bims-metlip 2022-04-17 papers

bims-metlip

Biomed News

on Methods and protocols in metabolomics and lipidomics

Issue of 2022–04–17
twenty-six papers selected by
Sofia Costa, Icahn School of Medicine at Mount Sinai

automRm: An R Package for Fully Automatic LC-QQQ-MS Data Preprocessing Powered by Machine Learning.
BAFinder: A Software for Unknown Bile Acid Identification Using Accurate Mass LC-MS/MS in Positive and Negative Modes.
Coupling Stable Isotope Labeling and Liquid Chromatography-Trapped Ion Mobility Spectrometry-Time-of-Flight-Tandem Mass Spectrometry for De Novo Mosquito Ovarian Lipid Studies.
Molecular networking and collision cross section prediction for structural isomer and unknown compound identification in plant metabolomics: a case study applied to Zhanthoxylum heitzii extracts.
Mass recalibration for desorption electrospray ionization mass spectrometry imaging using endogenous reference ions.
Development of a liquid chromatography mass spectrometry method for the determination of vitamin K1, menaquinone-4, menaquinone-7 and vitamin K1-2,3 epoxide in serum of individuals without vitamin K supplements.
Liquid chromatography-tandem mass spectrometry based quantification of arginine metabolites including polyamines in different sample matrices.
Goslin 2.0 Implements the Recent Lipid Shorthand Nomenclature for MS-Derived Lipid Structures.
Ultrafast liquid chromatography-tandem mass spectrometry determination of donepezil in human plasma: application to a bioequivalence study.
Simultaneous quantification of trimethoprim metabolites in pediatric plasma.
A novel LC-MS/MS method for simultaneous estimation of acalabrutinib and its active metabolite acalabrutinib M27 in human plasma and application to a human pharmacokinetic study.
Targeted Lipidomics for Characterization of PUFAs and Eicosanoids in Extracellular Vesicles.
Development and validation of a sensitive LC-MS/MS method for pioglitazone: application towards pharmacokinetic and tissue distribution study in rats.
Validation-based model selection for 13C metabolic flux analysis with uncertain measurement errors.
Paper spray-atmospheric pressure photoionization-high resolution mass spectrometry for the direct analysis of neutral fluorinated compounds in waterproof impregnation sprays.
Real-time analysis of metabolites in vivo by online extraction electrospray ionization mass spectrometry coupled to microdialysis.
Analytical and Structural Tools of Lipid Hydroperoxides: Present State and Future Perspectives.
Retraction: High-throughput metabolomics identifies serum metabolic signatures in acute kidney injury using LC-MS combined with pattern recognition approach.
Identification of key lipid metabolites during metabolic dysregulation in the diabetic retinopathy disease mouse model and efficacy of Keluoxin capsule using an UHPLC-MS-based non-targeted lipidomics approach.
Simultaneous determination of poly- and perfluoroalkyl substances and organophosphorus flame retardants in serum by ultra performance liquid chromatography-tandem mass spectrometry.
Evaluation of fresh, frozen, and lyophilized fecal samples by SPME and derivatization methods using GC×GC-TOFMS.
Simultaneous determination of 12 illicit drugs in human plasma by the PRiME clover-shaped nano-titania functionalized covalent organic frameworks pass-through cleanup procedure followed by ultra-performance liquid chromatography-tandem mass spectrometry.
Simultaneous determination of 16 urinary metabolites of organophosphate flame retardants and organophosphate pesticides by solid phase extraction and ultra performance liquid chromatography coupled to tandem mass spectrometry.
LC-HRMS based method for suspect/non-targeted screening for biomarkers of chemical exposure in human urine.
Unravelling Prostate Cancer Heterogeneity Using Spatial Approaches to Lipidomics and Transcriptomics.
Biomarkers in disease diagnosis and the role of LC-MS and NMR: A Review.

Anal Chem. 2022 Apr 12.

automRm: An R Package for Fully Automatic LC-QQQ-MS Data Preprocessing Powered by Machine Learning.

Daniel Eilertz, Michael Mitterer, Joerg M Buescher.

Preprocessing of liquid chromatography-mass spectrometry (LC-MS) raw data facilitates downstream statistical and biological data analyses. In the case of targeted LC-MS data, consistent recognition of chromatographic peaks is a main challenge, in particular, for low abundant signals. Fully automatic preprocessing is faster than manual peak review and does not depend on the individual operator. Here, we present the R package automRm for fully automatic preprocessing of LC-MS data recorded in MRM mode. Using machine learning (ML) for detection of chromatographic peaks and quality control of reported results enables the automatic recognition of complex patterns in raw data. In addition, this approach renders automRm generally applicable to a wide range of analytical methods including hydrophilic interaction liquid chromatography (HILIC), which is known for sample-to-sample variations in peak shape and retention time. We demonstrate the impact of the choice of training data set, of the applied ML algorithm, and of individual peak characteristics on automRm's ability to correctly report chromatographic peaks. Next, we show that automRm can replicate results obtained by manual peak review on published data. Moreover, automRm outperforms alternative software solutions regarding the variation in peak integration among replicate measurements and the number of correctly reported peaks when applied to a HILIC-MS data set. The R package is freely available from gitlab (https://gitlab.gwdg.de/joerg.buescher/automrm).

DOI: https://doi.org/10.1021/acs.analchem.1c05224
Anal Chem. 2022 Apr 11.

BAFinder: A Software for Unknown Bile Acid Identification Using Accurate Mass LC-MS/MS in Positive and Negative Modes.

Yan Ma, Yang Cao, Xiaocui Song, Yuanying Zhang, Jing Li, Yankai Wang, Xiaoqing Wu, Xiangbing Qi.

