bims-metlip 2025-01-05 papers

bims-metlip

Biomed News

on Methods and protocols in metabolomics and lipidomics

Issue of 2025–01–05
twenty-six papers selected by
Sofia Costa, Matterworks

Validated LC-MS/MS Method for the Determination of Paxalisib on Mouse Dried Blood Spots: An Application to Pharmacokinetic Study in Mice.
Simultaneous Determination of Vitamins A and E and Their Generated Metabolites in Human Serum by LC-MS/MS.
A Simple and Sensitive LC-MS/MS Method for the Determination of Mobocertinib and Its Metabolite Desmethyl-Mobocertinib in Human Plasma and Its Application to Clinical Pharmacokinetic Study.
Streamlined Vitamin D Metabolite Fingerprinting Analysis Using Isotope-Coded Multiplexing MS with Cost-Effective One-Pot Double Derivatization.
Enalomics: A Mass Spectrometry-Based Approach for Profiling, Identifying, and Semiquantifying Enals in Biological Samples.
Highly Sensitive LC-MS/MS Method for Determination of Dexamethasone in Rat Plasma and Brain Tissue: An Application to Pharmacokinetic Study in Rats.
Column Screening and Development of HILIC and RPLC Methods Coupled to Tandem Mass Spectrometry for the Monitoring of Albumin on Cysteine 34 Exposed to Mustard Agents.
Glial Biologist's Guide to Mass Spectrometry-Based Lipidomics: A Tutorial From Sample Preparation to Data Analysis.
Evaluation of the Impact of HIFU on Peptide Bond Formation: A Study Using SPE-LC-MS/MS Methodology.
Advancing characterization of pyrolysis products: Comprehensive gas chromatography methods for analytes in gas and liquid phases.
Bioanalysis of protein-unbound prednisolone in serum using equilibrium dialysis followed by liquid chromatography-tandem mass spectrometry.
Protomix: a Python package for 1H-NMR metabolomics data preprocessing.
Liquid Chromatography Combined With Tandem Mass Spectrometry for the Pharmacokinetic and Metabolism Studies of PROTAC ARV-471 in Rats.
Development of a liquid chromatography-mass spectrometry based targeted metabolomics method for discovering diagnostic biomarkers in Kawasaki disease.
Non-targeted LC-MS metabolomics reveals serum metabolites for high-altitude adaptation in Tibetan donkeys.
Untargeted metabolomics combined with lipidomics revealed the effects of myocardial infarction and exercise rehabilitation on blood circulation metabolism of patients based on liquid chromatography-mass spectrometry.
Universal, untargeted detection of bacteria in tissues using metabolomics workflows.
OligoDistiller: A Platform Agnostic Software Tool for MS and MS2 Data Analysis of Complex Oligonucleotides and Their Impurities.
Non-suppressed ion chromatography-tandem electrospray mass spectrometry using a short column for simultaneous analysis of dichloroacetic acid, trichloroacetic acid, and bromate: aqueous ammonia as the eluent additive.
FREDA: A Web Application for the Processing, Analysis, and Visualization of Fourier-Transform Mass Spectrometry Data.
Development and thorough evaluation of a multi-omics sample preparation workflow for comprehensive LC-MS/MS-based metabolomics, lipidomics and proteomics datasets.
Identification of serum biomarkers for cystic echinococcosis in sheep through untargeted metabolomic analysis using LC-MS/MS technology.
A Doped Surface Ionization Method for Ion Mobility Spectrometry.
An improved matrix deposition technique for thin layer chromatography coupled to MALDI-TOF mass spectrometry (TLC-MALDI).
NMRformer: A Transformer-Based Deep Learning Framework for Peak Assignment in 1D 1H NMR Spectroscopy.
Computational Methods for Data Integration and Imputation of Missing Values in Omics Datasets.

Biomed Chromatogr. 2025 Feb;39(2): e6071

Validated LC-MS/MS Method for the Determination of Paxalisib on Mouse Dried Blood Spots: An Application to Pharmacokinetic Study in Mice.

Ashok Zakkula, M Akiful Haque.

  Paxalisib is a dual PI3K/mTOR inhibitor, being used in advanced cancer treatment. In this research, we report a validated LC-MS/MS method for quantifying paxalisib from mouse dried blood spot (DBS). We validated the method in-line with the FDA guidelines. Liquid-liquid extraction technique was used to extract paxalisib from the DBS discs. We used a Chromolith RP-18 end cap (100 × 4.6 mm) column and isocratic mobile phase for the chromatographic separation of paxalisib and the internal standard (IS, dasatinib). The flow was 0.80 mL/min. In the optimized chromatographic conditions, the retention of paxalisib and the IS was ~2.13 and 2.06 min, respectively. Each injection total run time was 2.50 min. The MS/MS ion transitions monitored were m/z 383.2 → 309.1 and 488.1 → 410.1 for paxalisib and the IS, respectively. We have used a broad calibration range (1.24-3762 ng/mL) with a determination coefficient (r2) of 0.995. All the validation parameters assessed met the acceptance criteria, and hematocrit had no effect on DBS Paxalisib concentrations. We have used the validated method to derive the intravenous and oral pharmacokinetic parameters by quantifying paxalisib in mouse blood and correlated with mice pharmacokinetic data.

Keywords:  DBS; LC–MS/MS; method validation; mouse blood; paxalisib; pharmacokinetics

DOI:  https://doi.org/10.1002/bmc.6071
Biomed Chromatogr. 2025 Jan;39(1): e6064

Simultaneous Determination of Vitamins A and E and Their Generated Metabolites in Human Serum by LC-MS/MS.

Yongjuan Jia, Xingli Liu, Chunran Liu, Yongmei Chen, Wei Li.

  In the context of personalized and precision medicine, simultaneous monitoring of different forms of vitamins A and E and their metabolites could help us better understand the status of vitamins A and E in the body. The aim of this study was to establish a method for simultaneous determination of 13 kinds of vitamins A and E and their metabolites in human serum. Serum samples were directly detected by LC-MS/MS after deproteinization. Chromatographic and mass spectrometry parameters were optimized to achieve good separation and sensitivity for these analytes, especially for isomers. Finally, all analytes were effectively separated on Kinetex biphenyl stationary phase. The method covered a large profile of vitamins A and E and their metabolites in a run time only of 10 min. Good linearities were achieved in the quantitative range for each analyte with the correlation coefficients higher than 0.9916. The recoveries were in the range of 78.8%-111.6% with the intraday and interday precisions within 9.6%. This method was simple, sensitive, and accurate and had been successfully applied for the determination of vitamins A and E and their metabolites in human serum samples and could provide technical support for clinical nutritional evaluation of these vitamins.

