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Gao S, Zhou X, Yue M, Zhu S, Liu Q, Zhao XE. Advances and perspectives in chemical isotope labeling-based mass spectrometry methods for metabolome and exposome analysis. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.117022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
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2
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Armbruster MR, Mostafa ME, Caldwell RN, Grady SF, Arnatt CK, Edwards JL. Isobaric 6-plex and tosyl dual tagging for the determination of positional isomers and quantitation of monounsaturated fatty acids using rapid UHPLC-MS/MS. Analyst 2023; 148:297-304. [PMID: 36533920 DOI: 10.1039/d2an01699k] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Isobaric labelling of fatty acids is complicated by chromatographic co-elution of double bond isomers. This produces contaminated spectra which can mask important biological changes. Here two derivatization strategies are combined to improve throughput and produce MS2 reporters which change mass depending on double bond position. A 6-plex isobaric tag is attached to the acid group, followed by the tosylation of the double bond using chloramine-T. These two derivatizations allowed for the chromatographic resolution of nearly all investigated isomers using a 3.5 minute ultrafast method. Further isomer differentiation is achieved upon fragmentation as reporter masses scale with the double bond location. This occurs by a dual-fragmentation route which reveals the isobaric labelling and fragments along the double bond of each analyte. These unique fragments allowed for accurate quantitation of co-isolated double bond isomers where traditional isobaric tags would experience ratio distortion. Saturated and monounsaturated fatty acids were characterized by this rapid 6-plex method and produced an average signal RSD of 9.3% and R2 of 0.99. The method was then used to characterize fatty acid dysregulation upon inhibition of stearoyl CoA desaturase with CAY10566.
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Affiliation(s)
- Michael R Armbruster
- Department of Chemistry and Biochemistry, Saint Louis University, 3501 Laclede Ave, St. Louis, MO, 63103, USA.
| | - Mahmoud Elhusseiny Mostafa
- Department of Chemistry and Biochemistry, Saint Louis University, 3501 Laclede Ave, St. Louis, MO, 63103, USA.
| | - Rhea N Caldwell
- Department of Chemistry and Biochemistry, Saint Louis University, 3501 Laclede Ave, St. Louis, MO, 63103, USA.
| | - Scott F Grady
- Department of Chemistry and Biochemistry, Saint Louis University, 3501 Laclede Ave, St. Louis, MO, 63103, USA.
| | - Christopher K Arnatt
- Department of Chemistry and Biochemistry, Saint Louis University, 3501 Laclede Ave, St. Louis, MO, 63103, USA.
| | - James L Edwards
- Department of Chemistry and Biochemistry, Saint Louis University, 3501 Laclede Ave, St. Louis, MO, 63103, USA.
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3
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Sivanich MK, Gu T, Tabang DN, Li L. Recent advances in isobaric labeling and applications in quantitative proteomics. Proteomics 2022; 22:e2100256. [PMID: 35687565 PMCID: PMC9787039 DOI: 10.1002/pmic.202100256] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 05/21/2022] [Accepted: 06/07/2022] [Indexed: 12/30/2022]
Abstract
Mass spectrometry (MS) has emerged at the forefront of quantitative proteomic techniques. Liquid chromatography-mass spectrometry (LC-MS) can be used to determine abundances of proteins and peptides in complex biological samples. Several methods have been developed and adapted for accurate quantification based on chemical isotopic labeling. Among various chemical isotopic labeling techniques, isobaric tagging approaches rely on the analysis of peptides from MS2-based quantification rather than MS1-based quantification. In this review, we will provide an overview of several isobaric tags along with some recent developments including complementary ion tags, improvements in sensitive quantitation of analytes with lower abundance, strategies to increase multiplexing capabilities, and targeted analysis strategies. We will also discuss limitations of isobaric tags and approaches to alleviate these restrictions through bioinformatic tools and data acquisition methods. This review will highlight several applications of isobaric tags, including biomarker discovery and validation, thermal proteome profiling, cross-linking for structural investigations, single-cell analysis, top-down proteomics, along with applications to different molecules including neuropeptides, glycans, metabolites, and lipids, while providing considerations and evaluations to each application.
