatography (GC) is a separation technique commonly developed for targeted in situ analyses in planetary space missions. It is coupled with low-resolution mass spectrometry to obtain additional structural information and allow compound identification. However, ground-based analyses of extraterrestrial samples have shown the presence of large molecular diversities. For future targeted in situ analyses, it is therefore essential to develop new technologies. High resolution mass spectrometry (HRMS) is currently being spatialized using FT-orbitrap-MS technology. In this contribution, the coupling of gas chromatography with FT-orbitrap-MS is studied for targeted amino acid analyses. The method for enantioselective separation of amino acids was optimized on a standard mixture comprising 47 amino acid enantiomers. Different ionization modes were optimized, chemical ionization with three different reactive gasses (NH3, CH4 and NH3/CH4) and electron impact ionization at different electron energies. Single ion and full scan monitoring modes were compared, and detection and quantification limits were estimated by internal calibration under the optimized conditions. The GC-FT-orbitrap-MS demonstrated its ability to separate 47 amino acid enantiomers with minimal co-elution. Furthermore, due to the high mass resolution and accuracy of FT-orbitrap-MS, with mass extraction, the S/N is close to zero, allowing average LOD values of 10⁻7 M, orders of magnitude lower than conventional GC-MS techniques. Finally, these conditions were tested for enantioselective analysis of amino acids on an analog of a pre-cometary organic material showing similarities to that of extraterrestrial materials.

Keywords:  Amino acids; Cometary ice analogs; GC-FT-Orbitrap-MS; Gas chromatography; High-resolution mass spectrometry

DOI:  https://doi.org/10.1016/j.chroma.2023.464118
Drug Metab Dispos. 2023 Jun 09. pii: DMD-MR-2022-001069. [Epub ahead of print]

Recent advances in mass spectrometry-based spatially resolved molecular imaging of drug disposition and metabolomics.

Yu Chen, Ying Liu, Ximei Li, Yan He, Weiwei Li, Ying Peng, Jiang Zheng.

  Mass spectrometric imaging (MSI) is a non-targeted, tag-free, high-throughput, and highly responsive analytical approach. The highly accurate molecular visualization detection technology enables to provide qualitative and quantitative analyses of biological tissues or cells scanned by mass spectrometry in situ, extracting known and unknown multiple compounds, and simultaneously assessing relative contents of targeting molecules by monitoring their molecular ions, and pinpointing the spatial locations of those molecules distributed. Five mass spectrometric imaging techniques and their characteristics are introduced in the review, including matrix-assisted laser desorption ionization (MALDI) mass spectrometry, secondary ion mass spectrometry (SIMS), desorption electrospray ionization (DESI) mass spectrometry, laser ablation electrospray ionization (LAESI) mass spectrometry, and laser ablation inductively coupled plasma (LA-ICP) mass spectrometry. The mass spectrometry-based techniques provide the possibility for spatial metabolomics with the capability of high throughput and precision detection. The approaches have been widely employed to spatially image not only metabolome of endogenous amino acids, peptides, proteins, neurotransmitters, and lipids, but also the disposition of exogenous chemicals, such as pharmaceutical agents, environmental pollutants, toxicants, natural products, and heavy metals. The techniques also provide us with spatial distribution imaging of analytes in single cells, tissue microregions, organs, and whole animals. Significance Statement The review article includes an overview of five commonly used mass spectrometers for spatial imaging and describes the advantages and disadvantages of each. Examples of the technology applications cover drug disposition, diseases, and omics. Technical aspects of relative and absolute quantification by mass spectrometric imaging and challenges for future new applications are discussed as well. The reviewed knowledge anticipates to benefit the development of new drugs and to better understand biochemical processes related to physiology and diseases.

Keywords:  Spatial signaling; drug disposition; mass spectrometry; metabolomics

DOI:  https://doi.org/10.1124/dmd.122.001069
Molecules. 2023 May 23. pii: 4268. [Epub ahead of print]28(11):

Validation and Simultaneous Monitoring of 311 Pesticide Residues in Loamy Sand Agricultural Soils by LC-MS/MS and GC-MS/MS, Combined with QuEChERS-Based Extraction.

