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Chu LX, Wang WJ, Gu XP, Wu P, Gao C, Zhang Q, Wu J, Jiang DW, Huang JQ, Ying XW, Shen JM, Jiang Y, Luo LH, Xu JP, Ying YB, Chen HM, Fang A, Feng ZY, An SH, Li XK, Wang ZG. Spatiotemporal multi-omics: exploring molecular landscapes in aging and regenerative medicine. Mil Med Res 2024; 11:31. [PMID: 38797843 PMCID: PMC11129507 DOI: 10.1186/s40779-024-00537-4] [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: 12/15/2023] [Accepted: 05/07/2024] [Indexed: 05/29/2024] Open
Abstract
Aging and regeneration represent complex biological phenomena that have long captivated the scientific community. To fully comprehend these processes, it is essential to investigate molecular dynamics through a lens that encompasses both spatial and temporal dimensions. Conventional omics methodologies, such as genomics and transcriptomics, have been instrumental in identifying critical molecular facets of aging and regeneration. However, these methods are somewhat limited, constrained by their spatial resolution and their lack of capacity to dynamically represent tissue alterations. The advent of emerging spatiotemporal multi-omics approaches, encompassing transcriptomics, proteomics, metabolomics, and epigenomics, furnishes comprehensive insights into these intricate molecular dynamics. These sophisticated techniques facilitate accurate delineation of molecular patterns across an array of cells, tissues, and organs, thereby offering an in-depth understanding of the fundamental mechanisms at play. This review meticulously examines the significance of spatiotemporal multi-omics in the realms of aging and regeneration research. It underscores how these methodologies augment our comprehension of molecular dynamics, cellular interactions, and signaling pathways. Initially, the review delineates the foundational principles underpinning these methods, followed by an evaluation of their recent applications within the field. The review ultimately concludes by addressing the prevailing challenges and projecting future advancements in the field. Indubitably, spatiotemporal multi-omics are instrumental in deciphering the complexities inherent in aging and regeneration, thus charting a course toward potential therapeutic innovations.
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Affiliation(s)
- Liu-Xi Chu
- Affiliated Cixi Hospital, Wenzhou Medical University, Ningbo, 315300, Zhejiang, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Wen-Jia Wang
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Xin-Pei Gu
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou, 510515, China
- Department of Human Anatomy, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, Shandong, China
| | - Ping Wu
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Chen Gao
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Quan Zhang
- Integrative Muscle Biology Laboratory, Division of Regenerative and Rehabilitative Sciences, University of Tennessee Health Science Center, Memphis, TN, 38163, United States
| | - Jia Wu
- Key Laboratory for Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Da-Wei Jiang
- Affiliated Cixi Hospital, Wenzhou Medical University, Ningbo, 315300, Zhejiang, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Jun-Qing Huang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Institute of Imaging Diagnosis and Minimally Invasive Intervention Research, the Fifth Affiliated Hospital of Wenzhou Medical University, Lishui Hospital of Zhejiang University, Lishui, 323000, Zhejiang, China
| | - Xin-Wang Ying
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Jia-Men Shen
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Yi Jiang
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Li-Hua Luo
- School and Hospital of Stomatology, Wenzhou Medical University, Wenzhou, 324025, Zhejiang, China
| | - Jun-Peng Xu
- Affiliated Cixi Hospital, Wenzhou Medical University, Ningbo, 315300, Zhejiang, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Yi-Bo Ying
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Hao-Man Chen
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Ao Fang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Zun-Yong Feng
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and College of Design and Engineering, National University of Singapore, Singapore, 119074, Singapore.
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore.
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.
- Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), Singapore, 138673, Singapore.
| | - Shu-Hong An
- Department of Human Anatomy, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, Shandong, China.
| | - Xiao-Kun Li
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
| | - Zhou-Guang Wang
- Affiliated Cixi Hospital, Wenzhou Medical University, Ningbo, 315300, Zhejiang, China.
