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Rincon Pabon JP, Akbar Z, Politis A. MSe Collision Energy Optimization for the Analysis of Membrane Proteins Using HDX-cIMS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1383-1389. [PMID: 38842540 PMCID: PMC11228973 DOI: 10.1021/jasms.4c00093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/09/2024] [Accepted: 06/05/2024] [Indexed: 06/07/2024]
Abstract
Hydrogen/deuterium exchange mass spectrometry (HDX-MS) has evolved as an essential technique in structural proteomics. The use of ion mobility separation (IMS) coupled to HDX-MS has increased the applicability of the technique to more complex systems and has been shown to improve data quality and robustness. The first step when running any HDX-MS workflow is to confirm the sequence and retention time of the peptides resulting from the proteolytic digestion of the nondeuterated protein. Here, we optimized the collision energy ramp of HDMSE experiments for membrane proteins using a Waters SELECT SERIES cIMS-QTOF system following an HDX workflow using Phosphorylase B, XylE transporter, and Smoothened receptor (SMO) as model systems. Although collision energy (CE) ramp 10-50 eV gave the highest amount of positive identified peptides when using Phosphorylase B, XylE, and SMO, results suggest optimal CE ramps are protein specific, and different ramps can produce a unique set of peptides. We recommend cIMS users use different CE ramps in their HDMSE experiments and pool the results to ensure maximum peptide identifications. The results show how selecting an appropriate CE ramp can change the sequence coverage of proteins ranging from 4 to 94%.
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Affiliation(s)
- Juan Pablo Rincon Pabon
- Faculty of Biology, Medicine and Health, Division of Molecular and Cellular Function, The University of Manchester, Manchester M13 9PT, U.K
- Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester M1 7DN, U.K
| | - Zulaikha Akbar
- Faculty of Biology, Medicine and Health, Division of Molecular and Cellular Function, The University of Manchester, Manchester M13 9PT, U.K
- Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester M1 7DN, U.K
| | - Argyris Politis
- Faculty of Biology, Medicine and Health, Division of Molecular and Cellular Function, The University of Manchester, Manchester M13 9PT, U.K
- Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester M1 7DN, U.K
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2
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Wartmann Y, Boxler MI, Kraemer T, Steuer AE. Impact of three different peak picking software tools on the quality of untargeted metabolomics data. J Pharm Biomed Anal 2024; 248:116302. [PMID: 38865927 DOI: 10.1016/j.jpba.2024.116302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 06/07/2024] [Accepted: 06/08/2024] [Indexed: 06/14/2024]
Abstract
Data quality and control parameters are becoming more important in metabolomics. For peak picking, open-source or commercial solutions are used. Other publications consider different software solutions or data acquisition types for peak picking, a combination, including proposed and new quality parameters for the process of peak picking, does not exist. This study tries to examine the performance of three different software in terms of reproducibility and quality of their output while also considering new quality parameters to gain a better understanding of resulting feature lists in metabolomics data. We saw best recovery of spiked analytes in MS-DIAL. Reproducibility over multiple projects was good among all software. The total number of features found was consistent for DDA and full scan acquisition in MS-DIAL but full scan data leading to considerably more features in MZmine and Progenesis Qi. Feature linearity proved to be a good quality parameter. Features in MS-DIAL and MZmine, showed good linearity while Progenesis Qi produced large variation, especially in full scan data. Peak width proved to be a very powerful filtering criteria revealing many features in MZmine and Progenesis Qi to be of questionable peak width. Additionally, full scan data appears to produce a disproportionally higher number of short features. This parameter is not yet available in MS-DIAL. Finally, the manual classification of true positive features proved MS-DIAL to perform significantly better in DDA data (62 % true positive) than the two other software in either mode. We showed that currently popular solutions MS-DIAL and MZmine perform well in targeted analysis of spiked analytes as well as in classic untargeted analysis. The commercially available solution Progenesis Qi does not hold any advantage over the two in terms of quality parameters, of which we proposed peak width as a new parameter and showed that already proposed parameters such as feature linearity in samples of increasing concentration are advisable to use.
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Affiliation(s)
- Yannick Wartmann
- Department of Forensic Pharmacology and Toxicology, Zurich Institute of Forensic Medicine,University of Zurich, Winterthurerstrasse 190/52, Zurich 8057, Switzerland
| | - Martina I Boxler
- Department of Forensic Pharmacology and Toxicology, Zurich Institute of Forensic Medicine,University of Zurich, Winterthurerstrasse 190/52, Zurich 8057, Switzerland
| | - Thomas Kraemer
- Department of Forensic Pharmacology and Toxicology, Zurich Institute of Forensic Medicine,University of Zurich, Winterthurerstrasse 190/52, Zurich 8057, Switzerland
| | - Andrea E Steuer
- Department of Forensic Pharmacology and Toxicology, Zurich Institute of Forensic Medicine,University of Zurich, Winterthurerstrasse 190/52, Zurich 8057, Switzerland.
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3
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Lemmink IB, Straub LV, Bovee TFH, Mulder PPJ, Zuilhof H, Salentijn GI, Righetti L. Recent advances and challenges in the analysis of natural toxins. ADVANCES IN FOOD AND NUTRITION RESEARCH 2024; 110:67-144. [PMID: 38906592 DOI: 10.1016/bs.afnr.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/23/2024]
Abstract
Natural toxins (NTs) are poisonous secondary metabolites produced by living organisms developed to ward off predators. Especially low molecular weight NTs (MW<∼1 kDa), such as mycotoxins, phycotoxins, and plant toxins, are considered an important and growing food safety concern. Therefore, accurate risk assessment of food and feed for the presence of NTs is crucial. Currently, the analysis of NTs is predominantly performed with targeted high pressure liquid chromatography tandem mass spectrometry (HPLC-MS/MS) methods. Although these methods are highly sensitive and accurate, they are relatively expensive and time-consuming, while unknown or unexpected NTs will be missed. To overcome this, novel on-site screening methods and non-targeted HPLC high resolution mass spectrometry (HRMS) methods have been developed. On-site screening methods can give non-specialists the possibility for broad "scanning" of potential geographical regions of interest, while also providing sensitive and specific analysis at the point-of-need. Non-targeted chromatography-HRMS methods can detect unexpected as well as unknown NTs and their metabolites in a lab-based approach. The aim of this chapter is to provide an insight in the recent advances, challenges, and perspectives in the field of NTs analysis both from the on-site and the laboratory perspective.
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Affiliation(s)
- Ids B Lemmink
- Laboratory of Organic Chemistry, Wageningen University & Research, Wageningen, The Netherlands; Wageningen Food Safety Research, Wageningen University & Research, Wageningen, The Netherlands
| | - Leonie V Straub
- Laboratory of Organic Chemistry, Wageningen University & Research, Wageningen, The Netherlands; Wageningen Food Safety Research, Wageningen University & Research, Wageningen, The Netherlands
| | - Toine F H Bovee
- Wageningen Food Safety Research, Wageningen University & Research, Wageningen, The Netherlands
| | - Patrick P J Mulder
- Wageningen Food Safety Research, Wageningen University & Research, Wageningen, The Netherlands
| | - Han Zuilhof
- Laboratory of Organic Chemistry, Wageningen University & Research, Wageningen, The Netherlands; School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin, P.R. China
| | - Gert Ij Salentijn
- Laboratory of Organic Chemistry, Wageningen University & Research, Wageningen, The Netherlands; Wageningen Food Safety Research, Wageningen University & Research, Wageningen, The Netherlands.
| | - Laura Righetti
- Laboratory of Organic Chemistry, Wageningen University & Research, Wageningen, The Netherlands; Wageningen Food Safety Research, Wageningen University & Research, Wageningen, The Netherlands.
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Kelly JT, McNamara LE, Hoover ME, Rubenstein HM, Houthuijs K, Martens J. Development of Nontargeted Workflow of Occupational Exposure by Infrared Ion Spectroscopy and Silicone Wristbands' Passive Sampling. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:829-833. [PMID: 38564189 DOI: 10.1021/jasms.3c00400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
A new approach using orthogonal analytical techniques is developed for chemical identification. High resolution mass spectrometry and infrared ion spectroscopy are applied through a 5-level confidence paradigm to demonstrate the effectiveness of nontargeted workflow for the identification of hazardous organophosphates. Triphenyl phosphate is used as a surrogate organophosphate for occupational exposure, and silicone wristbands are used to represent personal samplers. Spectral data of a target compound is combined with spectral data of the sodium adduct and quantum chemical calculations to achieve a confirmed identification. Here, we demonstrate a nontargeted workflow that identifies organophosphate exposure and provides a mechanism for selecting validated methods for quantitative analyses.
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Affiliation(s)
- John T Kelly
- Savannah River National Laboratory, 301 Gateway Drive, Aiken, South Carolina 29803, United States
| | - Louis E McNamara
- Savannah River National Laboratory, 301 Gateway Drive, Aiken, South Carolina 29803, United States
| | - Megan E Hoover
- Savannah River National Laboratory, 301 Gateway Drive, Aiken, South Carolina 29803, United States
| | - H Mitchell Rubenstein
- United States Air Force - Air Force Research Laboratory, 711th Human Performance Wing, 2510 Fifth Street, Area B, Building 840, Wright-Patterson AFB, Ohio 45433, United States
| | - Kas Houthuijs
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - Jonathan Martens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
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5
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Lawlor K, Clausen J, Johnston A, Edge A, Wolff K, Castrignanò E, Couchman L. A review of analytical parameters in 'rapid' liquid chromatographic methods for bioanalysis: Can we do better? J Chromatogr A 2024; 1721:464803. [PMID: 38547680 DOI: 10.1016/j.chroma.2024.464803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 02/22/2024] [Accepted: 03/06/2024] [Indexed: 04/13/2024]
Abstract
Rapid bioanalysis is beneficial to many applications. However, how 'rapid' a method is, or could be, is often an unanswered question. In this statistical review, the authors have assessed multiple pre-analytical (i.e. sample preparation), and analytical method parameters specifically for liquid chromatography to assist researchers in developing and validating 'rapid' bioanalytical methods. We restricted the search to urine and plasma matrices only. Data were extracted from over 2,000 recent studies and evaluated to assess how these parameters affected the 'on-instrument' analysis time. In addition to methods using ultra-violet (UV) detection, there were a large number of mass spectrometric (MS) methods, allowing additional review of the differences between high- and low-resolution MS on analysis time. We observed that most (N = 922, 70 %) methods used 5 or 10 cm columns, and that whilst uptake of ultra-high performance (U)HPLC columns was good, the use of sub-5 cm columns and/or flow rates in excess of 1 mL/min was incredibly rare (N = 25, 3 %). The detector of choice for quantitative (U)HPLC-MS remains the triple quadrupole, although a number of groups report the use of high-resolution MS for such methods.