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Affiliation(s)
| | - Ting‐Jia Gu
- School of PharmacyUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
| | | | - Lingjun Li
- Department of ChemistryUniversity of Wisconsin‐MadisonMadisonWisconsinUSA,School of PharmacyUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
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4
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Fadil F, Samol C, Berger RS, Kellermeier F, Gronwald W, Oefner PJ, Dettmer K. Isotope Ratio Outlier Analysis (IROA) for HPLC-TOFMS-Based Metabolomics of Human Urine. Metabolites 2022; 12:741. [PMID: 36005614 PMCID: PMC9414531 DOI: 10.3390/metabo12080741] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/04/2022] [Accepted: 08/10/2022] [Indexed: 11/16/2022] Open
Abstract
Metabolic fingerprinting by mass spectrometry aims at the comprehensive, semiquantitative analysis of metabolites. Isotope dilution, if successfully implemented, may provide a more reliable, relative quantification. Therefore, the 13C labeled yeast extract of the IROA TruQuant kit was added as an internal standard (IS) to human urine samples measured in full-scan mode on a high-performance liquid chromatography-time-of-flight mass spectrometer (HPLC-TOFMS) system. The isotope ratio approach enabled the analysis of 112 metabolites. The correlation with reference data did not improve significantly using 12C/13C ratios compared to absolute 12C peak areas. Moreover, using an intricate 13C-labeled standard increased the complexity of the mass spectra, which made correct signal annotation more challenging. On the positive side, the ratio approach helps to reduce batch effects, but it does not perform better than computational methods such as the "removebatcheffect" function in the R package Limma.
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Affiliation(s)
| | | | | | | | | | | | - Katja Dettmer
- Institute of Functional Genomics, University of Regensburg, 93053 Regensburg, Germany
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5
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Armbruster M, Grady SF, Arnatt CK, Edwards JL. Isobaric 4-Plex Tagging for Absolute Quantitation of Biological Acids in Diabetic Urine Using Capillary LC-MS/MS. ACS MEASUREMENT SCIENCE AU 2022; 2:287-295. [PMID: 35726255 PMCID: PMC9204807 DOI: 10.1021/acsmeasuresciau.1c00061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 06/15/2023]
Abstract
Isobaric labeling in mass spectrometry enables multiplexed absolute quantitation and high throughput, while minimizing full scan spectral complexity. Here, we use 4-plex isobaric labeling with a fixed positive charge tag to improve quantitation and throughput for polar carboxylic acid metabolites. The isobaric tag uses an isotope-encoded neutral loss to create mass-dependent reporters spaced 2 Da apart and was validated for both single- and double-tagged analytes. Tags were synthesized in-house using deuterated formaldehyde and methyl iodide in a total of four steps, producing cost-effective multiplexing. No chromatographic deuterium shifts were observed for single- or double-tagged analytes, producing consistent reporter ratios across each peak. Perfluoropentanoic acid was added to the sample to drastically increase retention of double-tagged analytes on a C18 column. Excess tag was scavenged and extracted using hexadecyl chloroformate after reaction completion. This allowed for removal of excess tag that typically causes ion suppression and column overloading. A total of 54 organic acids were investigated, producing an average linearity of 0.993, retention time relative standard deviation (RSD) of 0.58%, and intensity RSD of 12.1%. This method was used for absolute quantitation of acid metabolites comparing control and type 1 diabetic urine. Absolute quantitation of organic acids was achieved by using one isobaric lane for standards, thereby allowing for analysis of six urine samples in two injections. Quantified acids showed good agreement with previous work, and six significant changes were found. Overall, this method demonstrated 4-plex absolute quantitation of acids in a complex biological sample.