Keywords:  LC–MS/MS; metabolites; serum; vitamin A; vitamin E

DOI:  https://doi.org/10.1002/bmc.6064
Biomed Chromatogr. 2025 Feb;39(2): e6063

A Simple and Sensitive LC-MS/MS Method for the Determination of Mobocertinib and Its Metabolite Desmethyl-Mobocertinib in Human Plasma and Its Application to Clinical Pharmacokinetic Study.

Fan Tang, Xiaoli Hou, Jiajie Chen, Yasen Cao, Yixia Wang, Hong Cheng.

  Mobocertinib is a potent selective tyrosine kinase inhibitor approved for the treatment of non-small cell lung cancer with activating EGFR exon 20 insertions. The aim of this study was to develop a procedure for liquid chromatography tandem mass spectrometry (LC-MS/MS) for the determination of mobocertinib and its metabolite desmethyl-mobocertinib in human plasma. The human plasma samples were precipitated with acetonitrile and analyzed using a Waters ACQUITY BEH C18 column coupled to a triple quadrupole mass spectrometer. Separation was executed using the acetonitrile-0.1% formic acid solution with gradient elution, at a flow rate of 0.4 mL/min. Mobocertinib and desmethyl-mobocertinib were monitored by multiple reaction monitoring (MRM) with m/z 586.5 > 72.2 and 572.4 > 473.2, respectively. The procedure demonstrated excellent linearity (r > 0.997) within the concentration range of 0.1-200 ng/mL for both analytes. Precision in relative standard deviation was < 9.37% for mobocertinib and < 12.03% for desmethyl-mobocertinib. Accuracy in relative error was within -7.23% to 9.18% for mobocertinib and -2.78% to 9.87% for desmethyl-mobocertinib. Extraction recovery was > 80% for both analytes. The validated LC-MS/MS method was successfully applied to the pharmacokinetic study of mobocertinib and desmethyl-mobocertinib in healthy human volunteers with K2EDTA as anticoagulant after a single dose of mobocertinib (160 mg).

Keywords:  LC‐MS/MS; clinical pharmacokinetics; desmethyl‐mobocertinib; mobocertinib

DOI:  https://doi.org/10.1002/bmc.6063
ACS Omega. 2024 Dec 24. 9(51): 50660-50670

Streamlined Vitamin D Metabolite Fingerprinting Analysis Using Isotope-Coded Multiplexing MS with Cost-Effective One-Pot Double Derivatization.

Pascal Schorr, Caroline S Stokes, Dietrich A Volmer.

In this study, we extended a previously developed one-pot double derivatization reaction to establish the first routine isotope-coded multiplex derivatization for vitamin D and its metabolites for application in clinical environments, using commercial reagents, without the need for specialized reagents and advanced synthesis requirements. The original derivatization process consisted of using both a Cookson-type reagent and derivatization of hydroxyl groups. Initially, the analytes are derivatized by a Diels-Alder reaction using 4-phenyl-1,2,4-triazoline-3,5-dione (PTAD), followed by acetylation using acetic anhydride, catalyzed by 4-dimethylaminopyridine at room temperature. To enable sample multiplexing, we utilized acetic anhydride as well as the d 3- isotopologue of acetic anhydride, generating d 3- and d 6-products of the investigated vitamin D3 metabolites. This approach not only allowed for the simultaneous measurement of two samples within a single LC-MS/MS run but also improved the LC separation of the important 25-hydroxyvitamin D3 epimers (3α-25(OH)D3 and 3β-25(OH)D3) on a conventional C-18 column, addressing a significant challenge in vitamin D analysis. Typically, the separation of these epimers after PTAD derivatization cannot be performed on C-18 columns, necessitating the use of pentafluorophenylpropyl (PFP) stationary phases. However, PFP columns are not as stable as C-18 in long-term use, wherein the acetylation of the C-3 hydroxyl group provided a solution by enhancing chromatographic selectivity and achieving the baseline separation of the metabolites 24,25(OH)2D3, 3α-25(OH)D3, 3β-25(OH)D3, and vitamin D3 using a C-18 column with methanol/water gradient elution. The described duplex derivatization was tested on 40 serum samples of patients with chronic liver diseases (CLD). Additionally, the method was evaluated in terms of linearity, accuracy, precision, and interferences between heavy and light tag samples using both commercial quality control samples and in-house quality control and calibration samples.

DOI: https://doi.org/10.1021/acsomega.4c08675
Anal Chem. 2025 Jan 02.

Enalomics: A Mass Spectrometry-Based Approach for Profiling, Identifying, and Semiquantifying Enals in Biological Samples.

Congyu Ma, Wen Zhang, Jialong Jing, Zhe Wang, Ning Sheng, Zhuoling An, Jinlan Zhang.

Human cells generate a bulk of aldehydes during lipid peroxidation (LPO), influencing critical cellular processes, such as oxidative stress, protein modification, and DNA damage. Enals, highly reactive α,β-unsaturated aldehydic metabolites, are implicated in various human pathologies, especially neurodegenerative disorders, cancer, and cardiovascular diseases. Despite their importance, endogenous enals remain poorly characterized, primarily due to their instability and low abundance. Herein, we introduced "enalomics," a mass spectrometry (MS)-based approach for profiling, identifying, and semiquantifying enals in biological samples. Derivatization with 2,4-dinitrophenylhydrazine and treatment with ascorbic acid stabilized enals in biological matrices and provided a unique MS fragment ([M-H-47]-) for reliable enal identification. Utilizing precursor ion scanning, dynamic multiple reaction monitoring, high-resolution MS, and mathematical correlations between retention times and carbon numbers of enals, we identified 157 enals (127 newly reported) with tissue-specific profiles in rats and 29 enals (24 newly reported) in human plasma. To the best of our knowledge, this represents the comprehensive analysis of enals, i.e., "enalomics," in biological samples. Enalomics demonstrated significant alterations in enal metabolism in rats with myocardial injury, highlighting the potential of medium- and short-chain plasma enals as sensitive diagnostic biomarkers. Further application of enalomics in patients with myocardial infarction (MI) identified 14 plasma diagnostic biomarkers. Receiver operating characteristic curves showed good discrimination (area under curve ≥ 0.8603, p ≤ 0.0043). This research advances the understanding of LPO products and emphasizes the roles of enals in human diseases, offering good prospects for early screening, diagnosis, and clinical interventions targeting LPO products in MI patients.