Most LC-MS based bile acid analyses target common bile acids. The identification of unknown bile acids remains challenging in untargeted experiments. Here, a software named BAFinder was developed to improve the identification of unknown bile acids from accurate mass LC-MS/MS data in both the positive and negative ESI modes. A wide variety of bile acid structures were covered in BAFinder, including oxidized bile acids and sugar conjugates that were often ignored. The annotation of unknown bile acids was based on a thorough investigation of MS/MS fragmentation patterns of 84 bile acid reference standards in both modes. Specifically, BAFinder took the peak alignment result and MS/MS spectra, grouped candidate features in positive and negative modes, searched their representative MS/MS spectra against a MS/MS library, and used characteristic product ions and neutral losses to annotate bile acids not covered in the library. Finally, the number of hydroxyl groups and double bonds, conjugation, and isomer information of bile acids were reported with four different levels of annotation confidence. The use of BAFinder was demonstrated through successful application to the analysis of human plasma and urine samples, in which a total of 112 and 244 bile acids were annotated and 75 and 111 of them were confirmed with standards or synthesized compounds, respectively. The software is freely available at https://bafinder.github.io/.

DOI: https://doi.org/10.1021/acs.analchem.1c05648
Anal Chem. 2022 Apr 14.

Coupling Stable Isotope Labeling and Liquid Chromatography-Trapped Ion Mobility Spectrometry-Time-of-Flight-Tandem Mass Spectrometry for De Novo Mosquito Ovarian Lipid Studies.

Lilian V Tose, Cesar E Ramirez, Veronika Michalkova, Marcela Nouzova, Fernando G Noriega, Francisco Fernandez-Lima.

There is a need to better understand lipid metabolism during mosquito ovarian development. Lipids are the major source of energy supporting ovarian follicles development in mosquitoes. In this paper, we describe the complementary use of stable isotope labeling (SIL) and high-resolution mass spectrometry-based tools for the investigation of de novo triglycerides (TG) and diglycerides (DG) during the ovarian previtellogenic (PVG) stage (4-6 days posteclosion) of female adult Aedes aegypti. Liquid chromatography coupled to high-resolution trapped ion mobility spectrometry-parallel accumulation sequential fragmentation-time-of-flight tandem mass spectrometry (LC-TIMS-PASEF-TOF MS/MS) allowed the separation and quantification of nonlabeled and 2H/13C-labeled TG and DG species. Three SIL strategies were evaluated (H2O/2H2O with 50:50 and 95:5 mixtures, 13C-sucrose, and 13C-glucose). Results showed wide applicability with no signs of lipid ovarian impairment by SIL induced toxicity. The analytical workflow based on LC-TIMS-TOF MS/MS provided high confidence and high reproducibility for lipid DG and TG identification and SIL incorporation based on their separation by retention time (RT), collision cross section (CCS), and accurate m/z. In addition, the SIL fatty acid chain incorporation was evaluated using PASEF MS/MS. The 2H/13C incorporation into the mosquito diet provided information on how TG lipids are consumed, stored, and recycled during the PVG stage of ovarian development.

DOI: https://doi.org/10.1021/acs.analchem.1c05090
Anal Bioanal Chem. 2022 Apr 13.

Molecular networking and collision cross section prediction for structural isomer and unknown compound identification in plant metabolomics: a case study applied to Zhanthoxylum heitzii extracts.

Valentina Calabrese, Isabelle Schmitz-Afonso, Candice Prevost, Carlos Afonso, Abdelhakim Elomri.

  Mass spectrometry-based plant metabolomics allow large-scale analysis of a wide range of compounds and the discovery of potential new active metabolites with minimal sample preparation. Despite recent tools for molecular networking, many metabolites remain unknown. Our objective is to show the complementarity of collision cross section (CCS) measurements and calculations for metabolite annotation in a real case study. Thus, a systematic and high-throughput investigation of root, bark, branch, and leaf of the Gabonese plant Zhanthoxylum heitzii was performed through ultra-high performance liquid chromatography high-resolution tandem mass spectrometry (UHPLC-QTOF/MS). A feature-based molecular network (FBMN) was employed to study the distribution of metabolites in the organs of the plants and discover potential new components. In total, 143 metabolites belonging to the family of alkaloids, lignans, polyphenols, fatty acids, and amino acids were detected and a semi-quantitative analysis in the different organs was performed. A large proportion of medical plant phytochemicals is often characterized by isomerism and, in the absence of reference compounds, an additional dimension of gas phase separation can result in improvements to both quantitation and compound annotation. The inclusion of ion mobility in the ultra-high performance liquid chromatography mass spectrometry workflow (UHPLC-IMS-MS) has been used to collect experimental CCS values in nitrogen and helium (CCSN2 and CCSHe) of Zhanthoxylum heitzii features. Due to a lack of reference data, the investigation of predicted collision cross section has enabled comparison with the experimental values, helping in dereplication and isomer identification. Moreover, in combination with mass spectra interpretation, the comparison of experimental and theoretical CCS values allowed annotation of unknown features. The study represents a practical example of the potential of modern mass spectrometry strategies in the identification of medicinal plant phytochemical components.

Keywords:  Collision cross section; Liquid chromatography ion mobility mass spectrometry; Metabolomics; Molecular networks; Zhanthoxylum heitzii

DOI:  https://doi.org/10.1007/s00216-022-04059-7
BMC Bioinformatics. 2022 Apr 15. 23(1): 133

Mass recalibration for desorption electrospray ionization mass spectrometry imaging using endogenous reference ions.

Paolo Inglese, Helen Xuexia Huang, Vincen Wu, Matthew R Lewis, Zoltan Takats.

BACKGROUND: Mass spectrometry imaging (MSI) data often consist of tens of thousands of mass spectra collected from a sample surface. During the time necessary to perform a single acquisition, it is likely that uncontrollable factors alter the validity of the initial mass calibration of the instrument, resulting in mass errors of magnitude significantly larger than their theoretical values. This phenomenon has a two-fold detrimental effect: (a) it reduces the ability to interpret the results based on the observed signals, (b) it can affect the quality of the observed signal spatial distributions.
RESULTS: We present a post-acquisition computational method capable of reducing the observed mass drift by up to 60 ppm in biological samples, exploiting the presence of typical molecules with a known mass-to-charge ratio. The procedure, tested on time-of-flight and Orbitrap mass spectrometry analyzers interfaced to a desorption electrospray ionization (DESI) source, improves the molecular annotation quality and the spatial distributions of the detected ions.
CONCLUSION: The presented method represents a robust and accurate tool for performing post-acquisition mass recalibration of DESI-MSI datasets and can help to increase the reliability of the molecular assignment and the data quality.