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Institute of Imaging Diagnosis and Minimally Invasive Intervention Research, the Fifth Affiliated Hospital of Wenzhou Medical University, Lishui Hospital of Zhejiang University, Lishui, 323000, Zhejiang, China.
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2
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Hsieh WC, Budiarto BR, Wang YF, Lin CY, Gwo MC, So DK, Tzeng YS, Chen SY. Spatial multi-omics analyses of the tumor immune microenvironment. J Biomed Sci 2022; 29:96. [DOI: 10.1186/s12929-022-00879-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 11/02/2022] [Indexed: 11/16/2022] Open
Abstract
AbstractIn the past decade, single-cell technologies have revealed the heterogeneity of the tumor-immune microenvironment at the genomic, transcriptomic, and proteomic levels and have furthered our understanding of the mechanisms of tumor development. Single-cell technologies have also been used to identify potential biomarkers. However, spatial information about the tumor-immune microenvironment such as cell locations and cell–cell interactomes is lost in these approaches. Recently, spatial multi-omics technologies have been used to study transcriptomes, proteomes, and metabolomes of tumor-immune microenvironments in several types of cancer, and the data obtained from these methods has been combined with immunohistochemistry and multiparameter analysis to yield markers of cancer progression. Here, we review numerous cutting-edge spatial ‘omics techniques, their application to study of the tumor-immune microenvironment, and remaining technical challenges.
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Xu L, Li X, Li W, Chang K, Yang H, Tao N, Zhang P, Payne EM, Modavi C, Humphries J, Lu C, Abate AR. Microbowls with Controlled Concavity for Accurate Microscale Mass Spectrometry. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2108194. [PMID: 35045587 PMCID: PMC9028217 DOI: 10.1002/adma.202108194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/15/2021] [Indexed: 06/14/2023]
Abstract
Patterned surfaces can enhance the sensitivity of laser desorption ionization mass spectrometry by segregating and concentrating analytes, but their fabrication can be challenging. Here, a simple method to fabricate substrates patterned with micrometer-scale wells that yield more accurate and sensitive mass spectrometry measurements compared to flat surfaces is described. The wells can also concentrate and localize cells and beads for cell-based assays.
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Affiliation(s)
- Linfeng Xu
- Department of Bioengineering and Therapeutic SciencesUniversity of California, San FranciscoSan FranciscoCA94158USA
| | - Xiangpeng Li
- Department of Bioengineering and Therapeutic SciencesUniversity of California, San FranciscoSan FranciscoCA94158USA
| | - Wenzong Li
- Amyris Inc.5885 Hollis St #100EmeryvilleCA94608USA
| | - Kai‐chun Chang
- Department of Bioengineering and Therapeutic SciencesUniversity of California, San FranciscoSan FranciscoCA94158USA
| | - Hyunjun Yang
- Institute for Neurodegenerative DiseasesWeill Institute for NeurosciencesUniversity of CaliforniaSan FranciscoCA94158USA
| | | | - Pengfei Zhang
- Department of Bioengineering and Therapeutic SciencesUniversity of California, San FranciscoSan FranciscoCA94158USA
| | - Emory M. Payne
- Department of ChemistryUniversity of MichiganAnn ArborMI48104USA
| | - Cyrus Modavi
- Department of Bioengineering and Therapeutic SciencesUniversity of California, San FranciscoSan FranciscoCA94158USA
| | | | - Chia‐Wei Lu
- Amyris Inc.5885 Hollis St #100EmeryvilleCA94608USA
| | - Adam R. Abate
- Department of Bioengineering and Therapeutic SciencesUniversity of California, San FranciscoSan FranciscoCA94158USA
- Chan Zuckerberg BiohubSan FranciscoCA94158USA
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Lin CH, Su H, Hung CC, Lane HY, Shiea J. Characterization of Potential Protein Biomarkers for Major Depressive Disorder Using Matrix-Assisted Laser Desorption Ionization/Time-of-Flight Mass Spectrometry. Molecules 2021; 26:molecules26154457. [PMID: 34361610 PMCID: PMC8348063 DOI: 10.3390/molecules26154457] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 12/16/2022] Open
Abstract