DOI: https://doi.org/10.1021/acs.analchem.4c02842
Biomed Chromatogr. 2025 Jan;39(1): e6059

Highly Sensitive LC-MS/MS Method for Determination of Dexamethasone in Rat Plasma and Brain Tissue: An Application to Pharmacokinetic Study in Rats.

Rama Murthi Bestha, Ashok Zakkula, Madipelli Keerthana, Sandeep Kaddare, Niranjan Veerla, Ramesh Mullangi, Sreekanth Dittakavi.

  A highly sensitive and rapid LC-MS/MS method was developed and validated for the quantification of dexamethasone in rat plasma and brain tissue. Protein precipitation method was used for sample preparation. The separation of dexamethasone and the IS (labetalol) was achieved on an Atlantis dC18 column using an isocratic mobile phase (10 mM ammonium formate and acetonitrile, 25/75, v/v) delivered at 0.7 mL/min flow-rate. Dexamethasone and the IS were eluted at 1.03 and 1.06 min, respectively. The MS/MS transitions monitored were m/z 393.100 → 373.100 (dexamethasone) and 329.100 → 91.100 (IS). Method validation was performed as per FDA guidelines and all parameters met the acceptance criteria. The assay was validated with a quantification range of 0.05-1046 ng/mL in both matrices. The intraday and interday precision for were in the range of 2.62-7.28 and 2.76%-6.98% and 2.24-6.85 and 2.97%-6.37%, in plasma and brain tissue, respectively. Dexamethasone was stable in a series of stability conditions in both matrices. Post-intravenous administration to rats, dexamethasone concentrations in plasma and brain tissue were quantifiable up to 24 and 10 h, respectively. Dexamethasone half-life was ~2.30 h. Dexamethasone exhibited low clearance and moderate volume of distribution in plasma but in brain tissue the clearance and volume of distribution were high.

Keywords:  LC–MS/MS; dexamethasone; method validation; pharmacokinetics; rat brain tissue; rat plasma

DOI:  https://doi.org/10.1002/bmc.6059
J Sep Sci. 2025 Jan;48(1): e70065

Column Screening and Development of HILIC and RPLC Methods Coupled to Tandem Mass Spectrometry for the Monitoring of Albumin on Cysteine 34 Exposed to Mustard Agents.

Lorenzo Avigo, Audrey Combès, Charlotte Desoubries, Christine Albaret, Anne Bossée, Emmanuel Joubert, Valérie Pichon.

  Adduction on protein nucleophile sites by mustard agents can be monitored to assess detection of retrospective exposure to these agents. Cysteine 34 (Cys34) on human serum albumin was selected as the target of choice. This work targets di- and tripeptides adducted on Cys34 by sulfur mustard, sesquimustard, and nitrogen mustards separated in hydrophilic liquid chromatography (HILIC) and Reversed-Phase (RP) mode. The effect of several mobile phase additives on the mass spectrometry (MS) and MS/MS signal and on LC retention profile was studied. A mix of ammonium acetate and acetic acid offered satisfactory results in terms of MS sensitivity. Screening of HILIC columns was performed, and ZIC-HILIC stationary phase was selected for HILIC mode, and C18 stationary phase was used for RP analysis. Negative ionization mode leads to a higher S/N ratio compared to positive ionization mode. Adducted tripeptides were selected for the monitoring of mustard agents' exposure, allowing better sensitivity than their dipeptide homologues. The two developed chromatographic methods have similar sensitivities with LOQs ranging from 1.9 to 20.5 ng/mL for the reversed-phase liquid chromatography (RPLC)-ESI-(-)-MS/MS method and from 1.7 to 43.3 ng/mL for the HILIC-ESI-(-)-MS/MS method. The monitoring method should be selected based on the targeted mustard agent, and the remaining method can be a confirmation tool.

Keywords:  HILIC–MS/MS; RPLC–MS/MS; albumin adducts; biomarkers

DOI:  https://doi.org/10.1002/jssc.70065
Glia. 2025 Jan 03.

Glial Biologist's Guide to Mass Spectrometry-Based Lipidomics: A Tutorial From Sample Preparation to Data Analysis.

Caitlin E Randolph, Katherine A Walker, Ruilin Yu, Connor Beveridge, Palak Manchanda, Gaurav Chopra.

  Neurological diseases are associated with disruptions in the brain lipidome that are becoming central to disease pathogenesis. Traditionally perceived as static structural support in membranes, lipids are now known to be actively involved in cellular signaling, energy metabolism, and other cellular activities involving membrane curvature, fluidity, fusion or fission. Glia are critical in the development, health, and function of the brain, and glial regulation plays a major role in disease. The major pathways of glial dysregulation related to function are associated with downstream products of metabolism including lipids. Taking advantage of significant innovations and technical advancements in instrumentation, lipidomics has emerged as a popular omics discipline, serving as the prevailing approach to comprehensively define metabolic alterations associated with organismal development, damage or disease. A key technological platform for lipidomics studies is mass spectrometry (MS), as it affords large-scale profiling of complex biological samples. However, as MS-based techniques are often refined and advanced, the relative comfort level among biologists with this instrumentation has not followed suit. In this review, we aim to highlight the importance of the study of glial lipids and to provide a concise record of best practices and steps for MS-based lipidomics. Specifically, we outline procedures for glia lipidomics workflows ranging from sample collection and extraction to mass spectrometric analysis to data interpretation. To ensure these approaches are more accessible, this tutorial aims to familiarize glia biologists with sample handling and analysis techniques for MS-based lipidomics, and to guide non-experts toward generating high quality lipidomics data.

Keywords:  glial lipidomics; lipid identification; lipidomics data analysis; lipids in neurological disease; mass spectrometry‐based lipidomics; sample preparation

DOI:  https://doi.org/10.1002/glia.24665
Biomed Chromatogr. 2025 Feb;39(2): e6067

Evaluation of the Impact of HIFU on Peptide Bond Formation: A Study Using SPE-LC-MS/MS Methodology.

Jiale Liu, Rongfei Yuan, Qi Wang, Hai Qiao, Yuling Yang, Siyu Yang, Hua Zhang, Chang Chen.