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Affiliation(s)
- K Lawlor
- Department of Analytical, Environmental and Forensic Sciences, King's College London, London, SE1 9NH, UK; Analytical Services International, St. George's University of London, Cranmer Terrace, London, SW17 0RE, UK.
| | - J Clausen
- Analytical Services International, St. George's University of London, Cranmer Terrace, London, SW17 0RE, UK
| | - A Johnston
- Analytical Services International, St. George's University of London, Cranmer Terrace, London, SW17 0RE, UK
| | - A Edge
- Avantor Sciences, The Markham Centre, Station Road, Theale, Reading, RG7 4PE
| | - K Wolff
- Department of Analytical, Environmental and Forensic Sciences, King's College London, London, SE1 9NH, UK; Drug Control Centre, King's College London, London, SE1 9NH, UK
| | - E Castrignanò
- Department of Analytical, Environmental and Forensic Sciences, King's College London, London, SE1 9NH, UK; Drug Control Centre, King's College London, London, SE1 9NH, UK
| | - L Couchman
- Department of Analytical, Environmental and Forensic Sciences, King's College London, London, SE1 9NH, UK; Analytical Services International, St. George's University of London, Cranmer Terrace, London, SW17 0RE, UK
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6
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Sarkar S, Roy D, Chatterjee B, Ghosh R. Clinical advances in analytical profiling of signature lipids: implications for severe non-communicable and neurodegenerative diseases. Metabolomics 2024; 20:37. [PMID: 38459207 DOI: 10.1007/s11306-024-02100-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 02/06/2024] [Indexed: 03/10/2024]
Abstract
BACKGROUND Lipids play key roles in numerous biological processes, including energy storage, cell membrane structure, signaling, immune responses, and homeostasis, making lipidomics a vital branch of metabolomics that analyzes and characterizes a wide range of lipid classes. Addressing the complex etiology, age-related risk, progression, inflammation, and research overlap in conditions like Alzheimer's Disease, Parkinson's Disease, Cardiovascular Diseases, and Cancer poses significant challenges in the quest for effective therapeutic targets, improved diagnostic markers, and advanced treatments. Mass spectrometry is an indispensable tool in clinical lipidomics, delivering quantitative and structural lipid data, and its integration with technologies like Liquid Chromatography (LC), Magnetic Resonance Imaging (MRI), and few emerging Matrix-Assisted Laser Desorption Ionization- Imaging Mass Spectrometry (MALDI-IMS) along with its incorporation into Tissue Microarray (TMA) represents current advances. These innovations enhance lipidomics assessment, bolster accuracy, and offer insights into lipid subcellular localization, dynamics, and functional roles in disease contexts. AIM OF THE REVIEW The review article summarizes recent advancements in lipidomic methodologies from 2019 to 2023 for diagnosing major neurodegenerative diseases, Alzheimer's and Parkinson's, serious non-communicable cardiovascular diseases and cancer, emphasizing the role of lipid level variations, and highlighting the potential of lipidomics data integration with genomics and proteomics to improve disease understanding and innovative prognostic, diagnostic and therapeutic strategies. KEY SCIENTIFIC CONCEPTS OF REVIEW Clinical lipidomic studies are a promising approach to track and analyze lipid profiles, revealing their crucial roles in various diseases. This lipid-focused research provides insights into disease mechanisms, biomarker identification, and potential therapeutic targets, advancing our understanding and management of conditions such as Alzheimer's Disease, Parkinson's Disease, Cardiovascular Diseases, and specific cancers.
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Affiliation(s)
- Sutanu Sarkar
- Amity Institute of Biotechnology (AIBNK), Amity University, Rajarhat, Newtown Action Area 2, Kolkata, 700135, West Bengal, India
| | - Deotima Roy
- Amity Institute of Biotechnology (AIBNK), Amity University, Rajarhat, Newtown Action Area 2, Kolkata, 700135, West Bengal, India
| | - Bhaskar Chatterjee
- Amity Institute of Biotechnology (AIBNK), Amity University, Rajarhat, Newtown Action Area 2, Kolkata, 700135, West Bengal, India
| | - Rajgourab Ghosh
- Amity Institute of Biotechnology (AIBNK), Amity University, Rajarhat, Newtown Action Area 2, Kolkata, 700135, West Bengal, India.
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7
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Yuan Y, Huang L, Yu L, Yan X, Chen S, Bi C, He J, Zhao Y, Yang L, Ning L, Jin H, Yang R, Li Y. Clinical metabolomics characteristics of diabetic kidney disease: A meta-analysis of 1875 cases with diabetic kidney disease and 4503 controls. Diabetes Metab Res Rev 2024; 40:e3789. [PMID: 38501707 DOI: 10.1002/dmrr.3789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 01/01/2024] [Accepted: 01/31/2024] [Indexed: 03/20/2024]
Abstract
AIMS Diabetic Kidney Disease (DKD), one of the major complications of diabetes, is also a major cause of end-stage renal disease. Metabolomics can provide a unique metabolic profile of the disease and thus predict or diagnose the development of the disease. Therefore, this study summarises a more comprehensive set of clinical biomarkers related to DKD to identify functional metabolites significantly associated with the development of DKD and reveal their driving mechanisms for DKD. MATERIALS AND METHODS We searched PubMed, Embase, the Cochrane Library and Web of Science databases through October 2022. A meta-analysis was conducted on untargeted or targeted metabolomics research data based on the strategy of standardized mean differences and the process of ratio of means as the effect size, respectively. We compared the changes in metabolite levels between the DKD patients and the controls and explored the source of heterogeneity through subgroup analyses, sensitivity analysis and meta-regression analysis. RESULTS The 34 clinical-based metabolomics studies clarified the differential metabolites between DKD and controls, containing 4503 control subjects and 1875 patients with DKD. The results showed that a total of 60 common differential metabolites were found in both meta-analyses, of which 5 metabolites (p < 0.05) were identified as essential metabolites. Compared with the control group, metabolites glycine, aconitic acid, glycolic acid and uracil decreased significantly in DKD patients; cysteine was significantly higher. This indicates that amino acid metabolism, lipid metabolism and pyrimidine metabolism in DKD patients are disordered. CONCLUSIONS We have identified 5 metabolites and metabolic pathways related to DKD which can serve as biomarkers or targets for disease prevention and drug therapy.
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Affiliation(s)
- Yu Yuan
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Liping Huang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- College of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Lulu Yu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xingxu Yan
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Siyu Chen
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Chenghao Bi
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Junjie He
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yiqing Zhao
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Liu Yang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Li Ning
- Department Clinical Laboratory, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Hua Jin
- College of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Rongrong Yang
- Public Health Science and Engineering College, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yubo Li
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
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8
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Walmsley SJ, Guo J, Tarifa A, DeCaprio AP, Cooke MS, Turesky RJ, Villalta PW. Mass Spectral Library for DNA Adductomics. Chem Res Toxicol 2024; 37:302-310. [PMID: 38231175 PMCID: PMC10939812 DOI: 10.1021/acs.chemrestox.3c00302] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Endogenous electrophiles, ionizing and non-ionizing radiation, and hazardous chemicals present in the environment and diet can damage DNA by forming covalent adducts. DNA adducts can form in critical cancer driver genes and, if not repaired, may induce mutations during cell division, potentially leading to the onset of cancer. The detection and quantification of specific DNA adducts are some of the first steps in studying their role in carcinogenesis, the physiological conditions that lead to their production, and the risk assessment of exposure to specific genotoxic chemicals. Hundreds of different DNA adducts have been reported in the literature, and there is a critical need to establish a DNA adduct mass spectral database to facilitate the detection of previously observed DNA adducts and characterize newly discovered DNA adducts. We have collected synthetic DNA adduct standards from the research community, acquired MSn (n = 2, 3) fragmentation spectra using Orbitrap and Quadrupole-Time-of-Flight (Q-TOF) MS instrumentation, processed the spectral data and incorporated it into the MassBank of North America (MoNA) database, and created a DNA adduct portal Web site (https://sites.google.com/umn.edu/dnaadductportal) to serve as a central location for the DNA adduct mass spectra and metadata, including the spectral database downloadable in different formats. This spectral library should prove to be a valuable resource for the DNA adductomics community, accelerating research and improving our understanding of the role of DNA adducts in disease.
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Affiliation(s)
- Scott J Walmsley
- Institute for Health Informatics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Jingshu Guo
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Anamary Tarifa
- Forensic & Analytical Toxicology Facility, Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Anthony P DeCaprio
- Forensic & Analytical Toxicology Facility, Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Marcus S Cooke
- Oxidative Stress Group, Department of Molecular Biosciences, University of South Florida, Tampa, Florida 33620, United States
| | - Robert J Turesky
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Peter W Villalta
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
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Gerhardtova I, Jankech T, Majerova P, Piestansky J, Olesova D, Kovac A, Jampilek J. Recent Analytical Methodologies in Lipid Analysis. Int J Mol Sci 2024; 25:2249. [PMID: 38396926 PMCID: PMC10889185 DOI: 10.3390/ijms25042249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/09/2024] [Accepted: 02/11/2024] [Indexed: 02/25/2024] Open
Abstract
Lipids represent a large group of biomolecules that are responsible for various functions in organisms. Diseases such as diabetes, chronic inflammation, neurological disorders, or neurodegenerative and cardiovascular diseases can be caused by lipid imbalance. Due to the different stereochemical properties and composition of fatty acyl groups of molecules in most lipid classes, quantification of lipids and development of lipidomic analytical techniques are problematic. Identification of different lipid species from complex matrices is difficult, and therefore individual analytical steps, which include extraction, separation, and detection of lipids, must be chosen properly. This review critically documents recent strategies for lipid analysis from sample pretreatment to instrumental analysis and data interpretation published in the last five years (2019 to 2023). The advantages and disadvantages of various extraction methods are covered. The instrumental analysis step comprises methods for lipid identification and quantification. Mass spectrometry (MS) is the most used technique in lipid analysis, which can be performed by direct infusion MS approach or in combination with suitable separation techniques such as liquid chromatography or gas chromatography. Special attention is also given to the correct evaluation and interpretation of the data obtained from the lipid analyses. Only accurate, precise, robust and reliable analytical strategies are able to bring complex and useful lipidomic information, which may contribute to clarification of some diseases at the molecular level, and may be used as putative biomarkers and/or therapeutic targets.