Matrix-assisted laser desorption ionization/time-of-flight (MALDI-TOF) mass spectrometry is a sensitive analytical tool for characterizing various biomolecules in biofluids. In this study, MALDI-TOF was used to characterize potential plasma biomarkers for distinguishing patients with major depressive disorder (MDD) from patients with schizophrenia and healthy controls. To avoid interference from albumin—the predominant protein in plasma—the plasma samples were pretreated using acid hydrolysis. The results obtained by MALDI-TOF were also validated by electrospray ionization-quadrupole time-of-flight (ESI-QTOF) mass spectrometry. The analytical results were further treated with principal component analysis (PCA), hierarchical clustering analysis (HCA), and receiver operating characteristic (ROC) curve analysis. The statistical analyses showed that MDD patients could be distinguished from schizophrenia patients and healthy controls by the lack of apolipoprotein C1 (Apo C1), which, in fact, was detected in healthy controls and schizophrenia patients. This protein is suggested to be a potential plasma biomarker for distinguishing MDD patients from healthy controls and schizophrenia patients. Since sample preparation for MALDI-TOF is very simple, high-throughput plasma apolipoprotein analysis for clinical purposes is feasible.
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Affiliation(s)
- Chieh-Hsin Lin
- Department of Psychiatry, Kaohsiung Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Kaohsiung 833401, Taiwan;
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 404332, Taiwan
- School of Medicine, Chang Gung University, Taoyuan 333323, Taiwan
| | - Hung Su
- Department of Chemistry, National Sun Yat-Sen University, Kaohsiung 804351, Taiwan;
| | - Chung-Chieh Hung
- Department of Psychiatry & Brain Disease Research Center, China Medical University and Hospital, Taichung 404332, Taiwan;
| | - Hsien-Yuan Lane
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 404332, Taiwan
- Department of Psychiatry & Brain Disease Research Center, China Medical University and Hospital, Taichung 404332, Taiwan;
- Department of Psychology, College of Medical and Health Sciences, Asia University, Taichung 413305, Taiwan
- Correspondence: (H.-Y.L.); (J.S.)
| | - Jentaie Shiea
- Department of Chemistry, National Sun Yat-Sen University, Kaohsiung 804351, Taiwan;
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
- Correspondence: (H.-Y.L.); (J.S.)
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Houdová D, Soto J, Castro R, Rodrigues J, Soledad Pino-González M, Petković M, Bandosz TJ, Algarra M. Chemically heterogeneous carbon dots enhanced cholesterol detection by MALDI TOF mass spectrometry. J Colloid Interface Sci 2021. [DOI: https://doi.org/10.1016/j.jcis.2021.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Houdová D, Soto J, Castro R, Rodrigues J, Soledad Pino-González M, Petković M, Bandosz TJ, Algarra M. Chemically heterogeneous carbon dots enhanced cholesterol detection by MALDI TOF mass spectrometry. J Colloid Interface Sci 2021; 591:373-383. [PMID: 33631525 DOI: 10.1016/j.jcis.2021.02.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 02/08/2023]
Abstract
A binary system composed of carbon dots (CDs) and N-doped CDs (N-CDs) embedded in an organic matrix was used for the analysis of cholesterol by MALDI (matrix-assisted laser desorption and ionization time-of-flight) mass spectrometry, as a model for detection of small, biologically relevant molecules. The results showed that both CDs are sensitive to the cholesterol and can be used either alone or in a binary system with 2,5-dihydroxybenzoic acid (DHB) to enhance the detection process. It was found that both COOH and NH2 groups on CDs surface contributed to the enhancement in the cholesterol detection by MALDI mass spectrometry in the presence of inorganic cations. Nevertheless, in the presence of NaCl, N-CDs led to a better reproducibility of results. It was due to the coexistence of positive and negative charge on N-CDs surface that led to a homogeneous analyte/substrate distribution, which is an important detection parameter. The enhancing effect of carbon dots was linked to a negative Gibbs energy of the complex formation between CDs, Na+, cholesterol and DHB, and it was supported by theoretical calculations. Moreover, upon the addition of CDs/N-CDs, such features as a low ionization potential, vertical excitation, dipole moment and oscillator strength positively affected the cholesterol detection by MALDI in the presence of Na+.