DOI: https://doi.org/10.1186/s12859-022-04671-5
Clin Chem Lab Med. 2022 Apr 18.

Development of a liquid chromatography mass spectrometry method for the determination of vitamin K1, menaquinone-4, menaquinone-7 and vitamin K1-2,3 epoxide in serum of individuals without vitamin K supplements.

Andreas Meinitzer, Dietmar Enko, Sieglinde Zelzer, Florian Prüller, Nerea Alonso, Eva Fritz-Petrin, Markus Herrmann.

   OBJECTIVES: Vitamin K and metabolites have a beneficial role in blood coagulation, bone metabolism and growth. However, the determination of vitamin K concentrations in the blood in patients consuming a diet with naturally occurring vitamin K is currently challenging. We aim to develop a cost-effective and rapid method to measure vitamin K metabolites with potential application for clinics and research.
METHODS: We developed a simple liquid chromatography-tandem mass spectrometric (LC-MS/MS) method for the determination of vitamin K1, menaquinone-4 (MK-4), menaquinone-7 (MK-7) and vitamin K1-2,3 epoxide in human serum and validated the method in a study cohort of 162 patients tested for carbohydrate malabsorption and in 20 patients with oral phenprocoumon intake.
RESULTS: The overall precision (CVs) ranged between 4.8 and 17.7% in the specified working range (0.06-9.0 nmol/L for all analytes except for MK-7 with 0.04-6.16 nmol/L). In the malabsorption cohort samples, measured values were obtained for all different vitamin K metabolites except for vitamin K1-2,3 epoxide. This metabolite could be detected only in patients with phenprocoumon intake. The good performance of the method is especially achieved by the interaction of three factors: the use of lipase in the sample preparation, the use of an atypical fluorinated reversed phase column, and a logarithmic methanol gradient.
CONCLUSIONS: The described method is able to determine the concentration of four vitamin K metabolites in a time-efficient, simple and cost-effective manner. It can be suitable for both routine clinics and research.

Keywords:  mass spectrometry; menaquinon-4; menaquinon-7; vitamin K1; vitamin K1-2,3 epoxide

DOI:  https://doi.org/10.1515/cclm-2022-0192
J Chromatogr A. 2022 Apr 05. pii: S0021-9673(22)00216-3. [Epub ahead of print]1671 463021

Liquid chromatography-tandem mass spectrometry based quantification of arginine metabolites including polyamines in different sample matrices.

Mathias Langner, Ivona Mateska, Nicole Bechmann, Ben Wielockx, Triantafyllos Chavakis, Vasileia Ismini Alexaki, Mirko Peitzsch.

  The conditionally essential amino acid arginine and its metabolic products play an important role in different biological processes, such as metabolic regulation of the immune response, including macrophage activation and polarization and regulation of T cell function. Furthermore, the polyamine spermidine has a role in aging and age-related diseases. Additionally, altered polyamine metabolism may be associated with neurodegenerative diseases, while polyamine levels may present useful biomarkers associated with severity of Parkinson's disease or with progression of non-alcoholic fatty liver disease. In the present study, a simple, derivatization-free hydrophilic interaction liquid chromatography based tandem mass spectrometry (LC-MS/MS) method is described, that allows the accurate quantification of arginine and related amine, polyamine and acetylated polyamine metabolites in different experimental sample matrices, such as cell lysates, cell culture supernatants and tissues. Ten arginine metabolites, including citrulline, agmatine, ornithine, putrescine, spermidine, spermine, N1-acetylspermidine, N1-acetylspermine, N1,N12-diacetylspermine and arginine in conjunction with the metabolic cofactors S-adenosylhomocysteine and S-adenosylmethionine are simultaneously analyzed within a total LC-MS/MS run time of 9.5 min. The assay is suitable to quantify concentration ranges over multiple orders of magnitude for all metabolites with averaged accuracies observed at 103.2% ± 6.8%, 99.0% ± 4.2% and 100.4% ± 4.3% in cell lysates, cell culture supernatant and tissue extracts, respectively. Inter-day coefficients of variation ranged from 5.9 to 14.8% in cell lysates, 6.7 to 14.6% in cell culture supernatants and 5.3 to 12.0% in tissue extracts. The method was successfully applied to cell culture systems of different origin as well as different murine tissues and organs. The herein described LC-MS/MS method provides a simple tool for a fast and simultaneous analysis of arginine metabolites, including polyamines and their respective metabolic cofactors. Assay performance characteristics demonstrate suitability for applications in different experimental and preclinical settings.

Keywords:  Arginine metabolites; LC-MS/MS; Polyamines

DOI:  https://doi.org/10.1016/j.chroma.2022.463021
Anal Chem. 2022 Apr 11.

Goslin 2.0 Implements the Recent Lipid Shorthand Nomenclature for MS-Derived Lipid Structures.

Dominik Kopczynski, Nils Hoffmann, Bing Peng, Gerhard Liebisch, Friedrich Spener, Robert Ahrends.

Goslin is the first grammar-based computational library for the recognition/parsing and normalization of lipid names following the hierarchical lipid shorthand nomenclature. The new version Goslin 2.0 implements the latest nomenclature and adds an additional grammar to recognize systematic IUPAC-IUB fatty acyl names as stored, e.g., in the LIPID MAPS database and is perfectly suited to update lipid names in LIPID MAPS or HMDB databases to the latest nomenclature. Goslin 2.0 is available as a standalone web application with a REST API as well as C++, C#, Java, Python 3, and R libraries. Importantly, it can be easily included in lipidomics tools and scripts providing direct access to translation functions. All implementations are open source.

DOI: https://doi.org/10.1021/acs.analchem.1c05430
Transl Clin Pharmacol. 2022 Mar;30(1): 37-48

Ultrafast liquid chromatography-tandem mass spectrometry determination of donepezil in human plasma: application to a bioequivalence study.

Yan-Wen Huang, Li Ding, Yuan-Ming Chen, Wei-Chen Lin, Fei Lin, Yunsheng Hsieh.