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6
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Heininen J, Julku U, Myöhänen T, Kotiaho T, Kostiainen R. Multiplexed analysis of amino acids in mice brain microdialysis samples using isobaric labeling and liquid chromatography-high resolution tandem mass spectrometry. J Chromatogr A 2021; 1656:462537. [PMID: 34537659 DOI: 10.1016/j.chroma.2021.462537] [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: 05/27/2021] [Revised: 08/26/2021] [Accepted: 09/01/2021] [Indexed: 11/29/2022]
Abstract
We developed a new multiplexed reversed phase liquid chromatography-high resolution tandem mass spectrometric (LC-MS/MS) method. The method is based on isobaric labeling with a tandem mass tag (TMT10-plex) and stable isotope-labeled internal standards, and was used to analyze amino acids in mouse brain microdialysis samples. The TMT10-plex labeling of amino acids allowed analysis of ten samples in one LC-MS/MS run, significantly increasing the sample throughput. The method provides good chromatographic performance (peak half-width between 0.04-0.12 min), allowing separation of all TMT-labeled amino acids with acceptable resolution and high sensitivity (limits of detection typically around 10 nM). The use of stable isotope-labeled internal standards, together with TMT10-plex labeling, ensured good repeatability (relative standard deviation ≤ 12.1 %) and linearity (correlation coefficient > 0.994), indicating good quantitative performance of the multiplexed method. The method was applied to study the effect of d-amphetamine microdialysis perfusion on amino acid concentrations in the mouse brain. All amino acids were reliably detected and quantified, indicating that the method is sensitive enough to detect low concentrations of amino acids in brain microdialysis samples.
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Affiliation(s)
- Juho Heininen
- Drug Research Program and Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, Finland
| | - Ulrika Julku
- Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, Finland
| | - Timo Myöhänen
- Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, Finland
| | - Tapio Kotiaho
- Drug Research Program and Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, Finland; Department of Chemistry, Faculty of Science, University of Helsinki, P.O. Box. 55, FIN-00014, Finland
| | - Risto Kostiainen
- Drug Research Program and Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, Finland.
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7
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Guan S, Armbruster MR, Huang T, Edwards JL, Bythell BJ. Isomeric Differentiation and Acidic Metabolite Identification by Piperidine-Based Tagging, LC–MS/MS, and Understanding of the Dissociation Chemistries. Anal Chem 2020; 92:9305-9311. [DOI: 10.1021/acs.analchem.0c01640] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Shanshan Guan
- Department of Chemistry and Biochemistry, Ohio University, 391 Clippinger Laboratories, Athens, Ohio 45701, United States
- Department of Chemistry and Biochemistry, University of Missouri, 1 University Blvd, St. Louis, Missouri 63121, United States
| | - Michael R. Armbruster
- Department of Chemistry and Biochemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri 63102, United States
| | - Tianjiao Huang
- Department of Chemistry and Biochemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri 63102, United States
| | - James L. Edwards
- Department of Chemistry and Biochemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri 63102, United States
| | - Benjamin J. Bythell
- Department of Chemistry and Biochemistry, Ohio University, 391 Clippinger Laboratories, Athens, Ohio 45701, United States
- Department of Chemistry and Biochemistry, University of Missouri, 1 University Blvd, St. Louis, Missouri 63121, United States
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8
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Important Considerations for Sample Collection in Metabolomics Studies with a Special Focus on Applications to Liver Functions. Metabolites 2020; 10:metabo10030104. [PMID: 32178364 PMCID: PMC7142637 DOI: 10.3390/metabo10030104] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/05/2020] [Accepted: 03/07/2020] [Indexed: 12/16/2022] Open
Abstract
Metabolomics has found numerous applications in the study of liver metabolism in health and disease. Metabolomics studies can be conducted in a variety of biological matrices ranging from easily accessible biofluids such as urine, blood or feces, to organs, tissues or even cells. Sample collection and storage are critical steps for which standard operating procedures must be followed. Inappropriate sample collection or storage can indeed result in high variability, interferences with instrumentation or degradation of metabolites. In this review, we will first highlight important general factors that should be considered when planning sample collection in the study design of metabolomic studies, such as nutritional status and circadian rhythm. Then, we will discuss in more detail the specific procedures that have been described for optimal pre-analytical handling of the most commonly used matrices (urine, blood, feces, tissues and cells).