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Affiliation(s)
- Ivana Gerhardtova
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, SK-845 10 Bratislava, Slovakia
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, SK-842 15 Bratislava, Slovakia
| | - Timotej Jankech
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, SK-845 10 Bratislava, Slovakia
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, SK-842 15 Bratislava, Slovakia
| | - Petra Majerova
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, SK-845 10 Bratislava, Slovakia
| | - Juraj Piestansky
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, SK-845 10 Bratislava, Slovakia
- Toxicological and Antidoping Center, Faculty of Pharmacy, Comenius University in Bratislava, Odbojarov 10, SK-832 32 Bratislava, Slovakia
- Department of Galenic Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Odbojarov 10, SK-832 32 Bratislava, Slovakia
| | - Dominika Olesova
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, SK-845 10 Bratislava, Slovakia
- Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, SK-845 05 Bratislava, Slovakia
| | - Andrej Kovac
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, SK-845 10 Bratislava, Slovakia
- Department of Pharmacology and Toxicology, University of Veterinary Medicine and Pharmacy in Kosice, Komenskeho 68/73, SK-041 81 Kosice, Slovakia
| | - Josef Jampilek
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, SK-845 10 Bratislava, Slovakia
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, SK-842 15 Bratislava, Slovakia
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10
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Jung YH, Kim JH. Feature-Based Molecular Networking Combined with Multivariate Analysis for the Characterization of Glutathione Adducts as a Smoking Gun of Bioactivation. Anal Chem 2023; 95:17450-17457. [PMID: 37976220 DOI: 10.1021/acs.analchem.3c01094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Feature-based molecular networking (FBMN) is a powerful analytical tool for mass spectrometry (MS)-based untargeted metabolomics data analysis. FBMN plays an important role in drug metabolism studies, enabling the visualization of complex metabolomics data to achieve metabolite characterization. In this study, we propose a strategy for the characterization of glutathione (GSH) adducts formed via in vitro metabolic activation using FBMN assisted by multivariate analysis (MVA). Acetaminophen was used as a model substrate for method development, and the practical potential of the method was investigated by its application to 2-aminophenol (2-AP) and 2,4-dinitrochlorobenzene (DNCB). Two 2-AP GSH adducts and one DNCB GSH adduct were successfully characterized by forming networks with GSH even though the mass spectral information obtained for the parent compound was deficient. False positives were effectively filtered out by the variable influence on projection cutoff criteria obtained from orthogonal partial least-squares-discriminant analysis. The GSH adducts formed by enzymatic or nonenzymatic reactions were intuitively distinguished by the pie chart of FBMN results. In summary, our approach effectively characterizes GSH adducts, which serve as compelling evidence of bioactivation. It can be widely utilized to enhance risk assessment in the context of drug metabolism.
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Affiliation(s)
- Young-Heun Jung
- College of Pharmacy, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Ju-Hyun Kim
- College of Pharmacy, Yeungnam University, Gyeongsan 38541, Republic of Korea
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11
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Lekka P, Fragopoulou E, Terpou A, Dasenaki M. Exploring Human Metabolome after Wine Intake-A Review. Molecules 2023; 28:7616. [PMID: 38005338 PMCID: PMC10673339 DOI: 10.3390/molecules28227616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 10/21/2023] [Accepted: 10/24/2023] [Indexed: 11/26/2023] Open
Abstract
Wine has a rich history dating back to 2200 BC, originally recognized for its medicinal properties. Today, with the aid of advanced technologies like metabolomics and sophisticated analytical techniques, we have gained remarkable insights into the molecular-level changes induced by wine consumption in the human organism. This review embarks on a comprehensive exploration of the alterations in human metabolome associated with wine consumption. A great number of 51 studies from the last 25 years were reviewed; these studies systematically investigated shifts in metabolic profiles within blood, urine, and feces samples, encompassing both short-term and long-term studies of the consumption of wine and wine derivatives. Significant metabolic alterations were observed in a wide variety of metabolites belonging to different compound classes, such as phenolic compounds, lipids, organic acids, and amino acids, among others. Within these classes, both endogenous metabolites as well as diet-related metabolites that exhibited up-regulation or down-regulation following wine consumption were included. The up-regulation of short-chain fatty acids and the down-regulation of sphingomyelins after wine intake, as well as the up-regulation of gut microbial fermentation metabolites like vanillic and syringic acid are some of the most important findings reported in the reviewed literature. Our results confirm the intact passage of certain wine compounds, such as tartaric acid and other wine acids, to the human organism. In an era where the health effects of wine consumption are of growing interest, this review offers a holistic perspective on the metabolic underpinnings of this centuries-old tradition.
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Affiliation(s)
- Pelagia Lekka
- Food Chemistry Laboratory, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zographou, 15771 Athens, Greece;
| | - Elizabeth Fragopoulou
- School of Health Science and Education, Department of Nutrition and Dietetics, Harokopio University, 17671 Athens, Greece;
| | - Antonia Terpou
- Department of Agricultural Development, Agrofood and Management of Natural Resources, School of Agricultural Development, Nutrition & Sustainability, National and Kapodistrian University of Athens, 34400 Psachna, Greece;
| | - Marilena Dasenaki
- Food Chemistry Laboratory, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zographou, 15771 Athens, Greece;
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12
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Gossner MM, Perret-Gentil A, Britt E, Queloz V, Glauser G, Ladd T, Roe AD, Cleary M, Liziniewicz M, Nielsen LR, Ghosh SK, Bonello P, Eisenring M. A glimmer of hope - ash genotypes with increased resistance to ash dieback pathogen show cross-resistance to emerald ash borer. THE NEW PHYTOLOGIST 2023; 240:1219-1232. [PMID: 37345294 DOI: 10.1111/nph.19068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/18/2023] [Indexed: 06/23/2023]
Abstract
Plants rely on cross-resistance traits to defend against multiple, phylogenetically distinct enemies. These traits are often the result of long co-evolutionary histories. Biological invasions can force naïve plants to cope with novel, coincident pests, and pathogens. For example, European ash (Fraxinus excelsior) is substantially threatened by the emerald ash borer (EAB), Agrilus planipennis, a wood-boring beetle, and the ash dieback (ADB) pathogen, Hymenoscyphus fraxineus. Yet, plant cross-resistance traits against novel enemies are poorly explored and it is unknown whether naïve ash trees can defend against novel enemy complexes via cross-resistance mechanisms. To gain mechanistic insights, we quantified EAB performance on grafted replicates of ash genotypes varying in ADB resistance and characterized ash phloem chemistry with targeted and untargeted metabolomics. Emerald ash borer performed better on ADB-susceptible than on ADB-resistant genotypes. Moreover, changes in EAB performance aligned with differences in phloem chemical profiles between ADB-susceptible and ADB-resistant genotypes. We show that intraspecific variation in phloem chemistry in European ash can confer increased cross-resistance to invasive antagonists from different taxonomic kingdoms. Our study suggests that promotion of ADB-resistant ash genotypes may simultaneously help to control the ADB disease and reduce EAB-caused ash losses, which may be critical for the long-term stability of this keystone tree species.
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Affiliation(s)
- Martin M Gossner
- Forest Health & Biotic Interactions, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), 8903, Birmensdorf, Switzerland
- Institute of Terrestrial Ecosystems, ETH Zürich, 8092, Zurich, Switzerland
| | - Anouchka Perret-Gentil
- Forest Health & Biotic Interactions, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), 8903, Birmensdorf, Switzerland
| | - Elisabeth Britt
- Forest Health & Biotic Interactions, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), 8903, Birmensdorf, Switzerland
| | - Valentin Queloz
- Forest Health & Biotic Interactions, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), 8903, Birmensdorf, Switzerland
| | - Gaétan Glauser
- Neuchâtel Platform of Analytical Chemistry, University of Neuchâtel, 2000, Neuchâtel, Switzerland
| | - Tim Ladd
- Great Lakes Forestry Centre, Canadian Forest Service, Natural Resources Canada, ON P6A 2E5, Sault Ste. Marie, ON, Canada
| | - Amanda D Roe
- Great Lakes Forestry Centre, Canadian Forest Service, Natural Resources Canada, ON P6A 2E5, Sault Ste. Marie, ON, Canada
| | - Michelle Cleary
- Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, SE-234 22, Alnarp, Sweden
| | | | - Lene R Nielsen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, 1958, Frederiksberg C, Denmark
| | - Soumya K Ghosh
- Department of Plant Pathology, The Ohio State University, Columbus, 43210, OH, USA
| | - Pierluigi Bonello
- Department of Plant Pathology, The Ohio State University, Columbus, 43210, OH, USA
| | - Michael Eisenring
- Forest Health & Biotic Interactions, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), 8903, Birmensdorf, Switzerland
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13
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Atashi M, Reyes CDG, Sandilya V, Purba W, Ahmadi P, Hakim MA, Kobeissy F, Plazzi G, Moresco M, Lanuzza B, Ferri R, Mechref Y. LC-MS/MS Quantitation of HILIC-Enriched N-glycopeptides Derived from Low-Abundance Serum Glycoproteins in Patients with Narcolepsy Type 1. Biomolecules 2023; 13:1589. [PMID: 38002271 PMCID: PMC10669497 DOI: 10.3390/biom13111589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/18/2023] [Accepted: 10/20/2023] [Indexed: 11/26/2023] Open
Abstract
Glycoproteomic analysis is always challenging because of low abundance and complex site-specific heterogeneity. Glycoproteins are involved in various biological processes such as cell signaling, adhesion, and cell-cell communication and may serve as potential biomarkers when analyzing different diseases. Here, we investigate glycoproteins in narcolepsy type 1 (NT1) disease, a form of narcolepsy characterized by cataplexy-the sudden onset of muscle paralysis that is typically triggered by intense emotions. In this study, 27 human blood serum samples were analyzed, 16 from NT1 patients and 11 from healthy individuals serving as controls. We quantified hydrophilic interaction liquid chromatography (HILIC)-enriched glycopeptides from low-abundance serum samples of controls and NT1 patients via LC-MS/MS. Twenty-eight unique N-glycopeptides showed significant changes between the two studied groups. The sialylated N-glycopeptide structures LPTQNITFQTESSVAEQEAEFQSPK HexNAc6, Hex3, Neu5Ac2 (derived from the ITIH4 protein) and the structure IVLDPSGSMNIYLVLDGSDSIGASNFTGAK HexNAc5, Hex4, Fuc1 (derived from the CFB protein), with p values of 0.008 and 0.01, respectively, were elevated in NT1 samples compared with controls. In addition, the N-glycopeptide protein sources Ceruloplasmin, Complement factor B, and ITH4 were observed to play an important role in the complement activation and acute-phase response signaling pathways. This may explain the possible association between the biomarkers and pathophysiological effects.
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Affiliation(s)
- Mojgan Atashi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (M.A.); (C.D.G.R.); (V.S.); (W.P.); (P.A.); (M.A.H.)
| | - Cristian D. Gutierrez Reyes
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (M.A.); (C.D.G.R.); (V.S.); (W.P.); (P.A.); (M.A.H.)
| | - Vishal Sandilya
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (M.A.); (C.D.G.R.); (V.S.); (W.P.); (P.A.); (M.A.H.)
| | - Waziha Purba
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (M.A.); (C.D.G.R.); (V.S.); (W.P.); (P.A.); (M.A.H.)
| | - Parisa Ahmadi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (M.A.); (C.D.G.R.); (V.S.); (W.P.); (P.A.); (M.A.H.)
| | - Md. Abdul Hakim
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (M.A.); (C.D.G.R.); (V.S.); (W.P.); (P.A.); (M.A.H.)
| | - Firas Kobeissy
- Department of biochemistry and molecular genetics, Faculty of Biochemistry and Molecular Genetics, American University of Beirut, Beirut 11072020, Lebanon;
- Department of Neurobiology, Center for Neurotrauma, Multiomics & Biomarkers (CNMB), Neuroscience Institute, Morehouse School of Medicine, Atlanta, GE 30310, USA
| | - Giuseppe Plazzi
- IRCCS, Instituto delle Scienze Neurologiche di Bologna, 40124 Bologna, Italy; (G.P.); (M.M.)