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Affiliation(s)
- Dominika Houdová
- CQM-Centro de Química da Madeira, Universidade da Madeira, Campus da Penteada, 9020-105 Funchal, Portugal
| | - Juan Soto
- Department of Physical Chemistry. Faculty of Science, University of Málaga. Campus de Teatinos s/n, 29071 Malaga, Spain
| | - Rita Castro
- CQM-Centro de Química da Madeira, Universidade da Madeira, Campus da Penteada, 9020-105 Funchal, Portugal
| | - João Rodrigues
- CQM-Centro de Química da Madeira, Universidade da Madeira, Campus da Penteada, 9020-105 Funchal, Portugal
| | - Mª Soledad Pino-González
- Department of Organic Chemistry. Faculty of Science, University of Málaga. Campus de Teatinos s/n, 29071 Málaga, Spain
| | - Marijana Petković
- VINČA Institute of Nuclear Sciences-National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia.
| | - Teresa J Bandosz
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Ave, New York, NY, 10031, USA.
| | - Manuel Algarra
- Department of Inorganic Chemistry. Faculty of Science, University of Málaga. Campus de Teatinos s/n, 29071 Málaga, Spain.
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Monopoli A, Nacci A, Cataldi TRI, Calvano CD. Synthesis and Matrix Properties of α-Cyano-5-phenyl-2,4-pentadienic Acid (CPPA) for Intact Proteins Analysis by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry. Molecules 2020; 25:molecules25246054. [PMID: 33371472 PMCID: PMC7767571 DOI: 10.3390/molecules25246054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 01/06/2023] Open
Abstract
The effectiveness of a synthesized matrix, α-cyano-5-phenyl-2,4-pentadienic acid (CPPA), for protein analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in complex samples such as foodstuff and bacterial extracts, is demonstrated. Ultraviolet (UV) absorption along with laser desorption/ionization mass spectrometry (LDI-MS) experiments were systematically conducted in positive ion mode under standard Nd:YLF laser excitation with the aim of characterizing the matrix in terms of wavelength absorption and proton affinity. Besides, the results for standard proteins revealed that CPPA significantly enhanced the protein signals, reduced the spot-to-spot variability and increased the spot homogeneity. The CPPA matrix was successful employed to investigate intact microorganisms, milk and seed extracts for protein profiling. Compared to conventional matrices such as sinapinic acid (SA), α-cyano-4-hydroxycinnamic acid (CHCA) and 4-chloro-α-cyanocinnamic acid (CClCA), CPPA exhibited better signal-to-noise (S/N) ratios and a uniform response for most examined proteins occurring in milk, hazelnut and in intact bacterial cells of E. coli. These findings not only provide a reactive proton transfer MALDI matrix with excellent reproducibility and sensitivity, but also contribute to extending the battery of useful matrices for intact protein analysis.
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Affiliation(s)
- Antonio Monopoli
- Agenzia delle Dogane e dei Monopoli, Ufficio delle Dogane di Bari, Corso De Tullio, 70122 Bari, Italy;
| | - Angelo Nacci
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, Via Orabona, 70126 Bari, Italy; (A.N.); (T.R.I.C.)
| | - Tommaso R. I. Cataldi
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, Via Orabona, 70126 Bari, Italy; (A.N.); (T.R.I.C.)