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9
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Huang T, Armbruster MR, Coulton JB, Edwards JL. Chemical Tagging in Mass Spectrometry for Systems Biology. Anal Chem 2018; 91:109-125. [DOI: 10.1021/acs.analchem.8b04951] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Tianjiao Huang
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri 63103, United States
| | - Michael R. Armbruster
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri 63103, United States
| | - John B. Coulton
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri 63103, United States
| | - James L. Edwards
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri 63103, United States
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10
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Dethloff F, Bueschl C, Heumann H, Schuhmacher R, Turck CW. Partially 13C-labeled mouse tissue as reference for LC-MS based untargeted metabolomics. Anal Biochem 2018; 556:63-69. [PMID: 29958846 DOI: 10.1016/j.ab.2018.06.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 06/20/2018] [Accepted: 06/22/2018] [Indexed: 12/28/2022]
Abstract
The inclusion of stable isotope-labeled reference standards in the sample is an established method for the detection and relative quantification of metabolic features in untargeted metabolomics. In order to quantify as many metabolites as possible, the reference should ideally include the same metabolites in their stable isotope-labeled form as the sample under investigation. We present here an attempt to use partially 13C-labeled mouse material as internal standard for relative metabolite quantification of mouse and human samples in untargeted metabolomics. We fed mice for 14 days with a13C-labeled Ralstonia eutropha based diet. Tissue and blood amino acids from these mice showed 13C enrichment levels that ranged from 6% to 75%. We used MetExtract II software to automatically detect native and labeled peak pairs in an untargeted manner. In a dilution series and with the implementation of a correction factor, partially 13C-labeled mouse plasma resulted in accurate relative quantification of human plasma amino acids using liquid chromatography coupled to mass spectrometry, The coefficient of variation for the relative quantification is reduced from 27% without internal standard to 10% with inclusion of partially 13C-labeled internal standard. We anticipate the method to be of general use for the relative metabolite quantification of human specimens.
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Affiliation(s)
- Frederik Dethloff
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Christoph Bueschl
- Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Austria
| | | | - Rainer Schuhmacher
- Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Austria.
| | - Christoph W Turck
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany.
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11
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Zhao X, Hui DS, Lee R, Edwards JL. Ratiometric quantitation of thiol metabolites using non-isotopic mass tags. Anal Chim Acta 2018; 1037:274-280. [PMID: 30292302 DOI: 10.1016/j.aca.2018.02.057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 02/19/2018] [Accepted: 02/20/2018] [Indexed: 10/17/2022]
Abstract
Ratiometric quantitation is used in mass spectrometry to account for variations in ionization efficiencies due to heterogenous sample matrixes. Isotopes are most commonly used to achieve ratiometric quantitation because of their ability to co-elute chromatographically with each other and to have similar ionization efficiencies. In the work presented here, a new non-isotopic quantitative tagging approach is presented which allows chromatographic co-elution and similar ionization efficiencies. Using two variations of maleimide tags, t-butyl and cyclohexyl maleimide, thiols are quantified with a high degree of linearity up to five-fold concentration differences. Because these two tags have similar hydrophobcities, they elute simultaneously which allows them to be used for ratiometric quantitation. Beyond the five-fold linear range, signal compression is observed. This technique was able to quantify thiol changes in both in vitro pharmacological treatments as well as in vivo diabetic tissue.
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Affiliation(s)
- Xiaofeng Zhao
- Department of Chemistry and Biochemistry, Saint Louis University, 3501 Laclede Ave, Saint Louis, MO 63102, United States
| | - Dawn S Hui
- Department of Surgery, Center for Comprehensive Cardiovascular Care, Saint Louis University, St Louis, MO 63110, United States
| | - Richard Lee
- Department of Surgery, Center for Comprehensive Cardiovascular Care, Saint Louis University, St Louis, MO 63110, United States
| | - James L Edwards
- Department of Chemistry and Biochemistry, Saint Louis University, 3501 Laclede Ave, Saint Louis, MO 63102, United States.