  A liquid chromatography equipped with tandem mass spectrometric method using multi-stage flow rates was developed for the determination of donepezil in human plasma to support a randomized, crossover bioequivalence (BE) study in which healthy volunteers each received a single oral dose of the reference and test formulations of 10 mg donepezil hydrochloride. This integrated liquid chromatography with tandem mass spectrometry (LC-MS/MS) system with electrospray ionization and a deuterium-labeled internal standard (IS) were employed for the positive multiple-reaction-monitoring (MRM) analyses. The baseline separation using a high-resolution monolithic column under gradient and flexible flowrate conditions between donepezil and multiple interfering peaks from the extracted quality control, calibration standard and study plasma samples following simple protein precipitation extraction procedures was accomplished within 1.5 minutes. The ultrafast monolithic column performance in terms of chromatographic separation efficiency, peak asymmetry and resolution and retention time reproducibility was found to be sustainable. The linear dynamic range was detected over a concentration range of 0.2-50 ng/mL. The intra- and inter-day assay accuracy and precision were within 15% for the analyte in individual biological fluids. A positive correlation coefficient (r) greater than 0.995 for donepezil concentrations in study plasma samplers measured by the proposed and the other validated LC-MS/MS methods in support of a bioequivalence study was observed.

Keywords:  Bioequivalence; Donepezil; LC-MS/MS; Multi-stage Flow Rate

DOI:  https://doi.org/10.12793/tcp.2022.30.e1
J Chromatogr B Analyt Technol Biomed Life Sci. 2022 Apr 09. pii: S1570-0232(22)00136-2. [Epub ahead of print]1198 123232

Simultaneous quantification of trimethoprim metabolites in pediatric plasma.

Robert T Tessman, Whitney Nolte, Paul Toren, Kim Gibson, Linda Vu, Jennifer Goldman.

  The dual agent antibiotic, trimethoprim/sulfamethoxazole (TMP-SMX), has been prescribed to treat or prevent infections for over 50 years. However, there are no published validated analytical methods for the measurement of TMP metabolites in humans. We developed methodology enabling reliable quantification of TMP and 5 metabolites in human plasma. Chromatographic separation was achieved in less than 8 min using a biphenyl column. Analytes were detected in positive electrospray mode using a tandem Waters Xevo-TQ-XS mass spectrometer. Precision and accuracy values for all analytes were within 15% of nominal values during assay validation.

Keywords:  Idiosyncratic adverse drug reactions; Metabolism; Tandem mass spectrometry; Trimethoprim; Validated methodology

DOI:  https://doi.org/10.1016/j.jchromb.2022.123232
RSC Adv. 2022 Feb 22. 12(11): 6631-6639

A novel LC-MS/MS method for simultaneous estimation of acalabrutinib and its active metabolite acalabrutinib M27 in human plasma and application to a human pharmacokinetic study.

Venkat Rao Valluri, Naresh Kumar Katari, Chirag Khatri, Pankaj Kasar, Srinivasa Rao Polagani, Sreekanth Babu Jonnalagadda.

A simple, specific, selective and accurate bioanalytical method was developed and validated for simultaneous estimation of acalabrutinib and its active metabolite in human plasma using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Deuterated analogs of both the analytes were used as internal standards. The extraction of analytes and internal standards were evaluated from the human plasma by liquid-liquid extraction technique using methyl tertiary butyl ether (TBME). The separation of the analytes was carried out on Zorbax Eclipse XDB-C18 (150 × 4.6 mm, 5 μm) column with a mixture of acetonitrile and 10 mM ammonium formate in 0.1% formic acid buffer (65 : 35, v/v) as mobile phase at a flow rate of 1 mL min-1. The method linearity was determined in the widen concentration range from 5.000 ng mL-1 to 1600 ng mL-1 with r 2 > 0.99. The entire method validation was carried out as per the USFDA guidelines on bioanalytical method validation and all validation experiment results were found within acceptable limits. Clinical pharmacokinetic study of both the parent drug and its active metabolite was successfully performed on six healthy volunteers under fasting conditions by applying the present method.

DOI: https://doi.org/10.1039/d1ra09026g
Nutrients. 2022 Mar 22. pii: 1319. [Epub ahead of print]14(7):

Targeted Lipidomics for Characterization of PUFAs and Eicosanoids in Extracellular Vesicles.

Madlen Reinicke, Saikal Shamkeeva, Max Hell, Berend Isermann, Uta Ceglarek, Mitja L Heinemann.

  Lipids are increasingly recognized as bioactive mediators of extracellular vesicle (EV) functions. However, while EV proteins and nucleic acids are well described, EV lipids are insufficiently understood due to lack of adequate quantitative methods. We adapted an established targeted and quantitative mass spectrometry (LC-MS/MS) method originally developed for analysis of 94 eicosanoids and seven polyunsaturated fatty acids (PUFA) in human plasma. Additionally, the influence of freeze-thaw (FT) cycles, injection volume, and extraction solvent were investigated. The modified protocol was applied to lipidomic analysis of differently polarized macrophage-derived EVs. We successfully quantified three PUFAs and eight eicosanoids within EVs. Lipid extraction showed reproducible PUFA and eicosanoid patterns. We found a particularly high impact of FT cycles on EV lipid profiles, with significant reductions of up to 70%. Thus, repeated FT will markedly influence analytical results and may alter EV functions, emphasizing the importance of a standardized sample pretreatment protocol for the analysis of bioactive lipids in EVs. EV lipid profiles differed largely depending on the polarization of the originating macrophages. Particularly, we observed major changes in the arachidonic acid pathway. We emphasize the importance of a standardized sample pretreatment protocol for the analysis of bioactive lipids in EVs.

Keywords:  eicosanoids; extracellular vesicles; pre-analytics; quantitative lipidomics

DOI:  https://doi.org/10.3390/nu14071319
RSC Adv. 2021 Mar 16. 11(19): 11437-11443

Development and validation of a sensitive LC-MS/MS method for pioglitazone: application towards pharmacokinetic and tissue distribution study in rats.