- Centro Interdipartimentale di Ricerca S.M.A.R.T., 70126 Bari, Italy
| | - Cosima D. Calvano
- Centro Interdipartimentale di Ricerca S.M.A.R.T., 70126 Bari, Italy
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, Via Orabona, 70126 Bari, Italy
- Correspondence:
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Hydrogels as Drug Delivery Systems: A Review of Current Characterization and Evaluation Techniques. Pharmaceutics 2020; 12:pharmaceutics12121188. [PMID: 33297493 PMCID: PMC7762425 DOI: 10.3390/pharmaceutics12121188] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/18/2020] [Accepted: 11/19/2020] [Indexed: 12/15/2022] Open
Abstract
Owing to their tunable properties, controllable degradation, and ability to protect labile drugs, hydrogels are increasingly investigated as local drug delivery systems. However, a lack of standardized methodologies used to characterize and evaluate drug release poses significant difficulties when comparing findings from different investigations, preventing an accurate assessment of systems. Here, we review the commonly used analytical techniques for drug detection and quantification from hydrogel delivery systems. The experimental conditions of drug release in saline solutions and their impact are discussed, along with the main mathematical and statistical approaches to characterize drug release profiles. We also review methods to determine drug diffusion coefficients and in vitro and in vivo models used to assess drug release and efficacy with the goal to provide guidelines and harmonized practices when investigating novel hydrogel drug delivery systems.
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Yang H, Jackson SN, Woods AS, Goodlett DR, Ernst RK, Scott AJ. Streamlined Analysis of Cardiolipins in Prokaryotic and Eukaryotic Samples Using a Norharmane Matrix by MALDI-MSI. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2495-2502. [PMID: 32924474 PMCID: PMC8681877 DOI: 10.1021/jasms.0c00201] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Cardiolipins (CLs) are an important, regulated lipid class both in prokaryotic and eukaryotic cells, yet they remain largely unexplored by matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) in tissues. To date, no in-depth optimization studies of label-free visualization of CLs in complex biological samples have been reported. Here we report a streamlined modification to our previously reported MALDI-MSI method for detection of endogenous CLs in prokaryotic and eukaryotic cells based on preparation with norharmane (NRM) matrix. Notably, the use of NRM matrix permitted sensitive detection (4.7 pg/mm2) of spotted CL synthetic standards. By contrast, four other MALDI matrices commonly used for lipid analysis failed to generate CL ions. Using this NRM-based method, endogenous CLs were detected from two types of complex biological samples: dried bacterial arrays and mouse tissue sections. In both cases, using NRM resulted in a better signal/noise for CL ions than the other matrices. Furthermore, inclusion of a washing step improved CL detection from tissue and this combined tissue preparation method (washing and NRM matrix) was used to profile normal mouse lung. Mouse lung yielded 26 unique CLs that were mapped and identified. Consistent with previous findings, CLs containing polyunsaturated fatty acids (PUFAs) were found in abundance in the airway and vascular features of the lung. This work represents a comprehensive investigation of detection conditions for CL using MALDI-MSI in complex biological samples that resulted in a streamlined method that enables future studies of the biological role(s) of CL in tissue.
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Affiliation(s)
- Hyojik Yang
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore 21201, MD, USA
| | | | - Amina S. Woods
- Structural Biology Core, NIDA IRP, NIH, Baltimore 21224, MD, USA
- Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore 21205, MD, USA
| | - David R. Goodlett
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore 21201, MD, USA
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, 80-308, Poland, EU
| | - Robert K. Ernst
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore 21201, MD, USA
| | - Alison J. Scott
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore 21201, MD, USA
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Maastricht University, Maastricht 6229 ER, Netherlands, EU
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10
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Jayathirtha M, Dupree EJ, Manzoor Z, Larose B, Sechrist Z, Neagu AN, Petre BA, Darie CC. Mass Spectrometric (MS) Analysis of Proteins and Peptides. Curr Protein Pept Sci 2020; 22:92-120. [PMID: 32713333 DOI: 10.2174/1389203721666200726223336] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 05/12/2020] [Accepted: 05/28/2020] [Indexed: 01/09/2023]
Abstract
The human genome is sequenced and comprised of ~30,000 genes, making humans just a little bit more complicated than worms or flies. However, complexity of humans is given by proteins that these genes code for because one gene can produce many proteins mostly through alternative splicing and tissue-dependent expression of particular proteins. In addition, post-translational modifications (PTMs) in proteins greatly increase the number of gene products or protein isoforms. Furthermore, stable and transient interactions between proteins, protein isoforms/proteoforms and PTM-ed proteins (protein-protein interactions, PPI) add yet another level of complexity in humans and other organisms. In the past, all of these proteins were analyzed one at the time. Currently, they are analyzed by a less tedious method: mass spectrometry (MS) for two reasons: 1) because of the complexity of proteins, protein PTMs and PPIs and 2) because MS is the only method that can keep up with such a complex array of features. Here, we discuss the applications of mass spectrometry in protein analysis.