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12
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Atzrodt J, Derdau V, Kerr WJ, Reid M. Deuterium- und tritiummarkierte Verbindungen: Anwendungen in den modernen Biowissenschaften. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201704146] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Jens Atzrodt
- Isotope Chemistry and Metabolite Synthesis, Integrated Drug Discovery, Medicinal Chemistry; Industriepark Höchst, G876 65926 Frankfurt Deutschland
| | - Volker Derdau
- Isotope Chemistry and Metabolite Synthesis, Integrated Drug Discovery, Medicinal Chemistry; Industriepark Höchst, G876 65926 Frankfurt Deutschland
| | - William J. Kerr
- Department of Pure and Applied Chemistry, WestCHEM; University of Strathclyde; 295 Cathedral Street Glasgow Scotland G1 1XL Großbritannien
| | - Marc Reid
- Department of Pure and Applied Chemistry, WestCHEM; University of Strathclyde; 295 Cathedral Street Glasgow Scotland G1 1XL Großbritannien
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13
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Atzrodt J, Derdau V, Kerr WJ, Reid M. Deuterium- and Tritium-Labelled Compounds: Applications in the Life Sciences. Angew Chem Int Ed Engl 2018; 57:1758-1784. [PMID: 28815899 DOI: 10.1002/anie.201704146] [Citation(s) in RCA: 407] [Impact Index Per Article: 67.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 07/27/2017] [Indexed: 12/19/2022]
Abstract
Hydrogen isotopes are unique tools for identifying and understanding biological and chemical processes. Hydrogen isotope labelling allows for the traceless and direct incorporation of an additional mass or radioactive tag into an organic molecule with almost no changes in its chemical structure, physical properties, or biological activity. Using deuterium-labelled isotopologues to study the unique mass-spectrometric patterns generated from mixtures of biologically relevant molecules drastically simplifies analysis. Such methods are now providing unprecedented levels of insight in a wide and continuously growing range of applications in the life sciences and beyond. Tritium (3 H), in particular, has seen an increase in utilization, especially in pharmaceutical drug discovery. The efforts and costs associated with the synthesis of labelled compounds are more than compensated for by the enhanced molecular sensitivity during analysis and the high reliability of the data obtained. In this Review, advances in the application of hydrogen isotopes in the life sciences are described.
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Affiliation(s)
- Jens Atzrodt
- Isotope Chemistry and Metabolite Synthesis, Integrated Drug Discovery, Medicinal Chemistry, Industriepark Höchst, G876, 65926, Frankfurt, Germany
| | - Volker Derdau
- Isotope Chemistry and Metabolite Synthesis, Integrated Drug Discovery, Medicinal Chemistry, Industriepark Höchst, G876, 65926, Frankfurt, Germany
| | - William J Kerr
- Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde, 295 Cathedral Street, Glasgow, Scotland, G1 1XL, UK
| | - Marc Reid
- Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde, 295 Cathedral Street, Glasgow, Scotland, G1 1XL, UK
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14
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Luo X, Li L. Metabolomics of Small Numbers of Cells: Metabolomic Profiling of 100, 1000, and 10000 Human Breast Cancer Cells. Anal Chem 2017; 89:11664-11671. [DOI: 10.1021/acs.analchem.7b03100] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Xian Luo
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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15
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Kostidis S, Addie RD, Morreau H, Mayboroda OA, Giera M. Quantitative NMR analysis of intra- and extracellular metabolism of mammalian cells: A tutorial. Anal Chim Acta 2017. [PMID: 28622799 DOI: 10.1016/j.aca.2017.05.011] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Metabolomics analysis of body fluids as well as cells is depended on many factors. While several well-accepted standard operating procedures for the analysis of body fluids are available, the NMR based quantitative analysis of cellular metabolites is less well standardized. Experimental designs depend on the cell type, the quenching protocol and the applied post-acquisition workflow. Here, we provide a tutorial for the quantitative description of the metabolic phenotype of mammalian cells using NMR spectroscopy. We discuss all key steps of the process, starting from the selection of the appropriate culture medium, quenching techniques to arrest metabolism in a reproducible manner, the extraction of the intracellular components and the profiling of the culture medium. NMR data acquisition and methods for both qualitative and quantitative analysis are also provided. The suggested methods cover experiments for adherent cells and cells in suspension. We ultimately describe the application of the discussed workflow to a thyroid cancer cell line. Although this tutorial focuses on mammalian cells, the given guidelines and procedures may be adjusted for the analysis of other cell types.