Kusuma Kumari G, Praveen Thaggikuppe Krishnamurthy, Ravi Kiran Ammu V V V, Kurawattimath Vishwanath, S T Narenderan, B Babu, Nagappan Krishnaveni.

In the present study, a sensitive LC-MS/MS method was developed and validated to measure pioglitazone (PGZ) concentrations in rat plasma and tissues. The chromatographic separation was achieved by using a YMC Pro C18 column (100 mm × 4.6 mm, 3μ) with a mobile phase consisting of formic acid (0.1% v/v) and acetonitrile (5 : 95) at a flow rate of 0.7 mL min-1 and injection volume of 10 μL (IS: rosiglitazone). Mass spectrometric detection was done using triple quadrupole mass spectrometry using the ESI interface operating in a positive ionization mode. The developed method was validated over a linearity range of 1-500 ng mL-1 with detection and a lower quantification limit of 0.5 ng mL-1 and 1 ng mL-1. The method accuracy ranged from 95.89-98.78% (inter-day) & 93.39-97.68% (intra-day) with a precision range of 6.09-8.12% for inter-day & 7.55-9.87% for intra-day, respectively. The PGZ shows the highest C max of 495.03 ng mL-1 in plasma and the lowest C max, 24.50 ± 2.71 ng mL-1 in bone. The maximum T max of 5.00 ± 0.49 h was observed in bone and a minimum of 1.01 ± 0.05 h in plasma. The AUC(0-24 h and 0-∞) values are highest in plasma (1056.58 ± 65.78 & 1069.38 ± 77.50 ng h-1 mL-1) and lowest in brain (166.93 ± 15.70 &167.12 ± 16.77 ng h-1 mL-1), and the T 1/2 was highest in plasma (5.62 ± 0.74 h) and lowest in kidney (2.78 ± 0.19). The developed method was successfully used to measure the PGZ pharmacokinetic and tissue distribution. Further, the developed method could be utilized for validating target organ (adipose tissue) specific delivery of PGZ (nano-formulations) in addition to conventional dosage forms.

DOI: https://doi.org/10.1039/d1ra01126j
PLoS Comput Biol. 2022 Apr 11. 18(4): e1009999

Validation-based model selection for 13C metabolic flux analysis with uncertain measurement errors.

Nicolas Sundqvist, Nina Grankvist, Jeramie Watrous, Jain Mohit, Roland Nilsson, Gunnar Cedersund.

Accurate measurements of metabolic fluxes in living cells are central to metabolism research and metabolic engineering. The gold standard method is model-based metabolic flux analysis (MFA), where fluxes are estimated indirectly from mass isotopomer data with the use of a mathematical model of the metabolic network. A critical step in MFA is model selection: choosing what compartments, metabolites, and reactions to include in the metabolic network model. Model selection is often done informally during the modelling process, based on the same data that is used for model fitting (estimation data). This can lead to either overly complex models (overfitting) or too simple ones (underfitting), in both cases resulting in poor flux estimates. Here, we propose a method for model selection based on independent validation data. We demonstrate in simulation studies that this method consistently chooses the correct model in a way that is independent on errors in measurement uncertainty. This independence is beneficial, since estimating the true magnitude of these errors can be difficult. In contrast, commonly used model selection methods based on the χ2-test choose different model structures depending on the believed measurement uncertainty; this can lead to errors in flux estimates, especially when the magnitude of the error is substantially off. We present a new approach for quantification of prediction uncertainty of mass isotopomer distributions in other labelling experiments, to check for problems with too much or too little novelty in the validation data. Finally, in an isotope tracing study on human mammary epithelial cells, the validation-based model selection method identified pyruvate carboxylase as a key model component. Our results argue that validation-based model selection should be an integral part of MFA model development.

DOI: https://doi.org/10.1371/journal.pcbi.1009999
Anal Chim Acta. 2022 Apr 29. pii: S0003-2670(22)00291-4. [Epub ahead of print]1204 339720

Paper spray-atmospheric pressure photoionization-high resolution mass spectrometry for the direct analysis of neutral fluorinated compounds in waterproof impregnation sprays.

R Seró, J F Ayala-Cabrera, F J Santos, E Moyano.

  In this work, paper spray (PS) is combined with atmospheric pressure photoionization-mass spectrometry (PS-APPI-MS) for the determination of non-polar and low polar compounds, such as the neutral per- and polyfluorinated alkyl substances (PFAS). The proposed PS-APPI-MS method has been developed for the analysis of fluorotelomer alcohols (FTOHs), fluoroctanesulfonamides (FOSAs) and fluorooctane sulfonamido-ethanols (FOSEs), using both negative ion mode and high-resolution mass spectrometry (HRMS). The most critical working parameters (i.e., UV-krypton lamp position, sample drying time, spray dopant solvent and spray voltage) have been evaluated to study both the ionization behaviour and ionization efficiency. The best results were achieved using dopant-assisted PS-APPI-HRMS with toluene as dopant solvent. The most intense ions observed in the mass spectra, [M‒H]‒ for FOSAs and [M+O2]‒• for FTOHs and FOSEs, were selected and proposed for fast screening and quantitative analysis of target compounds in waterproof impregnation sprays samples using internal standard calibration method and being able to detect down to μg L-1 levels. The satisfactory values of the method quality parameters (detection capability, repeatability, trueness and linearity) demonstrated the good performance of the PS-APPI-HRMS method and allowed the identification and quantitation of some FTOHs (6:2 FTOH, 7-Me-6:2 FTOH, 8:2 FTOH, 10:2 FTOH) and N-MeFOSE at mg L-1 in some of the waterproof impregnation spray products analyzed. This low-cost PS-APPI-HRMS method allows a fast screening, with minimum sample preparation, of non-polar and low polar compounds simultaneously, which can significantly improve the throughput on routine laboratories.

Keywords:  Ambient mass spectrometry; Atmospheric pressure photoionization; Fluorocotanesulfonamides and sulfonamido-ethanols; Fluorotelomer alcohols; High-resolution mass spectrometry; Paper spray

DOI:  https://doi.org/10.1016/j.aca.2022.339720
Anal Chim Acta. 2022 May 01. pii: S0003-2670(22)00331-2. [Epub ahead of print]1205 339760

Real-time analysis of metabolites in vivo by online extraction electrospray ionization mass spectrometry coupled to microdialysis.