  High-intensity focused ultrasound (HIFU) is a noninvasive soft tissue ablation technique, which utilizes ultrasound energy to induce thermal coagulation necrosis in targeted tissues. Whether this high energy causes side effects in vivo, such as the formation of peptide bonds, has not been fully investigated. Glycylglycine is the simplest dipeptide and hence is often used as a model compound for peptide studies. In this study, we developed and validated a sensitive quantification method based on ion-exchange solid-phase extraction, liquid chromatography, and tandem mass spectrometry (SPE-LC-MS/MS) for the analysis of glycylglycine without derivatization, and then used it to evaluate whether HIFU promoted peptide bond formation in aqueous solution (without enzymes) and plasma (with enzymes). The results showed that strong cation exchange SPE significantly reduced the matrix effect and improved the sensitivity of the LC-MS/MS method. No formation of glycylglycine in the aqueous solution or plasma was observed following HIFU irradiation.

Keywords:  HIFU; LC‐MS/MS; SPE; glycylglycine; peptide bond formation

DOI:  https://doi.org/10.1002/bmc.6067
J Chromatogr A. 2024 Dec 27. pii: S0021-9673(24)01014-8. [Epub ahead of print]1741 465641

Advancing characterization of pyrolysis products: Comprehensive gas chromatography methods for analytes in gas and liquid phases.

Bernardo A Souto, Bingxin Hai, Justice Asomaning, David C Bressler.

  The development of biofuel technologies depends on the accurate identification and quantification of products from the conversion processes. Given the complexity of the renewable resources, the availability of biomass, and the versatility of conversion methods, there is a need for characterization methods that provide rapid and reliable analysis for various products coming from different conversion processes with minimal sample preparation. This study develops and validates gas chromatography methods that use multiple detectors to analyze pyrolytic compounds in both gas and liquid phases efficiently in a single, rapid run. For gas products, flame ionization and thermal conductivity detectors were used for identification and quantification of organic and inorganic gases, with volume and mass concentrations showing <1 % error between calculated and referenced values. A method for analyzing liquid product containing hydrocarbons and fatty acids was developed without derivatization, using a simultaneous mass spectrometer for identification and a flame ionization detector for quantification. Validation against established methods demonstrated comparable results, utilizing less time. While the simultaneous dual detector feature provides a simple and rapid analytical tool for pyrolysis products, these methods are also adaptable to non-simultaneous instrument setups and are broadly applicable to any general pyrolysis products containing hydrocarbons and oxygenates, making them useful for improving the development of biofuel production technologies.

Keywords:  Biofuel characterization; Dual detector analysis; Gas chromatography; Hydrocarbon and fatty acids; Pyrolysis products

DOI:  https://doi.org/10.1016/j.chroma.2024.465641
J Chromatogr B Analyt Technol Biomed Life Sci. 2024 Dec 26. pii: S1570-0232(24)00449-5. [Epub ahead of print]1252 124440

Bioanalysis of protein-unbound prednisolone in serum using equilibrium dialysis followed by liquid chromatography-tandem mass spectrometry.

J E Möhlmann, M van Luin, E G W M Lentjes, A D R Huitema, A M Punt.

   INTRODUCTION: High-dose systemic prednisolone is the cornerstone treatment of many autoimmune- and inflammatory diseases. Since prednisolone shows non-linear protein binding at higher serum concentrations, quantification of the unbound prednisolone concentration is important to understand prednisolone pharmacokinetics. We developed a liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay to quantify protein-unbound prednisolone in serum.
METHODS: Protein-unbound prednisolone was obtained using an equilibrium dialysis technique. Prednisolone was extracted from the dialysate using methyl tert-butyl ether. After evaporation to dryness, the organic phase residue was reconstituted and ready for injection onto the LC-MS/MS. Prednisolone was analysed by selected reaction monitoring with MS/MS operating in positive ion mode.
RESULTS AND DISCUSSION: The equilibrium between bound and unbound prednisolone was stable after 24 h. The calibration model for prednisolone in serum ranged from 0.25 to 811 µg/L and had an average linearity of 0.998. The coefficient of variation (CV) for precision at the lower limit of quantification was ≤ 4.3 % and for the other quality control samples ≤ 7.8 %. Prednisolone protein binding showed no significant degradation after 30 months of storage at -80 °C and was not influenced by multiple cycles of freezing and thawing. The recovery for the tested matrix effects in serum ranged from 85 % to 115 % (CV 10.3 %) and throughout the validation, no carry-over was observed.
CONCLUSION: An LC-MS/MS assay for prednisolone in serum was developed and validated, with a successful equilibrium dialysis technique to obtain protein-unbound prednisolone prior to quantification. This assay is considered suitable for pharmacokinetic studies.

Keywords:  Equilibrium dialysis; LC-MS/MS; Pharmacokinetics; Prednisolone; Protein unbound; Unbound fraction

DOI:  https://doi.org/10.1016/j.jchromb.2024.124440
Bioinform Adv. 2025 ;5(1): vbae192

Protomix: a Python package for 1H-NMR metabolomics data preprocessing.

Mohammed Zniber, Youssef Fatihi, Tan-Phat Huynh.

Motivation: NMR-based metabolomics is a field driven by technological advancements, necessitating the use of advanced preprocessing tools. Despite this need, there is a remarkable scarcity of comprehensive and user-friendly preprocessing tools in Python. To bridge this gap, we have developed Protomix-a Python package designed for metabolomics research. Protomix offers a set of automated, efficient, and user-friendly signal-preprocessing steps, tailored to streamline and enhance the preprocessing phase in metabolomics studies.
Results: This package presents a comprehensive preprocessing pipeline compatible with various data analysis tools. It encompasses a suite of functionalities for data extraction, preprocessing, and interactive visualization. Additionally, it includes a tutorial in the form of a Python Jupyter notebook, specifically designed for the analysis of 1D 1H-NMR metabolomics data related to prostate cancer and benign prostatic hyperplasia.
Availability and implementation: Protomix can be accessed at https://github.com/mzniber/protomix and https://protomix.readthedocs.io/en/latest/index.html.

DOI: https://doi.org/10.1093/bioadv/vbae192
Biomed Chromatogr. 2025 Feb;39(2): e6068

Liquid Chromatography Combined With Tandem Mass Spectrometry for the Pharmacokinetic and Metabolism Studies of PROTAC ARV-471 in Rats.

Wenbin Huang, Hongjian Zhang, Yayun Zhou, Xuechao Liu, Qilei Zhang, Xiaopeng Ma.