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Affiliation(s)
- Sarantos Kostidis
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2300RC, Leiden, The Netherlands.
| | - Ruben D Addie
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2300RC, Leiden, The Netherlands; Department of Pathology, Leiden University Medical Center, Albinusdreef 2, 2300RC, Leiden, The Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Albinusdreef 2, 2300RC, Leiden, The Netherlands
| | - Oleg A Mayboroda
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2300RC, Leiden, The Netherlands
| | - Martin Giera
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2300RC, Leiden, The Netherlands
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16
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Madji Hounoum B, Blasco H, Emond P, Mavel S. Liquid chromatography–high-resolution mass spectrometry-based cell metabolomics: Experimental design, recommendations, and applications. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2015.08.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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17
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Yang S, Wang M, Chen L, Yin B, Song G, Turko IV, Phinney KW, Betenbaugh MJ, Zhang H, Li S. QUANTITY: An Isobaric Tag for Quantitative Glycomics. Sci Rep 2015; 5:17585. [PMID: 26616285 PMCID: PMC4663469 DOI: 10.1038/srep17585] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 11/02/2015] [Indexed: 12/15/2022] Open
Abstract
Glycan is an important class of macromolecules that play numerous biological functions. Quantitative glycomics - analysis of glycans at global level - however, is far behind genomics and proteomics owing to technical challenges associated with their chemical properties and structural complexity. As a result, technologies that can facilitate global glycan analysis are highly sought after. Here, we present QUANTITY (Quaternary Amine Containing Isobaric Tag for Glycan), a quantitative approach that can not only enhance detection of glycans by mass spectrometry, but also allow high-throughput glycomic analysis from multiple biological samples. This robust tool enabled us to accomplish glycomic survey of bioengineered Chinese Hamster Ovary (CHO) cells with knock-in/out enzymes involved in protein glycosylation. Our results demonstrated QUANTITY is an invaluable technique for glycan analysis and bioengineering.
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Affiliation(s)
- Shuang Yang
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Meiyao Wang
- Institute for Bioscience and Biotechnology Research, University of Maryland College Park, Rockville, MD, USA.,Analytical Biotechnology, MedImmune LLC, Gaithersburg, MD, USA
| | - Lijun Chen
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Bojiao Yin
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Guoqiang Song
- School of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, China
| | - Illarion V Turko
- Institute for Bioscience and Biotechnology Research, University of Maryland College Park, Rockville, MD, USA.,Biomolecular Measurement Division, National Institute of Standard and Technology, Gaithersburg, MD, USA
| | - Karen W Phinney
- Biomolecular Measurement Division, National Institute of Standard and Technology, Gaithersburg, MD, USA
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Shuwei Li
- Institute for Bioscience and Biotechnology Research, University of Maryland College Park, Rockville, MD, USA
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18
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Li Z, Tatlay J, Li L. Nanoflow LC–MS for High-Performance Chemical Isotope Labeling Quantitative Metabolomics. Anal Chem 2015; 87:11468-74. [DOI: 10.1021/acs.analchem.5b03209] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Zhendong Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G, Canada
| | - Jaspaul Tatlay
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G, Canada
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19
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Yuan W, Li S, Edwards JL. Extraction and Quantitation of Ketones and Aldehydes from Mammalian Cells Using Fluorous Tagging and Capillary LC-MS. Anal Chem 2015; 87:7660-6. [DOI: 10.1021/acs.analchem.5b01000] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Wei Yuan
- Institute
for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, Maryland 20850, United States,
- Department
of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Shuwei Li
- Institute
for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, Maryland 20850, United States,
- Department
of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - James L. Edwards
- Department
of Chemistry, Saint Louis University, St. Louis, Missouri 63103, United States
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20
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Li H, Qin Q, Qiao L, Shi X, Xu G. Preparation of mesoporous SiO2@azobenzene–COOH chemoselective nanoprobes for comprehensive mapping of amino metabolites in human serum. Chem Commun (Camb) 2015; 51:11321-4. [DOI: 10.1039/c5cc03756e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
mSiO2@azobenzene–COOH chemoselective nanoprobes were developed for comprehensive mapping of amino metabolites in complex biological samples with high specificity and sensitivity.