Tuo Li, Shumu Li, Junwen Shi, Xing Li, Jianan Liu, Hui Yang, Wenjing Wu, Lingyu Zhao, Zhenwen Zhao.

  In vivo and real-time analysis could reflect a more real biological state, which was of great significance to the study of complex life processes. In this work, we constructed an online extraction electrospray ionization (OE-ESI) ion source as the interface of microdialysis and mass spectrometry, which realized real-time analysis of metabolites in vivo without sample pretreatment process. The ion source was consisted of three coaxial capillaries, and the parameters of the ion source were optimized. The OE-ESI ion source could simultaneously extract, desalt and ionize the analyte, successfully perform MS analysis of analyte in high salt system, and overcome the ion suppression caused by salt ion. Compared with commercial ESI MS, the OE-ESI ion source had excellent salt tolerance and stability. MD-OE-ESI MS realized the real-time MS detection of metabolites in the living body, avoiding the complex desalting process. In the rat liver ischemia-reperfusion model, a total of 24 metabolites, including glucose, glutamate, glutamine, etc., were monitored in real time mode, and their concentrations had varying degrees of change during the experimental process compared with the control group. This platform, we believed, would be helpful for real-time monitoring of biological metabolites in vivo, and had great application prospects to study physiological processes.

Keywords:  In vivo; Mass spectrometry; Metabolites; Microdialysis

DOI:  https://doi.org/10.1016/j.aca.2022.339760
Molecules. 2022 Mar 25. pii: 2139. [Epub ahead of print]27(7):

Analytical and Structural Tools of Lipid Hydroperoxides: Present State and Future Perspectives.

Vassiliki G Kontogianni, Ioannis P Gerothanassis.

  Mono- and polyunsaturated lipids are particularly susceptible to peroxidation, which results in the formation of lipid hydroperoxides (LOOHs) as primary nonradical-reaction products. LOOHs may undergo degradation to various products that have been implicated in vital biological reactions, and thus in the pathogenesis of various diseases. The structure elucidation and qualitative and quantitative analysis of lipid hydroperoxides are therefore of great importance. The objectives of the present review are to provide a critical analysis of various methods that have been widely applied, and more specifically on volumetric methods, applications of UV-visible, infrared, Raman/surface-enhanced Raman, fluorescence and chemiluminescence spectroscopies, chromatographic methods, hyphenated MS techniques, NMR and chromatographic methods, NMR spectroscopy in mixture analysis, structural investigations based on quantum chemical calculations of NMR parameters, applications in living cells, and metabolomics. Emphasis will be given to analytical and structural methods that can contribute significantly to the molecular basis of the chemical process involved in the formation of lipid hydroperoxides without the need for the isolation of the individual components. Furthermore, future developments in the field will be discussed.

Keywords:  HPLC; IR; MS; NMR; Raman; fluorescence; hydroperoxides; lipids

DOI:  https://doi.org/10.3390/molecules27072139
RSC Adv. 2021 Jan 28. 11(10): 5722

Retraction: High-throughput metabolomics identifies serum metabolic signatures in acute kidney injury using LC-MS combined with pattern recognition approach.

Laura Fisher.

[This retracts the article DOI: 10.1039/C8RA01749B.].

DOI: https://doi.org/10.1039/d1ra90062e
RSC Adv. 2021 Jan 28. 11(10): 5491-5505

Identification of key lipid metabolites during metabolic dysregulation in the diabetic retinopathy disease mouse model and efficacy of Keluoxin capsule using an UHPLC-MS-based non-targeted lipidomics approach.

Nan Ge, Ling Kong, Ai-Hua Zhang, Ye Sun, Man-Qian Zhao, Bo Zhang, Lei Xu, Xiao Ke, Hui Sun, Xi-Jun Wang.

Diabetic retinopathy (DR) is an important complication of diabetes, and is currently the main cause of blindness among young adults in the world. Previous studies have shown that Keluoxin (KLX) capsules have a significant effect on DR in C57BL/KsJ/db-/- mice (db/db mice), however the unclear mechanism limits its further clinical application and actual value. Further research is urgently needed for the treatment of DR disease. Discovery of key lipid biomarkers and metabolic pathways can reveal and explore the molecular mechanisms related to DR development and discover the effect of Keluoxin (KLX) capsule against DR in db/db mice. Lipidomics has been used for characterizing the pathological conditions via identification of key lipid metabolites and the metabolic pathway. In this study, the high-throughput lipidomics using UHPLC-Q-TOF/MS combined with multivariate statistical analysis, querying multiple network databases and employing ingenuity pathway analysis (IPA) method for molecular target prediction. A total of 30 lipid biomarkers were identified and 7 metabolic pathways including arachidonic acid metabolism and steroid hormone biosynthesis were found. The preventive effect of KLX intervention can regulate 22 biomarkers such as LysoPA(16:0/0:0), prostaglandin D2, cortisol and γ-linolenic acid, etc. IPA platform has predicted that PI3K/MAPK pathway are closely related to DR development. It also showed that high-throughput lipidomics combined with multivariate statistical analysis could deep excavate of the biological significance of the big data, and can provide molecular targets information about the disease treatment.

DOI: https://doi.org/10.1039/d0ra00343c
Rapid Commun Mass Spectrom. 2022 Apr 11. e9312

Simultaneous determination of poly- and perfluoroalkyl substances and organophosphorus flame retardants in serum by ultra performance liquid chromatography-tandem mass spectrometry.

Jinhong Li, Qiang Li, Jiufeng Li, Yunhui Zhang.