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Monica Moresco
- IRCCS, Instituto delle Scienze Neurologiche di Bologna, 40124 Bologna, Italy; (G.P.); (M.M.)
| | - Bartolo Lanuzza
- Sleep Research Center, Department of Neurology IC, Oasi Research Institute-IRCCS, 94018 Tronia, Italy; (B.L.); (R.F.)
| | - Raffaele Ferri
- Sleep Research Center, Department of Neurology IC, Oasi Research Institute-IRCCS, 94018 Tronia, Italy; (B.L.); (R.F.)
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (M.A.); (C.D.G.R.); (V.S.); (W.P.); (P.A.); (M.A.H.)
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14
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Stincone P, Pakkir Shah AK, Schmid R, Graves LG, Lambidis SP, Torres RR, Xia SN, Minda V, Aron AT, Wang M, Hughes CC, Petras D. Evaluation of Data-Dependent MS/MS Acquisition Parameters for Non-Targeted Metabolomics and Molecular Networking of Environmental Samples: Focus on the Q Exactive Platform. Anal Chem 2023; 95:12673-12682. [PMID: 37578818 PMCID: PMC10469366 DOI: 10.1021/acs.analchem.3c01202] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 07/19/2023] [Indexed: 08/15/2023]
Abstract
Non-targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a widely used tool for metabolomics analysis, enabling the detection and annotation of small molecules in complex environmental samples. Data-dependent acquisition (DDA) of product ion spectra is thereby currently one of the most frequently applied data acquisition strategies. The optimization of DDA parameters is central to ensuring high spectral quality, coverage, and number of compound annotations. Here, we evaluated the influence of 10 central DDA settings of the Q Exactive mass spectrometer on natural organic matter samples from ocean, river, and soil environments. After data analysis with classical and feature-based molecular networking using MZmine and GNPS, we compared the total number of network nodes, multivariate clustering, and spectrum quality-related metrics such as annotation and singleton rates, MS/MS placement, and coverage. Our results show that automatic gain control, microscans, mass resolving power, and dynamic exclusion are the most critical parameters, whereas collision energy, TopN, and isolation width had moderate and apex trigger, monoisotopic selection, and isotopic exclusion minor effects. The insights into the data acquisition ergonomics of the Q Exactive platform presented here can guide new users and provide them with initial method parameters, some of which may also be transferable to other sample types and MS platforms.
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Affiliation(s)
- Paolo Stincone
- Cluster
of Excellence-Controlling Microbes to Fight Infection, University of Tübingen, Tübingen 72076, Germany
| | - Abzer K. Pakkir Shah
- Cluster
of Excellence-Controlling Microbes to Fight Infection, University of Tübingen, Tübingen 72076, Germany
| | - Robin Schmid
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Praha 6, Czech Republic
| | - Lana G. Graves
- Faculty
of Mathematics and Natural Sciences, Environmental Systems Analysis, University of Tübingen, Tübingen 72076, Germany
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin 12587, Germany
| | - Stilianos P. Lambidis
- Cluster
of Excellence-Controlling Microbes to Fight Infection, University of Tübingen, Tübingen 72076, Germany
| | - Ralph R. Torres
- University
of California San Diego, Scripps Institution of Oceanography, La Jolla, California 92093, United States
| | - Shu-Ning Xia
- Cluster
of Excellence-Controlling Microbes to Fight Infection, University of Tübingen, Tübingen 72076, Germany
| | - Vidit Minda
- Department
of Chemistry and Biochemistry, University
of Denver, Denver, Colorado 80210, United States
- Department
of Pharmacology and Pharmaceutical Sciences, University of Missouri−Kansas City, Kansas City, Missouri 64108, United States
| | - Allegra T. Aron
- Department
of Chemistry and Biochemistry, University
of Denver, Denver, Colorado 80210, United States
| | - Mingxun Wang
- Department
of Computer Science, University of California
Riverside, Riverside, California 92507, United States
| | - Chambers C. Hughes
- Cluster
of Excellence-Controlling Microbes to Fight Infection, University of Tübingen, Tübingen 72076, Germany
- Department
of Microbial Bioactive Compounds, Interfaculty Institute for Microbiology
and Infection Medicine, University of Tübingen, Tübingen 72076, Germany
- German
Center for Infection Research, Partner Site
Tübingen, Tübingen 72076, Germany
| | - Daniel Petras
- Cluster
of Excellence-Controlling Microbes to Fight Infection, University of Tübingen, Tübingen 72076, Germany
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15
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Assress H, Ferruzzi MG, Lan RS. Optimization of Mass Spectrometric Parameters in Data Dependent Acquisition for Untargeted Metabolomics on the Basis of Putative Assignments. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:1621-1631. [PMID: 37419493 PMCID: PMC10402710 DOI: 10.1021/jasms.3c00084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/09/2023]
Abstract
Optimization of mass spectrometric parameters for a data dependent acquisition (DDA) experiment is essential to increase the MS/MS coverage and hence increase metabolite identifications in untargeted metabolomics. We explored the influence of mass spectrometric parameters including mass resolution, radio frequency (RF) level, signal intensity threshold, number of MS/MS events, cycle time, collision energy, maximum ion injection time (MIT), dynamic exclusion, and automatic gain control (AGC) target value on metabolite annotations on an Exploris 480-Orbitrap mass spectrometer. Optimal annotation results were obtained by performing ten data dependent MS/MS scans with a mass isolation window of 2.0 m/z and a minimum signal intensity threshold of 1 × 104 at a mass resolution of 180,000 for MS and 30,000 for MS/MS, while maintaining the RF level at 70%. Furthermore, combining an AGC target value of 5 × 106 and MIT of 100 ms for MS and an AGC target value of 1 × 105 and an MIT of 50 ms for MS/MS scans provided an improved number of annotated metabolites. A 10 s exclusion duration and a two stepped collision energy were optimal for higher spectral quality. These findings confirm that MS parameters do influence metabolomics results, and propose strategies for increasing metabolite coverage in untargeted metabolomics. A limitation of this work is that our parameters were only optimized for one RPLC method on single matrix and may be different for other protocols. Additionally, no metabolites were identified at level 1 confidence. The results presented here are based on metabolite annotations and need to be validated with authentic standards.
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Affiliation(s)
- Hailemariam
Abrha Assress
- Arkansas
Children’s Nutrition Center, Little Rock, Arkansas 72202, United States
- Department
of Pediatrics, University of Arkansas for
Medical Sciences, Little
Rock, Arkansas 72205, United States
| | - Mario G. Ferruzzi
- Arkansas
Children’s Nutrition Center, Little Rock, Arkansas 72202, United States
- Department
of Pediatrics, University of Arkansas for
Medical Sciences, Little
Rock, Arkansas 72205, United States
| | - Renny S. Lan
- Arkansas
Children’s Nutrition Center, Little Rock, Arkansas 72202, United States
- Department
of Pediatrics, University of Arkansas for
Medical Sciences, Little
Rock, Arkansas 72205, United States
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16
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Ambli M, Deracinois B, Jenequin AS, Ravallec R, Cudennec B, Flahaut C. Impact of Bioinformatics Search Parameters for Peptides' Identification and Their Post-Translational Modifications: A Case Study of Proteolysed Gelatines from Beef, Pork, and Fish. Foods 2023; 12:2524. [PMID: 37444262 DOI: 10.3390/foods12132524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 06/16/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
Bioinformatics software, allowing the identification of peptides by the comparison of peptide fragmentation spectra obtained by mass spectrometry versus targeted databases or directly by de novo sequencing, is now mandatory in peptidomics/proteomics approaches. Programming the identification software requires specifying, among other things, the mass measurement accuracy of the instrument and the digestion enzyme used with the number of missed cleavages allowed. Moreover, these software algorithms are able to identify a large number of post-translational modifications (PTMs). However, peptide and PTM identifications are challenging in the agrofood field due to non-specific cleavage sites of physiological- or food-grade enzymes and the number and location of PTMs. In this study, we show the importance of customized software programming to obtain a better peptide and PTM identification rate in the agrofood field. A gelatine product and one industrial gelatine hydrolysate from three different sources (beef, pork, and fish), each digested by simulated gastrointestinal digestion, MS-grade trypsin, or both, were used to perform the comparisons. Two main points are illustrated: (i) the impact of the set-up of specific enzyme versus no specific enzyme use and (ii) the impact of a maximum of six PTMs allowed per peptide versus the standard of three. Prior knowledge of the composition of the raw proteins is an important asset for better identification of peptide sequences.
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Affiliation(s)
- Mouna Ambli
- UMR Transfrontalière BioEcoAgro-INRAe N° 1158, Univ. Artois, Univ. Lille, INRAe, Univ. Liège, UPJV, JUNIA, Univ. Littoral Côte d'Opale, ICV-Institut Charles Viollette, 62300 Lens, France
| | - Barbara Deracinois
- UMR Transfrontalière BioEcoAgro-INRAe N° 1158, Univ. Artois, Univ. Lille, INRAe, Univ. Liège, UPJV, JUNIA, Univ. Littoral Côte d'Opale, ICV-Institut Charles Viollette, 62300 Lens, France
| | - Anne-Sophie Jenequin
- UMR Transfrontalière BioEcoAgro-INRAe N° 1158, Univ. Artois, Univ. Lille, INRAe, Univ. Liège, UPJV, JUNIA, Univ. Littoral Côte d'Opale, ICV-Institut Charles Viollette, 62300 Lens, France
| | - Rozenn Ravallec
- UMR Transfrontalière BioEcoAgro-INRAe N° 1158, Univ. Artois, Univ. Lille, INRAe, Univ. Liège, UPJV, JUNIA, Univ. Littoral Côte d'Opale, ICV-Institut Charles Viollette, 62300 Lens, France
| | - Benoit Cudennec
- UMR Transfrontalière BioEcoAgro-INRAe N° 1158, Univ. Artois, Univ. Lille, INRAe, Univ. Liège, UPJV, JUNIA, Univ. Littoral Côte d'Opale, ICV-Institut Charles Viollette, 62300 Lens, France
| | - Christophe Flahaut
- UMR Transfrontalière BioEcoAgro-INRAe N° 1158, Univ. Artois, Univ. Lille, INRAe, Univ. Liège, UPJV, JUNIA, Univ. Littoral Côte d'Opale, ICV-Institut Charles Viollette, 62300 Lens, France
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17
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Sahu I, Zhu H, Buhrlage SJ, Marto JA. Proteomic approaches to study ubiquitinomics. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194940. [PMID: 37121501 PMCID: PMC10612121 DOI: 10.1016/j.bbagrm.2023.194940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/21/2023] [Accepted: 04/20/2023] [Indexed: 05/02/2023]
Abstract
As originally described some 40 years ago, protein ubiquitination was thought to serve primarily as a static mark for protein degradation. In the ensuing years, it has become clear that 'ubiquitination' is a structurally diverse and dynamic post-translational modification and is intricately involved in a myriad of signaling pathways in all eukaryote cells. And like other key pathways in the functional proteome, ubiquitin signaling is often disrupted, sometimes severely so, in human pathophysiology. As a result of its central role in normal physiology and human disease, the ubiquitination field is now represented across the full landscape of biomedical research from fundamental structural and biochemical studies to translational and clinical research. In recent years, mass spectrometry has emerged as a powerful technology for the detection and characterization of protein ubiquitination. Herein we detail qualitative and quantitative proteomic methods using a compare/contrast approach to highlight their strengths and weaknesses.