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Affiliation(s)
- Madhuri Jayathirtha
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Emmalyn J Dupree
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Zaen Manzoor
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Brianna Larose
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Zach Sechrist
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, "Alexandru Ioan Cuza" University of Iasi, Iasi, Romania
| | - Brindusa Alina Petre
- Laboratory of Biochemistry, Department of Chemistry, Al. I. Cuza University of Iasi, Iasi, Romania, Center for Fundamental Research and Experimental Development in Translation Medicine - TRANSCEND, Regional Institute of Oncology, Iasi, Romania
| | - Costel C Darie
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
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Klein AH, Ballard KR, Storey KB, Motti CA, Zhao M, Cummins SF. Multi-omics investigations within the Phylum Mollusca, Class Gastropoda: from ecological application to breakthrough phylogenomic studies. Brief Funct Genomics 2020; 18:377-394. [PMID: 31609407 DOI: 10.1093/bfgp/elz017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 07/06/2019] [Accepted: 07/15/2019] [Indexed: 12/22/2022] Open
Abstract
Gastropods are the largest and most diverse class of mollusc and include species that are well studied within the areas of taxonomy, aquaculture, biomineralization, ecology, microbiome and health. Gastropod research has been expanding since the mid-2000s, largely due to large-scale data integration from next-generation sequencing and mass spectrometry in which transcripts, proteins and metabolites can be readily explored systematically. Correspondingly, the huge data added a great deal of complexity for data organization, visualization and interpretation. Here, we reviewed the recent advances involving gastropod omics ('gastropodomics') research from hundreds of publications and online genomics databases. By summarizing the current publicly available data, we present an insight for the design of useful data integrating tools and strategies for comparative omics studies in the future. Additionally, we discuss the future of omics applications in aquaculture, natural pharmaceutical biodiscovery and pest management, as well as to monitor the impact of environmental stressors.
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Affiliation(s)
- Anne H Klein
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Kaylene R Ballard
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Kenneth B Storey
- Institute of Biochemistry & Department of Biology, Carleton University, Ottawa, ON, Canada K1S 5B6
| | - Cherie A Motti
- Australian Institute of Marine Science (AIMS), Cape Ferguson, Townsville Queensland 4810, Australia
| | - Min Zhao
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Scott F Cummins
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
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12
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Albishi T, Mikhael A, Shahidi F, Fridgen TD, Delmas M, Banoub J. Top-down lignomic matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry analysis of lignin oligomers extracted from date palm wood. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33:539-560. [PMID: 30506948 DOI: 10.1002/rcm.8368] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 11/23/2018] [Accepted: 11/26/2018] [Indexed: 06/09/2023]
Abstract
RATIONALE We report for the first time the top-down lignomic analysis of the virgin released lignin (VRL) oligomers obtained from the Saudi date palm wood (SDPW), using a matrix-assisted laser desorption/ionization time-of-flight/time-of-flight (MALDI-TOF/TOF) instrument. In addition, we are proposing new collision-induced dissociation tandem mass spectrometry (CID-MS/MS) fragmentation routes for this series of unreported VRL oligomers. METHODS We have used direct MALDI-TOF-MS analysis of the mixture of lignin oligomers without any chromatographic pre-separation. High-energy CID-MS/MS analyses were used to confirm the precursor ion structures. RESULTS