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Affiliation(s)
- Hua Li
- Key Lab of Separation Sciences for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian
- China
| | - Qian Qin
- Key Lab of Separation Sciences for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian
- China
| | - Lizhen Qiao
- Key Lab of Separation Sciences for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian
- China
| | - Xianzhe Shi
- Key Lab of Separation Sciences for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian
- China
| | - Guowang Xu
- Key Lab of Separation Sciences for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian
- China
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21
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Stable isotope-labeling studies in metabolomics: new insights into structure and dynamics of metabolic networks. Bioanalysis 2014; 6:511-24. [PMID: 24568354 DOI: 10.4155/bio.13.348] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The rapid emergence of metabolomics has enabled system-wide measurements of metabolites in various organisms. However, advances in the mechanistic understanding of metabolic networks remain limited, as most metabolomics studies cannot routinely provide accurate metabolite identification, absolute quantification and flux measurement. Stable isotope labeling offers opportunities to overcome these limitations. Here we describe some current approaches to stable isotope-labeled metabolomics and provide examples of the significant impact that these studies have had on our understanding of cellular metabolism. Furthermore, we discuss recently developed software solutions for the analysis of stable isotope-labeled metabolomics data and propose the bioinformatics solutions that will pave the way for the broader application and optimal interpretation of system-scale labeling studies in metabolomics.
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22
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Murphy JP, Everley RA, Coloff JL, Gygi SP. Combining amine metabolomics and quantitative proteomics of cancer cells using derivatization with isobaric tags. Anal Chem 2014; 86:3585-93. [PMID: 24611633 PMCID: PMC3983006 DOI: 10.1021/ac500153a] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
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Quantitative metabolomics and proteomics
technologies are powerful
approaches to explore cellular metabolic regulation. Unfortunately,
combining the two technologies typically requires different LC-MS
setups for sensitive measurement of metabolites and peptides. One
approach to enhance the analysis of certain classes of metabolites
is by derivatization with various types of tags to increase ionization
and chromatographic efficiency. We demonstrate here that derivatization
of amine metabolites with tandem mass tags (TMT), typically used in
multiplexed peptide quantitation, facilitates amino acid analysis
by standard nanoflow reversed-phase LC-MS setups used for proteomics.
We demonstrate that this approach offers the potential to perform
experiments at the MS1-level using duplex tags or at the MS2-level
using novel 10-plex reporter ion-containing isobaric tags for multiplexed
amine metabolite analysis. We also demonstrate absolute quantitative
measurements of amino acids conducted in parallel with multiplexed
quantitative proteomics, using similar LC-MS setups to explore cellular
amino acid regulation. We further show that the approach can also
be used to determine intracellular metabolic labeling of amino acids
from glucose carbons.