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Affiliation(s)
- Indrajit Sahu
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - He Zhu
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sara J Buhrlage
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA; Center for Emergent Drug Targets, USA.
| | - Jarrod A Marto
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA; Center for Emergent Drug Targets, USA.
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18
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Lepoittevin M, Blancart-Remaury Q, Kerforne T, Pellerin L, Hauet T, Thuillier R. Comparison between 5 extractions methods in either plasma or serum to determine the optimal extraction and matrix combination for human metabolomics. Cell Mol Biol Lett 2023; 28:43. [PMID: 37210499 DOI: 10.1186/s11658-023-00452-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/18/2023] [Indexed: 05/22/2023] Open
Abstract
BACKGROUND Although metabolomics continues to expand in many domains of research, methodological issues such as sample type, extraction and analytical protocols have not been standardized, impeding proper comparison between studies and future research. METHODS In the present study, five solvent-based and solid-phase extraction methods were investigated in both plasma and serum. All these extracts were analyzed using four liquid chromatography coupled with high resolution mass spectrometry (LC-MS) protocols, either in reversed or normal-phase and with both types of ionization. The performances of each method were compared according to putative metabolite coverage, method repeatability and also extraction parameters such as overlap, linearity and matrix effect; in both untargeted (global) and targeted approaches using fifty standard spiked analytes. RESULTS Our results verified the broad specificity and outstanding accuracy of solvent precipitation, namely methanol and methanol/acetonitrile. We also reveal high orthogonality between methanol-based methods and SPE, providing the possibility of increased metabolome coverage, however we highlight that such potential benefits must be weighed against time constrains, sample consumption and the risk of low reproducibility of SPE method. Furthermore, we highlighted the careful consideration about matrix choice. Plasma showed the most suitable in this metabolomics approach combined with methanol-based methods. CONCLUSIONS Our work proposes to facilitate rational design of protocols towards standardization of these approaches to improve the impact of metabolomics research.
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Affiliation(s)
- Maryne Lepoittevin
- Inserm Unit IRMETIST, UMR U1313, University of Poitiers, Faculty of Medicine and Pharmacy, 86073, Poitiers, France
| | | | - Thomas Kerforne
- Inserm Unit IRMETIST, UMR U1313, University of Poitiers, Faculty of Medicine and Pharmacy, 86073, Poitiers, France
- Cardio-Thoracic and Vascular Surgery Intensive Care Unit, Coordination of P.M.O. CHU Poitiers, 86021, Poitiers, France
| | - Luc Pellerin
- Inserm Unit IRMETIST, UMR U1313, University of Poitiers, Faculty of Medicine and Pharmacy, 86073, Poitiers, France
- Biochemistry Department CHU Poitiers, 86021, Poitiers, France
| | - Thierry Hauet
- Inserm Unit IRMETIST, UMR U1313, University of Poitiers, Faculty of Medicine and Pharmacy, 86073, Poitiers, France
- Biochemistry Department CHU Poitiers, 86021, Poitiers, France
- University Hospital Federation SUPPORT Tours Poitiers Limoges, 86021, Poitiers, France
| | - Raphael Thuillier
- Inserm Unit IRMETIST, UMR U1313, University of Poitiers, Faculty of Medicine and Pharmacy, 86073, Poitiers, France.
- Biochemistry Department CHU Poitiers, 86021, Poitiers, France.
- University Hospital Federation SUPPORT Tours Poitiers Limoges, 86021, Poitiers, France.
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19
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Calvete JJ, Lomonte B, Saviola AJ, Calderón Celis F, Ruiz Encinar J. Quantification of snake venom proteomes by mass spectrometry-considerations and perspectives. MASS SPECTROMETRY REVIEWS 2023. [PMID: 37155340 DOI: 10.1002/mas.21850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 11/24/2022] [Accepted: 03/30/2023] [Indexed: 05/10/2023]
Abstract
The advent of soft ionization mass spectrometry-based proteomics in the 1990s led to the development of a new dimension in biology that conceptually allows for the integral analysis of whole proteomes. This transition from a reductionist to a global-integrative approach is conditioned to the capability of proteomic platforms to generate and analyze complete qualitative and quantitative proteomics data. Paradoxically, the underlying analytical technique, molecular mass spectrometry, is inherently nonquantitative. The turn of the century witnessed the development of analytical strategies to endow proteomics with the ability to quantify proteomes of model organisms in the sense of "an organism for which comprehensive molecular (genomic and/or transcriptomic) resources are available." This essay presents an overview of the strategies and the lights and shadows of the most popular quantification methods highlighting the common misuse of label-free approaches developed for model species' when applied to quantify the individual components of proteomes of nonmodel species (In this essay we use the term "non-model" organisms for species lacking comprehensive molecular (genomic and/or transcriptomic) resources, a circumstance that, as we detail in this review-essay, conditions the quantification of their proteomes.). We also point out the opportunity of combining elemental and molecular mass spectrometry systems into a hybrid instrumental configuration for the parallel identification and absolute quantification of venom proteomes. The successful application of this novel mass spectrometry configuration in snake venomics represents a proof-of-concept for a broader and more routine application of hybrid elemental/molecular mass spectrometry setups in other areas of the proteomics field, such as phosphoproteomics, metallomics, and in general in any biological process where a heteroatom (i.e., any atom other than C, H, O, N) forms integral part of its mechanism.
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Affiliation(s)
- Juan J Calvete
- Evolutionary and Translational Venomics Laboratory, Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain
| | - Bruno Lomonte
- Unidad de Proteómica, Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Anthony J Saviola
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | | | - Jorge Ruiz Encinar
- Department of Physical and Analytical Chemistry, University of Oviedo, Oviedo, Spain
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20
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Lupolt SN, Newmeyer MN, Lyu Q, Prasse C, Nachman KE. Optimization of a method for collecting infant and toddler urine for non-target analysis using cotton pads and commercially available disposable diapers. JOURNAL OF EXPOSURE SCIENCE & ENVIRONMENTAL EPIDEMIOLOGY 2023:10.1038/s41370-023-00553-x. [PMID: 37149702 DOI: 10.1038/s41370-023-00553-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 05/08/2023]
Abstract
BACKGROUND Urine is an abundant and useful medium for measuring biomarkers related to chemical exposures in infants and children. Identification of novel biomarkers is greatly enhanced with non-targeted analysis (NTA), a powerful methodology for broad chemical analysis of environmental and biological specimens. However, collecting urine in non-toilet trained children presents many challenges, and contamination from specimen collection can impact NTA results. OBJECTIVES We optimized a caregiver-driven method for collecting urine from infants and children using cotton pads and commercially available disposable diapers for NTA and demonstrate its applicability to various children biomonitoring studies. METHODS Experiments were first performed to evaluate the effects of processing method (i.e., centrifuge vs. syringe), storage temperature, and diaper brand on recovery of urine absorbed to cotton pads. Caregivers of 11 children (<2 years) used and retained diapers (with cotton pads) to collect their child's urine for 24 h. Specimens were analyzed via a NTA method implementing an exclusion list of ions related to contamination from collection materials. RESULTS Centrifuging cotton pads through a small-pore membrane, compared to a manual syringe method, and storing diapers at 4 °C, compared to room temperature, resulted in larger volumes of recovered sample. This method was successfully implemented to recover urine from cotton pads collected in the field; between 5-9 diapers were collected per child in 24 h, and the total mean volume of urine recovered was 44.7 (range 26.7-71.1) mL. NTA yielded a list of compounds present in urine and/or stool that may hold promise as biomarkers of chemical exposures from a variety of sources. IMPACT STATEMENT Infant and children urine is a valuable matrix for studies of the early life exposome, in that numerous biological markers of exposure and outcome can be derived from a single analysis. Depending on the nature of the exposure study, it may be the case that a simple collection method that can be facilitated by caregivers of young children is desirable, especially when time-integrated samples or large volumes of urine are needed. We describe the process for development and results of an optimized method for urine collection and analysis using commercially available diapers and non-target analysis.
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Affiliation(s)
- Sara N Lupolt
- Department of Environmental Health & Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Risk Sciences and Public Policy Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Matthew N Newmeyer
- Department of Environmental Health & Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Qinfan Lyu
- Department of Environmental Health & Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Carsten Prasse
- Department of Environmental Health & Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Risk Sciences and Public Policy Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| | - Keeve E Nachman
- Department of Environmental Health & Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Risk Sciences and Public Policy Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Johns Hopkins Center for a Livable Future, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Department of Health Policy and Management, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
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21
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Ramabulana AT, Petras D, Madala NE, Tugizimana F. Mass spectrometry DDA parameters and global coverage of the metabolome: Spectral molecular networks of momordica cardiospermoides plants. Metabolomics 2023; 19:18. [PMID: 36920561 DOI: 10.1007/s11306-023-01981-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 02/15/2023] [Indexed: 03/16/2023]
Abstract
INTRODUCTION Molecular networking (MN) has emerged as a key strategy to organize and annotate untargeted tandem mass spectrometry (MS/MS) data generated using either data independent- or dependent acquisition (DIA or DDA). The latter presents a time-efficient approach where full scan (MS1) and MS2 spectra are obtained with shorter cycle times. However, there are limitations related to DDA parameters, some of which are (i) intensity threshold and (ii) collision energy. The former determines ion prioritization for fragmentation, and the latter defines the fragmentation of selected ions. These DDA parameters inevitably determine the coverage and quality of spectral data, which would affect the outputs of MN methods. OBJECTIVES This study assessed the extent to which the quality of the tandem spectral data relates to MN topology and subsequent implications in the annotation of metabolites and chemical classification relative to the different DDA parameters employed. METHODS Herein, characterising the metabolome of Momordica cardiospermoides plants, we employ classical MN performance indicators to investigate the effects of collision energies and intensity thresholds on the topology of generated MN and propagated annotations. RESULTS We demonstrated that the lowest predefined intensity thresholds and collision energies result in comprehensive molecular networks. Comparatively, higher intensity thresholds and collision energies resulted in fewer MS2 spectra acquisition, subsequently fewer nodes, and a limited exploration of the metabolome through MN. CONCLUSION Contributing to ongoing efforts and conversations on improving DDA strategies, this study proposes a framework in which multiple DDA parameters are utilized to increase the coverage of ions acquired and improve the global coverage of MN, propagated annotations, and the chemical classification performed.