  Proteolysis targeting chimera (PROTAC) is emerging as a promising medicinal modality, which has aroused widespread interest among the field of pharmaceutical manufacturing in the recent years. ARV-471 is an orally active PROTAC estrogen receptor degrader against breast cancer, which leads to the ubiquitylation and subsequent degradation of estrogen receptors via the proteasome. In this study, we developed a highly sensitive liquid chromatography tandem mass spectrometry method (LLOQ = 0.5 ng/mL) for the measurement of ARV-471 in rat plasma. The acetonitrile precipitated sample was separated on ACQUITY BEH C18 column using acetonitrile-0.1% formic acid as mobile phased with gradient elution. Multiple reactions monitoring in positive ESI mode was employed for the quantification of ARV-471 (m/z 724.4 → 396.2). The assay showed good linearity over the concentration range of 0.5-1000 ng/mL with correlation coefficient > 0.996. The assay was validated according to FDA guidance, and all the validation parameters were within the predefined acceptance criteria. After validation, the assay was applied to the pharmacokinetic study of ARV-471 in rats. Additionally, the metabolites in rat plasma were identified using liquid chromatography-high resolution mass spectrometry. Four metabolites were identified and characterized. Hydrolysis, glucuronidation and deamination were the main metabolic pathways of ARV-471 in rats.

Keywords:  ARV‐471; PROTAC; bioavailability; metabolism; pharmacokinetics

DOI:  https://doi.org/10.1002/bmc.6068
J Chromatogr A. 2024 Dec 20. pii: S0021-9673(24)00992-0. [Epub ahead of print]1741 465619

Development of a liquid chromatography-mass spectrometry based targeted metabolomics method for discovering diagnostic biomarkers in Kawasaki disease.

Xialin Luo, Jiaqi Tian, Qing Li, Zhonggan Jin, Xiaoyu Fan, Hong Zhang, Haitao Lv, Yi Ju.

  Kawasaki disease (KD) has emerged as the leading cause of acquired heart disease in children, primarily due to the absence of highly sensitive and specific biomarkers for early and accurate diagnosis. To address this issue, a simple and comprehensive targeted metabolomics method employing ultra high-performance liquid chromatography coupled with Q-TRAP mass spectrometry has been developed to identify new metabolite biomarkers for KD. This method enables the simultaneous quantification of 276 metabolites, covering 60 metabolic pathways, with a particular emphasis on metabolites relevant to KD. The use of nine ISs and commercial quality control samples significantly enhances both accuracy and precision. Through validation and application to serum samples from patients with KD, seventeen differential serum metabolites were identified. The altered metabolites are primarily associated with three functional metabolic pathways: tricarboxylic acid cycle, tryptophan metabolism, and bile acid metabolism, all of which are believed to be involved in the inflammatory and immune responses in KD patients. Ultimately, eight differential metabolites (indole-3-propionic acid, thiamine, indolepyruvic acid, levodopa, l-selenomethionine, isocitric acid, trans-aconitate, and N-acetylasparagine) were identified that could potentially serve as diagnostic biomarkers with the area under the curve values exceeding 0.9. Our targeted metabolomics approach demonstrates applicability in identifying potential metabolite biomarkers for KD and holds great promise in unraveling the intricate pathophysiology of the disease.

Keywords:  Kawasaki disease; Liquid chromatography; Mass spectrometry; Metabolite biomarkers; Metabolomics

DOI:  https://doi.org/10.1016/j.chroma.2024.465619
Sci Rep. 2025 Jan 02. 15(1): 46

Non-targeted LC-MS metabolomics reveals serum metabolites for high-altitude adaptation in Tibetan donkeys.

Jing Wang, Yulong Feng, Shibo Xu, Ngodrup Tenzin, Haiyu Han, Dehong Gong, Fengxin Liu, Yujiang Sun, Shuqin Liu.

  Tibetan donkeys inhabit the harsh environment of the Qinghai-Tibet Plateau. Research on serum metabolites related to their high-altitude adaptation is limited compared to other livestock. We used liquid chromatography-mass spectrometry (LC-MS) to analyze serum samples from healthy adult donkeys in Shigatse, Changdu, and Dezhou to evaluate the effects of high altitudes on serum metabolites. Metabolomics analysis identified 443 differential metabolites (DMs) across the three groups, meeting criteria of VIP ≥ 1, p-value < 0.05, and Fold-Change ≥ 1.2 or ≤ 0.5. Significant upregulation was observed in deoxycholic acid, vitamin A, vitamin C, flavin mononucleotide, n-acetylserotonin, N'-formyl-kynurenine, calcidiol, and adenosine monophosphate in the high-altitude group compared to the low-altitude control group. The DMs were involved in processes such as bile secretion, vitamin digestion and absorption, tryptophan metabolism, and parathyroid hormone synthesis, secretion, and action. All these are crucial for nutrient metabolism, immune function, and antioxidant stress response. This study constructed a metabolomics dataset of Tibetan donkey serum and revealed differential metabolites among donkeys from different geographic regions and environments. The results offer crucial insights into the adaptive regulatory mechanisms.

Keywords:  Dezhou donkey; High-altitude adaptation; Metabolomics; Tibetan donkey

DOI:  https://doi.org/10.1038/s41598-024-83544-8
J Pharm Biomed Anal. 2024 Dec 26. pii: S0731-7085(24)00693-9. [Epub ahead of print]255 116651

Untargeted metabolomics combined with lipidomics revealed the effects of myocardial infarction and exercise rehabilitation on blood circulation metabolism of patients based on liquid chromatography-mass spectrometry.

Na Wang, Huimin Li, Hao Wu, Zilin Xia, Dabing Ren, Yunmei Zhang, Yan Zhao, Hong Zhang, Ke Zhuang, Lunzhao Yi.

  Myocardial infarction (MI) is a major cause of death worldwide. Exercise rehabilitation (ER) is a powerful tool to improve life quality and prognosis of MI patients. Herein, we developed an untargeted metabolomics combined with lipidomics method to qualitatively and quantitatively detect metabolites in plasma. A total of 475 metabolites were annotated according to MS, MS/MS, and quantified by internal standard method. Moreover, medical statistical methods combined with chemometrics were used for metabolomics data mining and interpretation of clinical issues (matched Cohort 1, n = 90, Cohort 2, n = 6). The results illustrated that abnormal lipid metabolism is the most significant metabolic disorder for MI patients. And, three metabolic pathways, bile secretion, HIF-1 signaling pathway, and glutathione metabolism were uncovered in MI patients. Furthermore, glutamine, Phenylacetylglutamine (PAGln) and lysophosphatidylcholine (LPCs) were revealed as the essential biomarkers for ER of MI patients. Our findings revealed the metabolic landscape of MI and metabolic alterations after ER, will underlay potential applications of plasma metabolites in the detection of MI and optimization of ER program.