Six protonated lignin oligomer molecules were identified: [C19 H24 O8 + H]+ as H(8-O-4')G; [C50 H52 O19 + H]+ as H(8-O-4')H(8-O-4'')S(8-O-4''')S(8-O-4'''')G; [C58 H54 O18 + H]+ as H(8-O-4')H(8-O-4'')H(8-O-4''')G(8-O-4'''')S(8-O-4''''')G; [C58 H54 O19 + H]+ as H(8-O-4')H(8-O-4'')H(8-O-4''')S(8-O-4'''')S(8-O-4''''')G; [C61 H68 O25 + H]+ as H(8-O-4')G(8-O-4'')G(8-O-4''')S(8-O-4'''')S(8-O-4''''')G; and [C61 H68 O26 + H]+ as C(8-O-4')G(8-O-4'')G(8-O-4''')S(8-O-4'''')S(8-O-4''''')G units (H = coniferyl, S = sinapyl, and G = p-coumaryl). Two distonic cations were identified as [C39 H43 O15 + H]+• and [C40 H43 O16 + H]+• deriving from two tetrameric lignin oligomers. The high-energy MS/MS analyses allowed the confirmation of the proposed structures of this series of lignin oligomers. CONCLUSIONS To our knowledge, this is the first elucidation of the lignin structure of the Saudi seedling date palm wood that was accomplished using a top-down lignomic strategy that has not previously been published. The complex high-energy CID-MS/MS fragmentations presented herein are novel and have never been described before.
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Affiliation(s)
- Tasahil Albishi
- Department of Biochemistry, Memorial University of Newfoundland, St John's, Newfoundland, A1C 5X1, Canada
| | - Abanoub Mikhael
- Department of Chemistry, Memorial University of Newfoundland, St John's, Newfoundland, A1C 5X1, Canada
| | - Fereidoon Shahidi
- Department of Biochemistry, Memorial University of Newfoundland, St John's, Newfoundland, A1C 5X1, Canada
| | - Travis D Fridgen
- Department of Chemistry, Memorial University of Newfoundland, St John's, Newfoundland, A1C 5X1, Canada
| | - Michel Delmas
- Inp-Ensiacet, Chemical Engineering Laboratory 4, University of Toulouse, Allée Emile Monso, 31432, Toulouse, France
| | - Joseph Banoub
- Department of Biochemistry, Memorial University of Newfoundland, St John's, Newfoundland, A1C 5X1, Canada
- Department of Chemistry, Memorial University of Newfoundland, St John's, Newfoundland, A1C 5X1, Canada
- Science Branch, Special Projects, Fisheries and Oceans Canada, St John's, NL, A1C 5X1, Canada
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13
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Gao J, Meyer K, Borucki K, Ueland PM. Multiplex Immuno-MALDI-TOF MS for Targeted Quantification of Protein Biomarkers and Their Proteoforms Related to Inflammation and Renal Dysfunction. Anal Chem 2018; 90:3366-3373. [DOI: 10.1021/acs.analchem.7b04975] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jie Gao
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
| | - Klaus Meyer
- Bevital AS, Jonas Lies veg 87, Laboratory Building, Ninth Floor, 5021 Bergen, Norway
| | - Katrin Borucki
- Institute for Clinical Chemistry and Pathobiochemistry, Otto-von-Guericke University Magdeburg, Leipziger Strasse 44 , 39120 Magdeburg, Germany
| | - Per Magne Ueland
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
- Laboratory of Clinical Biochemistry, Haukeland University Hospital, 5021 Bergen, Norway
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14
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Park KM, Hyeon T, Kim MS, Moon JH. In Situ
Quantification and Profiling of Phosphatidylcholine in Mouse Brain Tissue by Matrix-assisted Laser Desorption Ionization with a Liquid Matrix. B KOREAN CHEM SOC 2017. [DOI: 10.1002/bkcs.11142] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Kyung Man Park
- Department of Chemistry; Seoul National University; Seoul 151-747 Korea
| | - Taeghwan Hyeon
- Center for Nanoparticle Research; Institute for Basic Science (IBS); Seoul 151-742 Korea
| | - Myung Soo Kim
- Center for Nanoparticle Research; Institute for Basic Science (IBS); Seoul 151-742 Korea
| | - Jeong Hee Moon
- Disease Target Structure Research Center; KRIBB; Daejeon 305-806 Korea
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15
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Chen BJ, Lam TC, Liu LQ, To CH. Post-translational modifications and their applications in eye research (Review). Mol Med Rep 2017; 15:3923-3935. [PMID: 28487982 DOI: 10.3892/mmr.2017.6529] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 02/22/2017] [Indexed: 02/05/2023] Open