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Affiliation(s)
| | - Daniel Petras
- CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Medicine, University of Tubingen, Auf der Morgenstelle 28, Tubingen, 72076, Germany
| | - Ntakadzeni E Madala
- Department of Biochemistry and Microbiology, University of Venda, Thohoyandou, South Africa
| | - Fidele Tugizimana
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg, South Africa.
- International Research and Development Division, Omnia Group, Ltd, Johannesburg, South Africa.
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22
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Awchi M, Sinues P, Datta AN, García-Gómez D, Singh KD. UHPLC-MS/MS-Based Identity Confirmation of Amino Acids Involved in Response to and Side Effects from Antiseizure Medications. J Proteome Res 2023; 22:990-995. [PMID: 36812155 PMCID: PMC9990125 DOI: 10.1021/acs.jproteome.2c00835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Real-time breath analysis using secondary electrospray ionization coupled with high-resolution mass spectrometry is a fast and noninvasive method to access the metabolic state of a person. However, it lacks the ability to unequivocally assign mass spectral features to compounds due to the absence of chromatographic separation. This can be overcomed by using exhaled breath condensate and conventional liquid chromatography-mass spectrometry (LC-MS) systems. In this study, to the best of our knowledge, we confirm for the first time the presence of six amino acids (GABA, Oxo-Pro, Asp, Gln, Glu, and Tyr) previously reported to be involved in response to and side effects from antiseizure medications in exhaled breath condensate and by extension in exhaled human breath. Raw data are publicly available at MetaboLights with the accession number MTBLS6760.
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Affiliation(s)
- Mo Awchi
- University Children's Hospital Basel, University of Basel, Spitalstrasse 33, 4056 Basel, Switzerland.,Department of Biomedical Engineering, University of Basel, Gewerbestrasse 14, 4123 Allschwil, Switzerland
| | - Pablo Sinues
- University Children's Hospital Basel, University of Basel, Spitalstrasse 33, 4056 Basel, Switzerland.,Department of Biomedical Engineering, University of Basel, Gewerbestrasse 14, 4123 Allschwil, Switzerland
| | - Alexandre N Datta
- University Children's Hospital Basel, University of Basel, Spitalstrasse 33, 4056 Basel, Switzerland
| | - Diego García-Gómez
- Department of Analytical Chemistry, University of Salamanca, Plaza de los Caídos s/n, 37008 Salamanca, Spain
| | - Kapil Dev Singh
- University Children's Hospital Basel, University of Basel, Spitalstrasse 33, 4056 Basel, Switzerland.,Department of Biomedical Engineering, University of Basel, Gewerbestrasse 14, 4123 Allschwil, Switzerland
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23
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Cajka T, Hricko J, Rudl Kulhava L, Paucova M, Novakova M, Kuda O. Optimization of Mobile Phase Modifiers for Fast LC-MS-Based Untargeted Metabolomics and Lipidomics. Int J Mol Sci 2023; 24:ijms24031987. [PMID: 36768308 PMCID: PMC9916776 DOI: 10.3390/ijms24031987] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 01/21/2023] Open
Abstract
Liquid chromatography-mass spectrometry (LC-MS) is the method of choice for the untargeted profiling of biological samples. A multiplatform LC-MS-based approach is needed to screen polar metabolites and lipids comprehensively. Different mobile phase modifiers were tested to improve the electrospray ionization process during metabolomic and lipidomic profiling. For polar metabolites, hydrophilic interaction LC using a mobile phase with 10 mM ammonium formate/0.125% formic acid provided the best performance for amino acids, biogenic amines, sugars, nucleotides, acylcarnitines, and sugar phosphate, while reversed-phase LC (RPLC) with 0.1% formic acid outperformed for organic acids. For lipids, RPLC using a mobile phase with 10 mM ammonium formate or 10 mM ammonium formate with 0.1% formic acid permitted the high signal intensity of various lipid classes ionized in ESI(+) and robust retention times. For ESI(-), the mobile phase with 10 mM ammonium acetate with 0.1% acetic acid represented a reasonable compromise regarding the signal intensity of the detected lipids and the stability of retention times compared to 10 mM ammonium acetate alone or 0.02% acetic acid. Collectively, we show that untargeted methods should be evaluated not only on the total number of features but also based on common metabolites detected by a specific platform along with the long-term stability of retention times.
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24
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Santorelli L, Caterino M, Costanzo M. Dynamic Interactomics by Cross-Linking Mass Spectrometry: Mapping the Daily Cell Life in Postgenomic Era. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:633-649. [PMID: 36445175 DOI: 10.1089/omi.2022.0137] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The majority of processes that occur in daily cell life are modulated by hundreds to thousands of dynamic protein-protein interactions (PPI). The resulting protein complexes constitute a tangled network that, with its continuous remodeling, builds up highly organized functional units. Thus, defining the dynamic interactome of one or more proteins allows determining the full range of biological activities these proteins are capable of. This conceptual approach is poised to gain further traction and significance in the current postgenomic era wherein the treatment of severe diseases needs to be tackled at both genomic and PPI levels. This also holds true for COVID-19, a multisystemic disease affecting biological networks across the biological hierarchy from genome to proteome to metabolome. In this overarching context and the current historical moment of the COVID-19 pandemic where systems biology increasingly comes to the fore, cross-linking mass spectrometry (XL-MS) has become highly relevant, emerging as a powerful tool for PPI discovery and characterization. This expert review highlights the advanced XL-MS approaches that provide in vivo insights into the three-dimensional protein complexes, overcoming the static nature of common interactomics data and embracing the dynamics of the cell proteome landscape. Many XL-MS applications based on the use of diverse cross-linkers, MS detection methods, and predictive bioinformatic tools for single proteins or proteome-wide interactions were shown. We conclude with a future outlook on XL-MS applications in the field of structural proteomics and ways to sustain the remarkable flexibility of XL-MS for dynamic interactomics and structural studies in systems biology and planetary health.
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Affiliation(s)
- Lucia Santorelli
- Department of Oncology and Hematology-Oncology, University of Milano, Milan, Italy.,IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Marianna Caterino
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy.,CEINGE-Biotecnologie Avanzate s.c.ar.l., Naples, Italy
| | - Michele Costanzo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy.,CEINGE-Biotecnologie Avanzate s.c.ar.l., Naples, Italy
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25
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Toward building mass spectrometry-based metabolomics and lipidomics atlases for biological and clinical research. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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26
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Ishii H, Shibuya M, Kusano K, Sone Y, Kamiya T, Wakuno A, Ito H, Miyata K, Sato F, Kuroda T, Yamada M, Leung GNW. Generic approach for the discovery of drug metabolites in horses based on data-dependent acquisition by liquid chromatography high-resolution mass spectrometry and its applications to pharmacokinetic study of daprodustat. Anal Bioanal Chem 2022; 414:8125-8142. [PMID: 36181513 DOI: 10.1007/s00216-022-04347-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/14/2022] [Accepted: 09/20/2022] [Indexed: 11/27/2022]
Abstract
In drug metabolism studies in horses, non-targeted analysis by means of liquid chromatography coupled with high-resolution mass spectrometry with data-dependent acquisition (DDA) has recently become increasingly popular for rapid identification of potential biomarkers in post-administration biological samples. However, the most commonly encountered problem is the presence of highly abundant interfering components that co-elute with the target substances, especially if the concentrations of these substances are relatively low. In this study, we evaluated the possibility of expanding DDA coverage for the identification of drug metabolites by applying intelligently generated exclusion lists (ELs) consisting of a set of chemical backgrounds and endogenous substances. Daprodustat was used as a model compound because of its relatively lower administration dose (100 mg) compared to other hypoxia-inducible factor stabilizers and the high demand in the detection sensitivity of its metabolites at the anticipated lower concentrations. It was found that the entire DDA process could efficiently identify both major and minor metabolites (flagged beyond the pre-set DDA threshold) in a single run after applying the ELs to exclude 67.7-99.0% of the interfering peaks, resulting in a much higher chance of triggering DDA to cover the analytes of interest. This approach successfully identified 21 metabolites of daprodustat and then established the metabolic pathway. It was concluded that the use of this generic intelligent "DDA + EL" approach for non-targeted analysis is a powerful tool for the discovery of unknown metabolites, even in complex plasma and urine matrices in the context of doping control.
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Affiliation(s)
- Hideaki Ishii
- Drug Analysis Department, Laboratory of Racing Chemistry, 1731-2 Tsuruta-machi, Utsunomiya, Tochigi, 320-0851, Japan.
- Department of Pharmaceutical Sciences, Tohoku University Hospital, 1-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8574, Japan.