Keywords:  Etabolomics; Exercise rehabilitation; LC-MS; Lipidomics; Myocardial infarction

DOI:  https://doi.org/10.1016/j.jpba.2024.116651
Nat Commun. 2025 Jan 02. 16(1): 165

Universal, untargeted detection of bacteria in tissues using metabolomics workflows.

Wei Chen, Min Qiu, Petra Paizs, Miriam Sadowski, Toma Ramonaite, Lieby Zborovsky, Raquel Mejias-Luque, Klaus-Peter Janßen, James Kinross, Robert D Goldin, Monica Rebec, Manuel Liebeke, Zoltan Takats, James S McKenzie, Nicole Strittmatter.

Fast and reliable identification of bacteria directly in clinical samples is a critical factor in clinical microbiological diagnostics. Current approaches require time-consuming bacterial isolation and enrichment procedures, delaying stratified treatment. Here, we describe a biomarker-based strategy that utilises bacterial small molecular metabolites and lipids for direct detection of bacteria in complex samples using mass spectrometry (MS). A spectral metabolic library of 233 bacterial species is mined for markers showing specificity at different phylogenetic levels. Using a univariate statistical analysis method, we determine 359 so-called taxon-specific markers (TSMs). We apply these TSMs to the in situ detection of bacteria using healthy and cancerous gastrointestinal tissues as well as faecal samples. To demonstrate the MS method-agnostic nature, samples are analysed using spatial metabolomics and traditional bulk-based metabolomics approaches. In this work, TSMs are found in >90% of samples, suggesting the general applicability of this workflow to detect bacterial presence with standard MS-based analytical methods.

DOI: https://doi.org/10.1038/s41467-024-55457-7
Anal Chem. 2024 Dec 29.

OligoDistiller: A Platform Agnostic Software Tool for MS and MS2 Data Analysis of Complex Oligonucleotides and Their Impurities.

Youzhong Liu, Jennifer L Lippens, Piotr Prostko, Ronald de Vries, Dirk Valkenborg, Thomas De Vijlder.

Oligonucleotides are currently one of the most rapidly advancing classes of therapeutic modalities. Understanding critical quality attributes, such as the impurity profile, stability, potential metabolites, and sequence conformity, is the key to their ultimate success. To obtain the information presented above, liquid chromatography-mass spectrometry (LC-MS) is often employed. However, data interpretation can be challenging due to multiple charge states, unknown species, chemical noises, and overlapping isotope envelopes (OIEs) of distinct but unresolved species. To address these challenges, we have developed an MS-platform agnostic, multifunctional R package and a web-tool for automated and interactive MS and MS2 data analysis, OligoDistiller. From the MS spectrum of a complex mixture of two synthetic strands, our tool OligoDistiller annotated and quantified 45 oligonucleotide-related features including 13 unknown impurities and 6 OIEs, which all together explained 90.8% of the detected peaks. Also, major product ions were assigned from the MS2 spectrum of a 47-mer DNA strand, covering 80.3% of the oligonucleotide sequence. We provide not only diverse isotope quality metrics for each annotated feature but also an interactive data review module allowing for direct inspection of the part of raw spectrum linked to a selected feature. This tool OligoDistiller is freely available at https://github.com/daniellyz/OligoDistiller.

DOI: https://doi.org/10.1021/acs.analchem.4c02667
Anal Methods. 2025 Jan 02.

Non-suppressed ion chromatography-tandem electrospray mass spectrometry using a short column for simultaneous analysis of dichloroacetic acid, trichloroacetic acid, and bromate: aqueous ammonia as the eluent additive.

Mingguo Peng, Jiali Chen, Shi Cheng, Huaicheng Zhang, Liangtao Pu, Erdeng Du, Qingfeng Cheng, Yanting Zuo, Aimin Li.

Dichloroacetic acid (DCAA), trichloroacetic acid (TCAA), and bromate (BrO3-) are disinfection byproducts (DBPs) formed during drinking water treatment and pose health risks. Rapid and reliable detection of these DBPs is essential for ensuring water safety. Non-suppressed ion chromatography (IC)-electrospray ionization mass spectrometry (IC-ESI-MS/MS) offers a promising approach for simultaneous analysis of organic haloacetic acids (HAAs) and inorganic oxyhalides, but previous methods using toxic methylamine can pose health risks. Herein, a new rapid non-suppressed IC-ESI-MS/MS method using a short AG18 guard column (13 μm, 2 mm × 50 mm) with aqueous ammonia as the alkaline modifier was developed for the simultaneous quantification of DCAA, TCAA, and BrO3-. This method allows direct sample injection without pretreatment and achieves sub-μg L-1 detection limits within 5 minutes. Aqueous ammonia (0.4 M) and acetonitrile were used as mobile phases in a gradient elution mode, providing good linearity (R2 >0.995), low limits of quantification (0.48-1.13 μg L-1), and high recoveries (76.3-107.3%). Intra-day (n = 9) and inter-day (3 days, n = 9) precision were validated with relative standard deviations of 5.8-8.9% and 6.4-7.7%, respectively. The method also demonstrated limited matrix interference from common water parameters such as Cl-, SO42-, HCO3-/CO32-, and natural organic matter (NOM), making it suitable for real water analysis. The applicability of this method was confirmed by monitoring DBP formation during the chlorination of NOM, showing that two-step chlorine dosing strategies reduce DBP formation compared to single-stage dosing. This newly established method provides a robust and efficient tool for DBP monitoring in drinking water treatment processes.

DOI: https://doi.org/10.1039/d4ay02007c
Rapid Commun Mass Spectrom. 2025 Apr 15. 39(7): e9980

FREDA: A Web Application for the Processing, Analysis, and Visualization of Fourier-Transform Mass Spectrometry Data.

David J Degnan, Daniel M Claborne, Amanda M White, Sarah M Akers, Natalie M Winans, Yuri E Corilo, Clayton W Strauch, Vanessa L Bailey, Lee Ann McCue, Kelly G Stratton, Lisa M Bramer.