Petros Tsiantas, Eleftheria Bempelou, Maria Doula, Helen Karasali.

  Soil can be contaminated by pesticide residues through agricultural practices, by direct application or through spray-drift in cultivations. The dissipation of those chemicals in the soil may pose risks to the environment and human health. A simple and sensitive multi-residue analytical method was optimized and validated for the simultaneous determination of 311 active substances of pesticides in agricultural soils. The method involves sample preparation with QuEChERS-based extraction, and determination of the analytes with a combination of GC-MS/MS and LC-MS/MS techniques. Calibration plots were linear for both detectors over the range of five concentration levels, using matrix-matched calibration standards. The obtained recoveries from fortified-soil samples ranged from 70 to 119% and from 72.6 to 119% for GC-MS/MS and LC-MS/MS, respectively, while precision values were <20% in all cases. As regards the matrix effect (ME), signal suppression was observed in the liquid chromatography (LC)-amenable compounds, which was further estimated to be negligible. The gas chromatography (GC)-amenable compounds showed enhancement in the chromatographic response estimated as medium or strong ME. The calibrated limit of quantification (LOQ) value was 0.01 μg g-1 dry weight for most of the analytes, while the corresponding calculated limit of determination (LOD) value was 0.003 μg g-1 d.w. The proposed method was subsequently applied to agricultural soils from Greece, and positive determinations were obtained, among which were non-authorized compounds. The results indicate that the developed multi-residue method is fit for the purpose of analyzing low levels of pesticides in soil, according to EU requirements.

Keywords:  GC-MS/MS; LC-MS/MS; matrix effect; method validation; multi-residue method; pesticide residues; soil

DOI:  https://doi.org/10.3390/molecules28114268
Front Pharmacol. 2023 ;14 1136735

Development of a UPLC-MS/MS method for simultaneous therapeutic drug monitoring of anti-hepatocellular carcinoma drugs and analgesics in human plasma.

Shijia Lu, Mingming Zhao, Limei Zhao, Guofei Li.

  In hepatocellular carcinoma treatment, sorafenib, oxaliplatin, 5-fluorouracil, capecitabine, lenvatinib, and donafenib are first-line drugs; regorafenib, apatinib, and cabozantinib are second-line drugs; and oxycodone, morphine, and fentanyl are commonly used analgesics. However, the high degree of inter- and intra-individual variability in the efficacy and toxicity of these drugs remains an urgent issue. Therapeutic drug monitoring (TDM) is the most reliable technical means for evaluating drug safety and efficacy. Therefore, we developed an ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method for simultaneous TDM of three chemotherapy drugs (5-fluorouracil, oxaliplatin, and capecitabin), six targeted drugs (sorafenib, donafenib, apatinib, cabozantinib, regorafenib, and lenvatinib), and three analgesics (morphine, fentanyl, and oxycodone). We extracted 12 analytes and isotope internal standards (ISs) from plasma samples by magnetic solid phase extraction (mSPE) and separated them using a ZORBAX Eclipse Plus C18 column with water containing 0.1% formic acid and methanol containing 0.1% formic acid as the mobile phase. The analytical performance of our method in terms of sensitivity, linearity, specificity, carryover, precision, limit of quantification, matrix effect, accuracy, dilution integrity, extraction recovery, stability, and crosstalk of all the analytes under different conditions met all the criteria stipulated by the guidelines of the Chinese Pharmacopoeia and U.S. Food and Drug Administration. The response function was estimated at 10.0-10 000.0 ng/mL for sorafenib, donafenib, apatinib, cabozantinib, regorafenib, and lenvatinib, and 20.0-20 000.0 ng/mL for 5-fluorouracil, oxaliplatin, capecitabin, morphine, fentanyl, and oxycodone, with a correlation of > 0.9956 for all compounds. The precision and accuracy of all analytes were < 7.21% and 5.62%, respectively. Our study provides empirical support for a simple, reliable, specific, and suitable technique for clinical TDM and pharmacokinetics.

Keywords:  UPLC-MS/MS; analgesics; chemotherapy and targeted drugs; hepatocellular carcinoma; human plasma; therapeutic drug monitoring

DOI:  https://doi.org/10.3389/fphar.2023.1136735