RATIONALE Poly- and perfluoroalkyl substances (PFASs) and organophosphorus flame retardants (OPFRs) are two types of emerging organic pollutants with potential human health hazards. Here, a rapid and sensitive method was developed for the determination of sixteen PFASs and seven OPFRs in human serum by ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS).
METHOD: After optimized the chromatographic and mass spectrometric conditions, respectively, 100 μL of serum sample was liquid-liquid extracted using 8 mL methyl tert butyl ether. The 23 targets were quantified within 8 mins. All targets were quantified by isotope internal standard method in both negative-ion mode and positive-ion mode by UPLC-MS/MS.
RESULTS: Method was validated in terms of sensitivity, linearity, precision, and accuracy. The limit of detection ranged between 0.004 and 0.650 ng/ml. Recoveries ranged from70.0% to 118.9% with a relative standard deviation lower than 20%. The developed method was successfully applied to analyze targeted analytes in human serum samples. 13 of 23 analytes were detected in over 50% of samples.
CONCLUSION: A sensitive and rapid method was developed to quantify 16 PFASs and 7 OPFRs in serum. Sensitivity, linearity, recovery, and precision were validated and found satisfactory. This method can be a valuable tool for evaluation of exposure to both PFASs and OPFRs with high separation efficiency and sensitivity.

DOI: https://doi.org/10.1002/rcm.9312
Metabolomics. 2022 Apr 15. 18(4): 25

Evaluation of fresh, frozen, and lyophilized fecal samples by SPME and derivatization methods using GC×GC-TOFMS.

Seo Lin Nam, Kieran Tarazona Carrillo, A Paulina de la Mata, Olle M de Bruin, Evgueni Doukhanine, James Harynuk.

   INTRODUCTION: Feces is a highly complex matrix containing thousands of metabolites. It also contains live bacteria and enzymes, and does not have a static chemistry. Consequently, proper control of pre-analytical parameters is critical to minimize unwanted variations in the samples. However, no consensus currently exists on how fecal samples should be stored/processed prior to analysis.
OBJECTIVE: The effects of sample handling conditions on fecal metabolite profiles and abundances were examined using comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (GC×GC-TOFMS).
METHODS: Solid-phase microextraction (SPME) and derivatization via trimethylsilylation (TMS) were employed as complementary techniques to evaluate fresh, frozen, and lyophilized fecal samples with expanded coverage of the fecal metabolome. The total number of detected peaks and the signal intensities were compared among the different handling conditions.
RESULTS: Our analysis revealed that the metabolic profiles of fecal samples depend greatly on sample handling and processing conditions, which had a more pronounced effect on results obtained by SPME than by TMS derivatization. Overall, lyophilization resulted in a greater amount of total and class-specific metabolites, which may be attributed to cell lysis and/or membrane disintegration.
CONCLUSIONS: A comprehensive comparison of the sample handling conditions provides a deeper understanding of the physicochemical changes that occur within the samples during freezing and lyophilization. Based on our results, snap-freezing at -80 °C would be preferred over lyophilization for handling samples in the field of fecal metabolomics as this imparts the least change from the fresh condition.

Keywords:  GC×GC-TOFMS; SPME; derivatization; feces; lyophilization; metabolomics; microbiome

DOI:  https://doi.org/10.1007/s11306-022-01881-z
J Chromatogr A. 2022 Apr 06. pii: S0021-9673(22)00217-5. [Epub ahead of print]1671 463022

Simultaneous determination of 12 illicit drugs in human plasma by the PRiME clover-shaped nano-titania functionalized covalent organic frameworks pass-through cleanup procedure followed by ultra-performance liquid chromatography-tandem mass spectrometry.

Yun Zhang, Yong-Gang Zhao, Yan Zhu, Jia-Wei Shi, Ting Cai, Shun Zhang.

  A rapid and sensitive method based on PRiME (process, robustness, improvements, matrix effects, ease of use) pass-through cleanup procedure and ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) for the simultaneous determination of 12 illicit drugs in human plasma was developed and validated. The clover-shaped nano-titania functionalized covalent organic frameworks (CSTF-COFs) has been evaluated in the PRiME pass-through cleanup procedure to remove blood phospholipids from plasma samples. Ion suppression effects can be dramatically reduced by CSTF-COFs based PRiME pass-through cleanup procedure. Under the optimal conditions, the results showed satisfactory recoveries between 85.8% and 109%. Acceptable precision and accuracy were also obtained with RSD values less than 15.0% and RE values below 13.3%. The limits of detections (LODs) of 12 illicit drugs were in the range of 0.018-0.360 µg/L. Furthermore, the PRiME CSTF-COFs cartridge could be conveniently regenerated and reused for 40-50 cycles. The proposed method was applied to real plasma samples from suspected drug abusers, which was proved to be reliable and robust for drug screening in clinical and forensic toxicology.

Keywords:  Functionalized covalent organic frameworks; Human plasma; Illicit drugs; PRiME pass-through cleanup procedure; Ultra-performance liquid chromatography-tandem mass spectrometry

DOI:  https://doi.org/10.1016/j.chroma.2022.463022
Chemosphere. 2022 Apr 12. pii: S0045-6535(22)01078-5. [Epub ahead of print] 134585

Simultaneous determination of 16 urinary metabolites of organophosphate flame retardants and organophosphate pesticides by solid phase extraction and ultra performance liquid chromatography coupled to tandem mass spectrometry.

Qi Lu, Nan Lin, Xiaomeng Cheng, Tao Yuan, Yan Zhang, Yu Gao, Yankai Xia, Yuning Ma, Ying Tian.

  Organophosphate flame retardants (OPFRs) and organophosphate pesticides (OPPs), pertaining to organophosphate esters, are ubiquitous in environment and have been verified to pose noticeable risks to human health. To evaluate human exposures to OPFRs and OPPs, a fast and sensitive approach based on a solid phase extraction (SPE) followed by the ultra-high-performance liquid chromatography coupled to tandem mass spectrometry (UPLC-MS/MS) detection has been developed for the simultaneous analysis of multiple organophosphorus metabolites in urine. The method allows the identification and quantification of ten metabolites of the most common OPFRs and all six dialkylphosphates (DAPs) of OPPs concerning the population exposure characteristics. The method provided good linearities (R2 = 0.998-0.999), satisfactory method detection limits (MDLs) (0.030-1.129 ng/mL) and only needed a small volume (200 μL) of urine. Recovery rates ranged 73.4-127.1% at three spiking levels (2, 10 and 25 ng/mL urine), with both intra- and inter-day precision less than 14%. The good correlations for DAPs in a cross-validation test with a previous gas chromatography-mass spectrometry (GC-MS) method and a good inter-laboratory agreement for several OPFR metabolites in a standard reference material (SRM 3673) re-enforced the precision and validity of our method. Finally, the established method was successfully applied to analyze 16 organophosphorus metabolites in 35 Chinese children's urine samples. Overall, by validating the method's sensitivity, accuracy, precision, reproducibility, etc., data reliability and robustness were ensured; and the satisfactory pilot application on real urine samples demonstrated feasibility and acceptability of this method for being implemented in large population-based studies.