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Affiliation(s)
- J Patrick Murphy
- Department of Cell Biology, Harvard Medical School , Boston, Massachusetts 02115, United States
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23
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León Z, García-Cañaveras JC, Donato MT, Lahoz A. Mammalian cell metabolomics: experimental design and sample preparation. Electrophoresis 2013; 34:2762-75. [PMID: 23436493 DOI: 10.1002/elps.201200605] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 01/08/2013] [Accepted: 01/20/2013] [Indexed: 12/19/2022]
Abstract
Metabolomics represents the global assessment of metabolites in a biological sample and reports the closest information to the phenotype of the biological system under study. Mammalian cell metabolomics has emerged as a promising tool with potential applications in many biotechnology and research areas. Metabolomics workflow includes experimental design, sampling, sample processing, metabolite analysis, and data processing. Given their influence on metabolite content and biological interpretation of data, a good experimental design and the appropriate choice of a sample processing method are prerequisites for success in any metabolomic study. The use of mammalian cells in the metabolomics field involves harder sample processing methods, including metabolism quenching and metabolite extraction, as compared to the use of body fluids, although such critical issues are frequently overlooked. This review aims to overview the common experimental procedures used in mammalian cell metabolomics based on mass spectrometry, by placing special emphasis on discussing sample preparation approaches, although other aspects, such as cell metabolomics applications, culture systems, cellular models, analytical platforms, and data analysis, are also briefly covered. This review intends to be a helpful tool to assist researchers in addressing decisions when planning a metabolomics study involving the use of mammalian cells.
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Affiliation(s)
- Zacarías León
- Unidad Analítica, Instituto de Investigación Sanitaria - Fundación Hospital La Fe, Valencia, Spain
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24
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Relative quantification of biomarkers using mixed-isotope labeling coupled with MS. Bioanalysis 2013; 4:2525-41. [PMID: 23157360 DOI: 10.4155/bio.12.208] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The identification and quantification of important biomarkers is a critical first step in the elucidation of biological systems. Biomarkers take many forms as cellular responses to stimuli and can be manifested during transcription, translation, and/or metabolic processing. Increasingly, researchers have relied upon mixed-isotope labeling (MIL) coupled with MS to perform relative quantification of biomarkers between two or more biological samples. MIL effectively tags biomarkers of interest for ease of identification and quantification within the mass spectrometer by using isotopic labels that introduce a heavy and light form of the tag. In addition to MIL coupled with MS, a number of other approaches have been used to quantify biomarkers including protein gel staining, enzymatic labeling, metabolic labeling, and several label-free approaches that generate quantitative data from the MS signal response. This review focuses on MIL techniques coupled with MS for the quantification of protein and small-molecule biomarkers.
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25
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Messana I, Cabras T, Iavarone F, Vincenzoni F, Urbani A, Castagnola M. Unraveling the different proteomic platforms. J Sep Sci 2012; 36:128-39. [PMID: 23212829 DOI: 10.1002/jssc.201200830] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 10/05/2012] [Accepted: 10/06/2012] [Indexed: 01/06/2023]
Abstract
This review is addressed to scientists working outside the field of proteomics and wishes to shed a light on the possibility offered by the latest proteomics strategies. Bottom-up and top-down platforms are critically examined outlining advantages and limitations of their application to qualitative and quantitative investigations. Discovery, directed and targeted proteomics as different options for the management of the MS instrument are defined emphasizing their integration in the experimental plan to accomplish meaningful results. The issue of data validation is analyzed and discussed. The most common qualitative proteomic platforms are described, with a particular emphasis on enrichment methods to elucidate PTMs codes (i.e. ubiquitin and histone codes). Label-free and labeled methods for relative and absolute quantification are critically compared. The possible contribution of proteomics platforms to the transition from structural proteomics to functional proteomics (study of the functional connections between different proteins) and to the challenging system biology (integrated study of all the functional cellular functions) is also briefly discussed.
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Affiliation(s)
- Irene Messana
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cagliari, Italy
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26
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Dayon L, Sonderegger B, Kussmann M. Combination of Gas-Phase Fractionation and MS3 Acquisition Modes for Relative Protein Quantification with Isobaric Tagging. J Proteome Res 2012; 11:5081-9. [DOI: 10.1021/pr300519c] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Loïc Dayon
- Proteomics and Metabonomics
Core, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Bernhard Sonderegger
- Proteomics and Metabonomics
Core, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Martin Kussmann
- Proteomics and Metabonomics
Core, Nestlé Institute of Health Sciences, Lausanne, Switzerland
- Faculty of Life Sciences, Ecole Polytechnique Fédérale Lausanne (EPFL), Lausanne, Switzerland
- Faculty of Science, Aarhus University (AU), Aarhus, Denmark
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