   RATIONALE: The high-resolution measurement capability of Fourier-transform mass spectrometry (FT-MS) has made it a necessity for exploring the molecular composition of complex organic mixtures, like soil, plant, aquatic, and petroleum samples. This demand has driven a need for informatics tools to explore and analyze FT-MS data in a robust and reproducible manner.
METHODS: FREDA is an interactive web application developed to enable spectrometrists to format, process, and explore their FT-MS data without the need for statistical programming expertise. FREDA was built to explore outputs from a molecular identification tool, like CoreMS, and provide a suite of methods to filter data, compute chemical properties of peaks, statistically compare samples and groups of samples, conduct exploratory data analysis, and download the results with a report detailing all steps conducted.
RESULTS: To demonstrate the utility of FREDA, an example analysis was conducted using FT-MS data from a soil microbiology study of samples collected in two different soil depths at the Sphagnum bog forest north of Grand Rapids, Minnesota. Differences between the two depths are observed using Kendrick, Gibbs free energy, and van Krevelen plots. G-tests are used to quantify a significant difference between the groups. All analyses and plotting are conducted using only the FREDA application.
CONCLUSIONS: FREDA is an open-source and readily available web application that allows users to explore and make statistically valid conclusions about their FT-MS data. The application is available online (https://map.emsl.pnnl.gov/app/freda) with a tutorial web series (https://youtu.be/k5HLE2kNSBY?si=yB6sGoyvzxrFf5MP) and freely accessible code on Github (https://github.com/EMSL-Computing/FREDA).

Keywords:  FT‐MS; exploratory data analysis; statistics; web application

DOI:  https://doi.org/10.1002/rcm.9980
Talanta. 2024 Dec 24. pii: S0039-9140(24)01824-1. [Epub ahead of print]286 127442

Development and thorough evaluation of a multi-omics sample preparation workflow for comprehensive LC-MS/MS-based metabolomics, lipidomics and proteomics datasets.

Lana Brockbals, Maiken Ueland, Shanlin Fu, Matthew P Padula.

  The importance of sample preparation selection if often overlooked particularly for untargeted multi-omics approaches that gained popularity in recent years. To minimize issues with sample heterogeneity and additional freeze-thaw cycles during sample splitting, multiple -omics datasets (e.g. metabolomics, lipidomics and proteomics) should ideally be generated from the same set of samples. For sample extraction, commonly biphasic organic solvent systems are used that require extensive multi-step protocols. Individual studies have recently also started to investigate monophasic (all-in-one) extraction procedures. The aim of the current study was to develop and systematically compare ten different mono- and biphasic extraction solvent mixtures for their potential to aid in the most comprehensive metabolomics, lipidomics and proteomics datasets. As the focus was on human postmortem tissue samples (muscle and liver tissue), four tissue homogenization parameters were also evaluated. Untargeted liquid chromatography mass spectrometry-based metabolomics, lipidomic and proteomics methods were utilized along with 1D sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and bicinchoninic acid (BCA) assay results. Optimal homogenization was found to be achieved by bead-homogenizing 20 mg of muscle or liver tissue with 200 μL (1:10 ratio) Water:Methanol (1:2) using 3 × 30 s pulses. The supernatant of the homogenate was further extracted. Comprehensive ranking, taking nine different processing parameters into account, showed that the monophasic extraction solvents, overall, showed better scores compared to the biphasic solvent systems, despite their recommendation for one or all of the -omics extractions. The optimal extraction solvent was found to be Methanol:Acetone (9:1), resulting in the most comprehensive metabolomics, lipidomics and proteomics datasets, showing the potential to be automated, hence, allowing for high-throughput analysis of samples and opening the door for comprehensive multi-omics results from routine clinical cases in the future.

Keywords:  Compound class identification; LC-MS/MS; Multi-omics; Postmortem tissue extraction; monophasic (all-in-one) extraction; untargeted -omics

DOI:  https://doi.org/10.1016/j.talanta.2024.127442
Parasit Vectors. 2024 Dec 30. 17(1): 547

Identification of serum biomarkers for cystic echinococcosis in sheep through untargeted metabolomic analysis using LC-MS/MS technology.

Xiao-Xia Wu, Wan-Li Ban, Li-Jiang Wu, Wen-Jing Qi, Mehdi Borhani, Xiao-Ying He, Xiao-Lei Liu, Ming-Yuan Liu, Jing Ding.

   BACKGROUND: Echinococcosis is a zoonotic disease caused by an Echinococcus tapeworm infection. While diagnostic methods for humans often rely on ultrasound imaging and immunodiagnostic techniques, diagnosis in intermediate hosts typically has no widely used diagnostic markers, hampering disease control efforts.
METHODS: The differences in serum metabolites of sheep infected with Echinococcus granulosus and a control group were analyzed using ultrahigh-performance liquid chromatography (UHPLC) separation with tandem mass spectrometry (MS/MS) detection. This provided a basis for the early diagnosis and pathogenetic study of cystic echinococcosis (CE) in intermediate hosts at the metabolomics level. Orthogonal projections to latent structures-discriminant analysis (OPLS-DA) were used to analyze different metabolites in the serum of the two groups. The differentially abundant metabolites were entered into the MetaboAnalyst 5.0 online analysis website for processing, and the top-15-ranked metabolic pathways were set to produce bubble plots and differential abundance score plots, with a significant difference of P < 0.05 and a false discovery rate (FDR) < 0.1 as the screening conditions.
RESULTS: Data analyses of serum samples from both groups identified a total of 1905 significantly different metabolites, where 841 metabolites were upregulated and 1064 metabolites were downregulated. Twelve metabolites were significantly upregulated and 21 metabolites were significantly downregulated in the experimental group. Then, the 1,7-dihydroxyxanthone, 2-methylbutyrylglycine, 3,3-dimethylglutaric acid, 5,12-dihydroxy-6,8,10,14,17-eicosapentaenoic acid, 9-hydroperoxy-10E,12Z,15Z-octadecatrienoic acid, and trimethylamine N-oxide 6 metabolites were selected as diagnostically valuable candidate biomarkers (area under the curve [AUC] > 0.7). These differential metabolites are involved in various metabolic pathways, including amino acid metabolites (arginine, L-isoleucine, L-valine) and fatty acid metabolism (fenugreek, arachidonic acid, linolenic acid). Compared with the control group, sheep in the CE group had increased serum levels of fenugreek acid, while all other metabolites such as glycine showed significantly reduced serum levels (P < 0.01).
CONCLUSIONS: Through non-targeted metabolomic analysis of the serum of CE-infected sheep, differential metabolites closely related to amino acid metabolism and the fatty acid metabolism pathway were identified. These differentially abundant metabolites can serve as biomarkers for diagnosing CE infection in intermediate sheep hosts.