| | - Mariko Shibuya
- Drug Analysis Department, Laboratory of Racing Chemistry, 1731-2 Tsuruta-machi, Utsunomiya, Tochigi, 320-0851, Japan
| | - Kanichi Kusano
- Veterinarian Section, Equine Department, Japan Racing Association, 6-11-1 Roppongi, Minato-ku, Tokyo, 105-0003, Japan
| | - Yu Sone
- Veterinarian Section, Equine Department, Japan Racing Association, 6-11-1 Roppongi, Minato-ku, Tokyo, 105-0003, Japan
| | - Takahiro Kamiya
- Equine Veterinary Clinic, Horse Racing School, Japan Racing Association, 835-1 Ne, Shiroi, Chiba, 270-1431, Japan
| | - Ai Wakuno
- Equine Veterinary Clinic, Horse Racing School, Japan Racing Association, 835-1 Ne, Shiroi, Chiba, 270-1431, Japan
| | - Hideki Ito
- Equine Veterinary Clinic, Horse Racing School, Japan Racing Association, 835-1 Ne, Shiroi, Chiba, 270-1431, Japan
| | - Kenji Miyata
- JRA Equestrian Park Utsunomiya Office, 321-4 Tokamicho, Utsunomiya, Tochigi, 320-0856, Japan
| | - Fumio Sato
- Clinical Veterinary Medicine Division, Equine Research Institute, Japan Racing Association, 1400-4, Shiba, Shimotsuke, Tochigi, 329-0412, Japan
| | - Taisuke Kuroda
- Clinical Veterinary Medicine Division, Equine Research Institute, Japan Racing Association, 1400-4, Shiba, Shimotsuke, Tochigi, 329-0412, Japan
| | - Masayuki Yamada
- Drug Analysis Department, Laboratory of Racing Chemistry, 1731-2 Tsuruta-machi, Utsunomiya, Tochigi, 320-0851, Japan
| | - Gary Ngai-Wa Leung
- Drug Analysis Department, Laboratory of Racing Chemistry, 1731-2 Tsuruta-machi, Utsunomiya, Tochigi, 320-0851, Japan
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27
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Jung YH, Lee DC, Kim JO, Kim JH. Untargeted metabolomics-assisted comparative cytochrome P450-dependent metabolism of fenbendazole in human and dog liver microsomes. Xenobiotica 2022; 52:986-996. [PMID: 36533905 DOI: 10.1080/00498254.2022.2160676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Fenbendazole (FBZ), a benzimidazole carbamate anthelmintic, has attracted attention for its antitumor activity. This study examined the metabolic characteristics of FBZ in humans compared with those in dogs. The phase I metabolites were identified in liver microsomal incubates using liquid chromatography-mass spectrometry (MS)-based untargeted metabolomics approaches. Seven metabolites of FBZ were identified by principal component analysis and orthogonal partial least square-discriminant analysis based on the global ion variables of the FBZ incubation groups. The chemical structure of the FBZ metabolites was suggested by examining the MS/MS spectrum and isotope distribution pattern. Cytochrome P450 (CYP) 1A1, CYP2D6, and CYP2J2 were the major isozymes responsible for the FBZ metabolism. No differences in the types of metabolites produced by the two species were noted. Multivariate analysis of human and dog incubation groups showed that five metabolites were relatively abundant in humans and the other two were not. In summary, the phase I metabolic profile of FBZ and the comparative metabolism between humans and dogs were examined using an untargeted metabolomics approach. This study suggests a successful investigation of FBZ metabolism in humans for conducting safety assessments regarding drug repositioning.
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Affiliation(s)
| | - Dong-Cheol Lee
- College of Pharmacy, Yeungnam University, Gyeongsan, Korea
| | - Jong Oh Kim
- College of Pharmacy, Yeungnam University, Gyeongsan, Korea
| | - Ju-Hyun Kim
- College of Pharmacy, Yeungnam University, Gyeongsan, Korea
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28
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Jia L, Wang H, Xu X, Wang H, Li X, Hu Y, Chen B, Liu M, Gao X, Li H, Guo D, Yang W. An off-line three-dimensional liquid chromatography/Q-Orbitrap mass spectrometry approach enabling the discovery of 1561 potentially unknown ginsenosides from the flower buds of Panax ginseng, Panax quinquefolius and Panax notoginseng. J Chromatogr A 2022; 1675:463177. [PMID: 35660315 DOI: 10.1016/j.chroma.2022.463177] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/21/2022] [Accepted: 05/24/2022] [Indexed: 01/05/2023]
Abstract
To comprehensively elucidate the herbal metabolites is crucial in natural products research to discover new lead compounds. Ginsenosides are an important class of bioactive components from the Panax plants exerting the significant tonifying effects. However, to identify new ginsenosides by the conventional strategies trends to be more and more difficult because of the large spans of acid-base property (the neutral and acidic saponins), molecular mass (400-1400 Da), and rather low content. Herein, an off-line multidimensional chromatography/high-resolution mass spectrometry approach was presented: ion exchange chromatography (IEC) as the first dimension of separation, hydrophilic interaction chromatography (HILIC) in the second dimension, and reversed-phase chromatography (RPC) for the third dimension which was hyphenated to a Q Exactive Q-Orbitrap mass spectrometer. By applying to the flower buds of P. ginseng (PGF), P. quinquefolius (PQF), and P. notoginseng (PNF), IEC using a PhenoSphereTM SAX column could fractionate the total extracts into the neutral (unretained) and acidic (retained) fractions, while HILIC (an XBridge Amide column) and RPC (BEH Shield RP18 column) achieved the hydrophilic interaction and hydrophobic interaction separations, respectively. Q-Orbitrap mass spectrometry offered rich structural information and complementary resolution to the co-eluting components, particular to those minor ones by including precursor ion lists in data-dependent acquisition. We could characterize 803 ginsenosides from PGF, 795 from PQF, and 833 from PNF, and 1561 thereof are potentially unknown. These results can indicate the great potential of this multidimensional approach in the ultra-deep characterization of complex herbal samples supporting the efficient discovery of potentially novel natural compounds.
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Affiliation(s)
- Li Jia
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin, 301617, China
| | - Hongda Wang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin, 301617, China
| | - Xiaoyan Xu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin, 301617, China
| | - Huimin Wang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin, 301617, China
| | - Xue Li
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin, 301617, China
| | - Ying Hu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin, 301617, China
| | - Boxue Chen
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin, 301617, China
| | - Meiyu Liu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin, 301617, China
| | - Xiumei Gao
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin, 301617, China; Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Ministry of Education, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin, 301617, China
| | - Huifang Li
- Thermo Fisher Scientific, Building #6, 27 Xinjinqiao Road, Pudong, Shanghai, 201206, China
| | - Dean Guo
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin, 301617, China; Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai, 201203, China.
| | - Wenzhi Yang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin, 301617, China.
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An online stepwise background subtraction-based ultra-high pressure liquid chromatography quadrupole time of flight tandem mass spectrometry dynamic detection integrated with metabolic molecular network strategy for intelligent characterization of the absorbed chemical-fingerprint of QiangHuoShengShi decoction in vivo. J Chromatogr A 2022; 1675:463172. [DOI: 10.1016/j.chroma.2022.463172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 05/20/2022] [Accepted: 05/20/2022] [Indexed: 01/31/2023]
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30
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Mi Y, Hu W, Li W, Wan S, Xu X, Liu M, Wang H, Mei Q, Chen Q, Yang Y, Chen B, Jiang M, Li X, Yang W, Guo D. Systematic Qualitative and Quantitative Analyses of Wenxin Granule via Ultra-High Performance Liquid Chromatography Coupled with Ion Mobility Quadrupole Time-of-Flight Mass Spectrometry and Triple Quadrupole–Linear Ion Trap Mass Spectrometry. Molecules 2022; 27:molecules27113647. [PMID: 35684583 PMCID: PMC9181919 DOI: 10.3390/molecules27113647] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/31/2022] [Accepted: 05/31/2022] [Indexed: 11/28/2022] Open
Abstract
Wenxin granule (WXG) is a popular traditional Chinese medicine (TCM) preparation for the treatment of arrhythmia disease. Potent analytical technologies are needed to elucidate its chemical composition and assess the quality differences among multibatch samples. In this work, both a multicomponent characterization and quantitative assay of WXG were conducted using two liquid chromatography–mass spectrometry (LC-MS) approaches. An ultra-high performance liquid chromatography–ion mobility quadrupole time-of-flight mass spectrometry (UHPLC/IM-QTOF-MS) approach combined with intelligent peak annotation workflows was developed to characterize the multicomponents of WXG. A hybrid scan approach enabling alternative data-independent and data-dependent acquisitions was established. We characterized 205 components, including 92 ginsenosides, 53 steroidal saponins, 14 alkaloids, and 46 others. Moreover, an optimized scheduled multiple reaction monitoring (sMRM) method was elaborated, targeting 24 compounds of WXG via ultra-high performance liquid chromatography–triple quadrupole linear ion trap mass spectrometry (UHPLC/QTrap-MS), which was validated based on its selectivity, precision, stability, repeatability, linearity, sensitivity, recovery, and matrix effect. By applying this method to 27 batches of WXG samples, the content variations of multiple markers from Notoginseng Radix et Rhizoma (21) and Codonopsis Radix (3) were depicted. Conclusively, we achieved the comprehensive multicomponent characterization and holistic quality assessment of WXG by targeting the non-volatile components.
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Affiliation(s)
- Yueguang Mi
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China; (Y.M.); (W.H.); (W.L.); (X.X.); (M.L.); (H.W.); (B.C.); (M.J.); (X.L.); (D.G.)
| | - Wandi Hu
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China; (Y.M.); (W.H.); (W.L.); (X.X.); (M.L.); (H.W.); (B.C.); (M.J.); (X.L.); (D.G.)
| | - Weiwei Li
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China; (Y.M.); (W.H.); (W.L.); (X.X.); (M.L.); (H.W.); (B.C.); (M.J.); (X.L.); (D.G.)
| | - Shiyu Wan
- Shenzhen Baoan Authentic TCM Therapy Hospital, Shenzhen 518101, China; (S.W.); (Q.M.); (Q.C.); (Y.Y.)
| | - Xiaoyan Xu
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China; (Y.M.); (W.H.); (W.L.); (X.X.); (M.L.); (H.W.); (B.C.); (M.J.); (X.L.); (D.G.)
| | - Meiyu Liu
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China; (Y.M.); (W.H.); (W.L.); (X.X.); (M.L.); (H.W.); (B.C.); (M.J.); (X.L.); (D.G.)
| | - Hongda Wang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China; (Y.M.); (W.H.); (W.L.); (X.X.); (M.L.); (H.W.); (B.C.); (M.J.); (X.L.); (D.G.)
| | - Quanxi Mei
- Shenzhen Baoan Authentic TCM Therapy Hospital, Shenzhen 518101, China; (S.W.); (Q.M.); (Q.C.); (Y.Y.)
| | - Qinhua Chen
- Shenzhen Baoan Authentic TCM Therapy Hospital, Shenzhen 518101, China; (S.W.); (Q.M.); (Q.C.); (Y.Y.)
| | - Yang Yang
- Shenzhen Baoan Authentic TCM Therapy Hospital, Shenzhen 518101, China; (S.W.); (Q.M.); (Q.C.); (Y.Y.)
| | - Boxue Chen
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China; (Y.M.); (W.H.); (W.L.); (X.X.); (M.L.); (H.W.); (B.C.); (M.J.); (X.L.); (D.G.)
| | - Meiting Jiang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China; (Y.M.); (W.H.); (W.L.); (X.X.); (M.L.); (H.W.); (B.C.); (M.J.); (X.L.); (D.G.)
| | - Xue Li
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China; (Y.M.); (W.H.); (W.L.); (X.X.); (M.L.); (H.W.); (B.C.); (M.J.); (X.L.); (D.G.)
| | - Wenzhi Yang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China; (Y.M.); (W.H.); (W.L.); (X.X.); (M.L.); (H.W.); (B.C.); (M.J.); (X.L.); (D.G.)
- Correspondence: ; Tel.: +86-022-5979-1833
| | - Dean Guo
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China; (Y.M.); (W.H.); (W.L.); (X.X.); (M.L.); (H.W.); (B.C.); (M.J.); (X.L.); (D.G.)