Keywords:  Organophosphate flame retardants; Organophosphate pesticides; Solid-phase extraction; UPLC-MS/MS; Urine metabolites

DOI:  https://doi.org/10.1016/j.chemosphere.2022.134585
Chemosphere. 2022 Apr 09. pii: S0045-6535(22)01043-8. [Epub ahead of print]300 134550

LC-HRMS based method for suspect/non-targeted screening for biomarkers of chemical exposure in human urine.

Žiga Tkalec, Garry Codling, Jana Klánová, Milena Horvat, Tina Kosjek.

  Every day we are exposed to a cocktail of anthropogenic compounds many of which are biologically active and capable of inducing negative effects. The simplest way to monitor contaminants in a population is via human biomonitoring (HBM), however conventional targeted approaches require foreknowledge of chemicals of concern, often have compound specific extractions and provide information only for those compounds. This study developed an extraction process for human biomarkers of interest (BoE) in urine that is less compound specific. Combining this with an ultra-high resolution mass spectrometer capable of operating in full scan, and a suspect and non-targeted analysis (SS/NTA) approach, this method provides a more holistic characterization of human exposure. Sample preparation development was based on enzymatically hydrolysed urine spiked with 34 native standards and extracted by solid-phase extraction (SPE). HRMS data was processed by MzMine2 and 80% of standards were identified in the final data matrix using typical NTA data processing procedures.

Keywords:  Biomonitoring; Exposome; HBM4EU; Non-targeted; Sample preparation; Xenobiotic

DOI:  https://doi.org/10.1016/j.chemosphere.2022.134550
Cancers (Basel). 2022 Mar 27. pii: 1702. [Epub ahead of print]14(7):

Unravelling Prostate Cancer Heterogeneity Using Spatial Approaches to Lipidomics and Transcriptomics.

Shadrack M Mutuku, Xander Spotbeen, Paul J Trim, Marten F Snel, Lisa M Butler, Johannes V Swinnen.

  Due to advances in the detection and management of prostate cancer over the past 20 years, most cases of localised disease are now potentially curable by surgery or radiotherapy, or amenable to active surveillance without treatment. However, this has given rise to a new dilemma for disease management; the inability to distinguish indolent from lethal, aggressive forms of prostate cancer, leading to substantial overtreatment of some patients and delayed intervention for others. Driving this uncertainty is the critical deficit of novel targets for systemic therapy and of validated biomarkers that can inform treatment decision-making and to select and monitor therapy. In part, this lack of progress reflects the inherent challenge of undertaking target and biomarker discovery in clinical prostate tumours, which are cellularly heterogeneous and multifocal, necessitating the use of spatial analytical approaches. In this review, the principles of mass spectrometry-based lipid imaging and complementary gene-based spatial omics technologies, their application to prostate cancer and recent advancements in these technologies are considered. We put in perspective studies that describe spatially-resolved lipid maps and metabolic genes that are associated with prostate tumours compared to benign tissue and increased risk of disease progression, with the aim of evaluating the future implementation of spatial lipidomics and complementary transcriptomics for prognostication, target identification and treatment decision-making for prostate cancer.

Keywords:  MALDI; biomarkers; lipidomics; lipids; mass spectrometry imaging; metabolomics; prostate cancer

DOI:  https://doi.org/10.3390/cancers14071702
Curr Pharm Des. 2022 Apr 08.

Biomarkers in disease diagnosis and the role of LC-MS and NMR: A Review.

Irtiza Ashaq, Aadil Ahmad Sheikh, Nikita Beri, Shruti Mittal, Mohd Javed Naim, Ozair Alam, Sandhya Bawa.

   BACKGROUND: Biomarker discovery is regarded as an essential tool to assess early disease diagnosis, disease progression, drug response, disease prevention, and drug target identification. The identification of biomarkers using different detection techniques and the characterization of these biomarkers is of great clinical importance. The integration of proteomics and metabolomics with LC-MS and NMR has every potential to map the early biochemical changes in diseases, making the identification of biomarkers facile. A vigorous and sentient technique is insisted upon to analyze an advanced biological system. The characteristics like susceptibility, explicitness, correctness, pace, and enhanced productiveness have led to the evolution of LC-MS for being a paramount methodical manifesto for biomarker analysis and discovery. The same technology has been employed to study large molecules such as nucleic acids and proteins. NMR allows nondestructive identification and quantification of an immense aggregate of unconventional metabolite biomarkers in both biofluids and tissues, therefore metabolomics based on NMR has demonstrated a substantial assurance in the diagnosis of a disease as well as biomarker discovery.
OBJECTIVES: This article highlights biomarker identification tools in different diseases and the current role of LC-MS and NMR in biomarker discovery for disease diagnosis.
METHODS: The role of LC-MS and NMR has been studied thoroughly as a disease diagnosis tool.
RESULTS: The advancements in Mass and 1H NMR analysis as well as their amalgamation and multifaceted scrutiny of statistical data commit increased efficiency in premature detection of disease, identification of impaired metabolic reactions, hence drug discovery.
CONCLUSION: The review focuses on the integration of biomarker identification for disease diagnostics using emerging high-throughput technologies and will be necessary to achieve the 'personalization' of treatment and disease prevention.

Keywords:  Biomarker; Disease diagnostics; Drug target Identification; LC-MS; NMR

DOI:  https://doi.org/10.2174/1381612828666220408233542