Keywords:   Echinococcus granulosus ; Biomarkers; LC–MS/MS; Non-targeted metabolomics; Serum

DOI:  https://doi.org/10.1186/s13071-024-06599-6
Rapid Commun Mass Spectrom. 2025 Mar 30. 39(6): e9974

A Doped Surface Ionization Method for Ion Mobility Spectrometry.

Jianhua Lin, Xiaoguang Gao, Jian Jia, Xiuli He.

   RATIONALE: Exhaled breath can be used for early warning of disease, with organic nitrogen compounds, including triethylamine (TEA), being linked to various medical conditions. Surface ionization ion mobility spectrometry (SI-IMS) facilitates the direct detection of TEA in exhaled breath. However, the presence of multiple ionization products of TEA poses challenges for both quantitative and qualitative analyses.
METHODS: A doped surface ionization (DSI) method consisting of surface ionization of dopants and gas-phase reaction of samples was proposed, and TEA was detected when combined with an ion mobility spectrometer. TEA at different concentrations and spiked by human breath was detected to evaluate the method's properties.
RESULTS: TEA with concentrations from 5.99 to 30.50 ppb and a relative humidity of 80% was detected. The peak intensity of the protonated TEA ions demonstrated a linear correlation with concentration, yielding a fitted correlation coefficient of R2 = 0.94. A standard deviation less than 0.066% was obtained with 10 replicate analyses of 29.92 ppb TEA, and the recovery rate of the sample was 93.57%.
CONCLUSIONS: The SI-IMS based on the DSI method has the advantages of excellent selective ionization, high accuracy and sensitivity, and remarkable repeatability for detecting TEA. It is a promising method for detecting specific organic nitrogen compounds in exhaled breath.

Keywords:  doped surface ionization; exhaled breath; ion mobility spectrometry; organic nitrogen compounds; triethylamine

DOI:  https://doi.org/10.1002/rcm.9974
J Chromatogr A. 2024 Dec 22. pii: S0021-9673(24)00998-1. [Epub ahead of print]1741 465625

An improved matrix deposition technique for thin layer chromatography coupled to MALDI-TOF mass spectrometry (TLC-MALDI).

Alexander Weng, René de Vaumas, Christoph Weise.

  Analytical thin layer chromatography (TLC) is a simple yet powerful chromatographic technique that is widely used for the qualitative characterization of complex mixtures such as plant extracts. For their qualitative and visual characterisation, a large number of more or less specific colour reactions are at hand and numerous reference substances are available as well. However, the identification of extract components by colour and the comparison of retention times is not straightforward. In contrast, the coupling of TLC with MALDI-TOF mass spectrometry can enable the identification of components and contribute to the optimization of TLC protocols. One of the most important steps for a successful TLC-MALDI process is the deposition of a sufficient amount of matrix onto the TLC plate. Standard methods such as the dip-coating protocol have major drawbacks. Here we present an improved and robust procedure for matrix application by means of matrix lines. The practicability of the method was tested on plant extracts from Agrostemma githago L. and Papaver somniferum L. (opium).

Keywords:  Improved matrix deposition; TLC-MALDI

DOI:  https://doi.org/10.1016/j.chroma.2024.465625
Anal Chem. 2025 Jan 02.

NMRformer: A Transformer-Based Deep Learning Framework for Peak Assignment in 1D 1H NMR Spectroscopy.

Zhouao Zhou, Xinli Liao, Xu Qiu, Yue Zhang, Jiyang Dong, Xiaobo Qu, Donghai Lin.

Metabolite identification from 1D 1H NMR spectra is a major challenge in NMR-based metabolomics. This study introduces NMRformer, a Transformer-based deep learning framework for accurate peak assignment and metabolite identification in 1D 1H NMR spectroscopy. Unlike traditional approaches, NMRformer interprets spectra as sequences of spectral peaks and integrates a self-attention mechanism and peak height ratios directly into the Transformer encoder layer. It has the capability to recognize and interpret long-range dependencies between peaks and to quickly identify peaks corresponding to identical metabolites. The effectiveness of NMRformer has been rigorously validated by analyzing real 1D 1H NMR spectra from a variety of cellular and biofluid samples. NMRformer achieved peak assignment accuracies above 88% and metabolite identification accuracies above 80% in four types of cellular samples. It also achieved peak assignment accuracies above 88% and metabolite identification accuracies above 80% in three types of biofluid samples. These results underscore the ability of NMRformer to significantly improve the accuracy and efficiency of peak assignment and metabolite identification in NMR-based metabolomics studies.

DOI: https://doi.org/10.1021/acs.analchem.4c05632
Proteomics. 2024 Dec 30. e202400100

Computational Methods for Data Integration and Imputation of Missing Values in Omics Datasets.

Yannis Schumann, Antonia Gocke, Julia E Neumann.

  Molecular profiling of different omic-modalities (e.g., DNA methylomics, transcriptomics, proteomics) in biological systems represents the basis for research and clinical decision-making. Measurement-specific biases, so-called batch effects, often hinder the integration of independently acquired datasets, and missing values further hamper the applicability of typical data processing algorithms. In addition to careful experimental design, well-defined standards in data acquisition and data exchange, the alleviation of these phenomena particularly requires a dedicated data integration and preprocessing pipeline. This review aims to give a comprehensive overview of computational methods for data integration and missing value imputation for omic data analyses. We provide formal definitions for missing value mechanisms and propose a novel statistical taxonomy for batch effects, especially in the presence of missing data. Based on an automated document search and systematic literature review, we describe 32 distinct data integration methods from five main methodological categories, as well as 37 algorithms for missing value imputation from five separate categories. Additionally, this review highlights multiple quantitative evaluation methods to aid researchers in selecting a suitable set of methods for their work. Finally, this work provides an integrated discussion of the relevance of batch effects and missing values in omics with corresponding method recommendations. We then propose a comprehensive three-step workflow from the study conception to final data analysis and deduce perspectives for future research. Eventually, we present a comprehensive flow chart as well as exemplary decision trees to aid practitioners in the selection of specific approaches for imputation and data integration in their studies.

Keywords:  algorithm; data integration; missing values; omics

DOI:  https://doi.org/10.1002/pmic.202400100