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai 201203, China
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Nevedomskaya E, Haendler B. From Omics to Multi-Omics Approaches for In-Depth Analysis of the Molecular Mechanisms of Prostate Cancer. Int J Mol Sci 2022; 23:ijms23116281. [PMID: 35682963 PMCID: PMC9181488 DOI: 10.3390/ijms23116281] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/24/2022] [Accepted: 06/01/2022] [Indexed: 02/01/2023] Open
Abstract
Cancer arises following alterations at different cellular levels, including genetic and epigenetic modifications, transcription and translation dysregulation, as well as metabolic variations. High-throughput omics technologies that allow one to identify and quantify processes involved in these changes are now available and have been instrumental in generating a wealth of steadily increasing data from patient tumors, liquid biopsies, and from tumor models. Extensive investigation and integration of these data have led to new biological insights into the origin and development of multiple cancer types and helped to unravel the molecular networks underlying this complex pathology. The comprehensive and quantitative analysis of a molecule class in a biological sample is named omics and large-scale omics studies addressing different prostate cancer stages have been performed in recent years. Prostate tumors represent the second leading cancer type and a prevalent cause of cancer death in men worldwide. It is a very heterogenous disease so that evaluating inter- and intra-tumor differences will be essential for a precise insight into disease development and plasticity, but also for the development of personalized therapies. There is ample evidence for the key role of the androgen receptor, a steroid hormone-activated transcription factor, in driving early and late stages of the disease, and this led to the development and approval of drugs addressing diverse targets along this pathway. Early genomic and transcriptomic studies have allowed one to determine the genes involved in prostate cancer and regulated by androgen signaling or other tumor-relevant signaling pathways. More recently, they have been supplemented by epigenomic, cistromic, proteomic and metabolomic analyses, thus, increasing our knowledge on the intricate mechanisms involved, the various levels of regulation and their interplay. The comprehensive investigation of these omics approaches and their integration into multi-omics analyses have led to a much deeper understanding of the molecular pathways involved in prostate cancer progression, and in response and resistance to therapies. This brings the hope that novel vulnerabilities will be identified, that existing therapies will be more beneficial by targeting the patient population likely to respond best, and that bespoke treatments with increased efficacy will be available soon.
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Affiliation(s)
| | - Bernard Haendler
- Correspondence: ; Tel.: +49-30-2215-41198; Fax: +49-30-468-18069
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Zheng T, Zhao Y, Li R, Huang M, Zhou A, Li Z, Wu H. Delineating the dynamic metabolic profile of Qi-Yu-San-Long decoction in rat urine using UPLC-QTOF-MSE coupled with a post-targeted screening strategy. J Pharm Anal 2022; 12:755-765. [PMID: 36320602 PMCID: PMC9615542 DOI: 10.1016/j.jpha.2022.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 04/27/2022] [Accepted: 05/16/2022] [Indexed: 11/24/2022] Open
Abstract
Qi-Yu-San-Long decoction (QYSLD) is a traditional Chinese medicine that has been clinically used in the treatment of non-small-cell lung cancer (NSCLC) for more than 20 years. However, to date, metabolic-related studies on QYSLD have not been performed. In this study, a post-targeted screening strategy based on ultra-performance liquid chromatography coupled with quadrupole time-of-flight full information tandem mass spectrometry (UPLC-QTOF-MSE) was developed to identify QYSLD-related xenobiotics in rat urine. The chemical compound database of QYSLD constituents was established from previous research, and metabolites related to these compounds were predicted in combination with their possible metabolic pathways. The metabolites were identified by extracted ion chromatograms using predicted m/z values as well as retention time, excimer ions, and fragmentation behavior. Overall, 85 QYSLD-related xenobiotics (20 prototype compounds and 65 metabolites) were characterized from rat urine. The main metabolic reactions and elimination features of QYSLD included oxidation, reduction, decarboxylation, hydrolysis, demethylation, glucuronidation, sulfation, methylation, deglycosylation, acetylation, and associated combination reactions. Of the identified molecules, 14 prototype compounds and 58 metabolites were slowly eliminated, thus accumulating in vivo over an extended period, while five prototypes and two metabolites were present in vivo for a short duration. Furthermore, one prototype and five metabolites underwent the process of “appearing-disappearing-reappearing” in vivo. Overall, the metabolic profile and characteristics of QYSLD in rat urine were determined, which is useful in elucidating the active components of the decoction in vivo, thus providing the basis for studying its mechanism of action. A post-targeted screening strategy based on UPLC-QTOF-MSE was developed. Twenty prototype compounds and 65 metabolites of QYSLD were identified in rat urine. The main metabolic reactions and elimination features of QYSLD were determined in vivo. Dynamic metabolic profiles of QYSLD-related xenobiotics at multiple time intervals were delineated.
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Data-Independent Acquisition Enables Robust Quantification of 400 Proteins in Non-Depleted Canine Plasma. Proteomes 2022; 10:proteomes10010009. [PMID: 35324581 PMCID: PMC8953371 DOI: 10.3390/proteomes10010009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/25/2022] [Accepted: 02/22/2022] [Indexed: 12/30/2022] Open
Abstract
Mass spectrometry-based plasma proteomics offers a major advance for biomarker discovery in the veterinary field, which has traditionally been limited to quantification of a small number of proteins using biochemical assays. The development of foundational data and tools related to sequential window acquisition of all theoretical mass spectra (SWATH)-mass spectrometry has allowed for quantitative profiling of a significant number of plasma proteins in humans and several animal species. Enabling SWATH in dogs enhances human biomedical research as a model species, and significantly improves diagnostic and disease monitoring capability. In this study, a comprehensive peptide spectral library specific to canine plasma proteome was developed and evaluated using SWATH for protein quantification in non-depleted dog plasma. Specifically, plasma samples were subjected to various orthogonal fractionation and digestion techniques, and peptide fragmentation data corresponding to over 420 proteins was collected. Subsequently, a SWATH-based assay was introduced that leveraged the developed resource and that enabled reproducible quantification of 400 proteins in non-depleted plasma samples corresponding to various disease conditions. The ability to profile the abundance of such a significant number of plasma proteins using a single method in dogs has the potential to accelerate biomarker discovery studies in this species.
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Tian Z, Liu F, Li D, Fernie AR, Chen W. Strategies for structure elucidation of small molecules based on LC–MS/MS data from complex biological samples. Comput Struct Biotechnol J 2022; 20:5085-5097. [PMID: 36187931 PMCID: PMC9489805 DOI: 10.1016/j.csbj.2022.09.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 09/03/2022] [Accepted: 09/03/2022] [Indexed: 11/06/2022] Open
Abstract
LC–MS/MS is a major analytical platform for metabolomics, which has become a recent hotspot in the research fields of life and environmental sciences. By contrast, structure elucidation of small molecules based on LC–MS/MS data remains a major challenge in the chemical and biological interpretation of untargeted metabolomics datasets. In recent years, several strategies for structure elucidation using LC–MS/MS data from complex biological samples have been proposed, these strategies can be simply categorized into two types, one based on structure annotation of mass spectra and for the other on retention time prediction. These strategies have helped many scientists conduct research in metabolite-related fields and are indispensable for the development of future tools. Here, we summarized the characteristics of the current tools and strategies for structure elucidation of small molecules based on LC–MS/MS data, and further discussed the directions and perspectives to improve the power of the tools or strategies for structure elucidation.
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Pettersen VK, Antunes LCM, Dufour A, Arrieta MC. Inferring early-life host and microbiome functions by mass spectrometry-based metaproteomics and metabolomics. Comput Struct Biotechnol J 2021; 20:274-286. [PMID: 35024099 PMCID: PMC8718658 DOI: 10.1016/j.csbj.2021.12.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 12/08/2021] [Accepted: 12/08/2021] [Indexed: 12/17/2022] Open
Abstract
Humans have a long-standing coexistence with microorganisms. In particular, the microbial community that populates the human gastrointestinal tract has emerged as a critical player in governing human health and disease. DNA and RNA sequencing techniques that map taxonomical composition and genomic potential of the gut community have become invaluable for microbiome research. However, deriving a biochemical understanding of how activities of the gut microbiome shape host development and physiology requires an expanded experimental design that goes beyond these approaches. In this review, we explore advances in high-throughput techniques based on liquid chromatography-mass spectrometry. These omics methods for the identification of proteins and metabolites have enabled direct characterisation of gut microbiome functions and the crosstalk with the host. We discuss current metaproteomics and metabolomics workflows for producing functional profiles, the existing methodological challenges and limitations, and recent studies utilising these techniques with a special focus on early life gut microbiome.
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Affiliation(s)
- Veronika Kuchařová Pettersen
- Research Group for Host-Microbe Interactions, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
- Pediatric Research Group, Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway
- Centre for New Antibacterial Strategies, UiT The Arctic University of Norway, Tromsø, Norway
| | - Luis Caetano Martha Antunes
- Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, Brazil
- National Institute of Science and Technology of Innovation on Diseases of Neglected Populations, Center for Technological Development in Health, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, Brazil
| | - Antoine Dufour
- Department of Physiology & Pharmacology, University of Calgary, Calgary, Canada
| | - Marie-Claire Arrieta
- Department of Physiology & Pharmacology, University of Calgary, Calgary, Canada
- Department of Pediatrics, University of Calgary, Calgary, AB, Canada
- International Microbiome Centre, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
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Partial-, Double-Enzymatic Dephosphorylation and EndoGluC Hydrolysis as an Original Approach to Enhancing Identification of Casein Phosphopeptides (CPPs) by Mass Spectrometry. Foods 2021; 10:foods10092134. [PMID: 34574245 PMCID: PMC8471704 DOI: 10.3390/foods10092134] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/02/2021] [Accepted: 09/06/2021] [Indexed: 01/07/2023] Open
Abstract
The identification of phosphopeptides is currently a challenge when they are part of a complex matrix of peptides, such as a milk protein enzymatic hydrolysate. This challenge increases with both the number of phosphorylation sites on the phosphopeptides and their amino acid length. Here, this paper reports a four-phase strategy from an enzymatic casein hydrolysate before a mass spectrometry analysis in order to enhance the identification of phosphopeptides and phosphosites: (i) the control protein hydrolysate, (ii) a two-step enzymatic dephosphorylation of the latter, allowing for the almost total dephosphorylation of peptides, (iii) a one-step enzymatic dephosphorylation, allowing for the partial dephosphorylation of the peptides and (iv) an additional endoGluC enzymatic hydrolysis, allowing for the cleavage of long-size peptides into shorter ones. The reverse-phase high-pressure liquid chromatography–tandem mass spectrometry (RP-HPLC-MS/MS) analyses of hydrolysates that underwent this four-phase strategy allowed for the identification of 28 phosphorylation sites (90%) out of the 31 referenced in UniprotKB/Swiss-Prot (1 June 2021), compared to 17 sites (54%) without the latter. The alpha-S2 casein phosphosites, referenced by their similarity in the UniProt database, were experimentally identified, whereas pSer148, pThr166 and pSer187 from a multiphosphorylated long-size kappa-casein were not. Data are available via ProteomeXchange with identifier PXD027132.
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