Abstract
Gene expression is the process by which genetic information is used for the synthesis of a functional gene product, and ultimately regulates cell function. The increase of biological complexity from genome to proteome is vast, and the post-translational modification (PTM) of proteins contribute to this complexity. The study of protein expression and PTMs has attracted attention in the post‑genomic era. Due to the limited capability of conventional biochemical techniques in the past, large‑scale PTM studies were technically challenging. The introduction of effective protein separation methods, specific PTM purification strategies and advanced mass spectrometers has enabled the global profiling of PTMs and the identification of a targeted PTM within the proteome. The present review provides an overview of current proteomic technologies being applied in eye research, with a particular focus on studies of PTMs in ocular tissues and ocular diseases.
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Affiliation(s)
- Bing-Jie Chen
- Department of Optometry and Visual Science, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Thomas Chuen Lam
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR, P.R. China
| | - Long-Qian Liu
- Department of Optometry and Visual Science, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Chi-Ho To
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR, P.R. China
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16
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Marsico ALM, Duncan B, Landis RF, Tonga GY, Rotello VM, Vachet RW. Enhanced Laser Desorption/Ionization Mass Spectrometric Detection of Biomolecules Using Gold Nanoparticles, Matrix, and the Coffee Ring Effect. Anal Chem 2017; 89:3009-3014. [PMID: 28193006 DOI: 10.1021/acs.analchem.6b04538] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Nanomaterials have been extensively used as alternate matrices to minimize the low molecular weight interferences observed in typical MALDI but such nanomaterials typically do not improve the spot-to-spot variability that is commonly seen. In this work, we demonstrate that nanoparticles and low matrix concentrations (<2.5 mg/mL) can be used to homogeneously concentrate analytes into a narrow ring by taking advantage of the "coffee ring" effect. Concentration of the samples in this way leads to enhanced signals when compared to conventional MALDI, with higher m/z analytes being enhanced to the greatest extent. Moreover, the ionization suppression often observed in samples with high salt concentrations can be overcome by preparing samples in this way. The ring that is formed is readily visible, allowing the laser to be focused only on spots that contain analyte. The coffee-ring effect represents a new mode by which nanomaterials can be used to enhance the MALDI-based detection of biomolecules.
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Affiliation(s)
- Alyssa L M Marsico
- Department of Chemistry, University of Massachusetts , Amherst, Massachusetts 01003, United States
| | - Bradley Duncan
- Department of Chemistry, University of Massachusetts , Amherst, Massachusetts 01003, United States
| | - Ryan F Landis
- Department of Chemistry, University of Massachusetts , Amherst, Massachusetts 01003, United States
| | - Gulen Yesilbag Tonga
- Department of Chemistry, University of Massachusetts , Amherst, Massachusetts 01003, United States
| | - Vincent M Rotello
- Department of Chemistry, University of Massachusetts , Amherst, Massachusetts 01003, United States
| | - Richard W Vachet
- Department of Chemistry, University of Massachusetts , Amherst, Massachusetts 01003, United States
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17
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Jiang K, Aloor A, Qu J, Xiao C, Wu Z, Ma C, Zhang L, Wang PG. Rapid and sensitive MALDI MS analysis of oligosaccharides by using 2-hydrazinopyrimidine as a derivative reagent and co-matrix. Anal Bioanal Chem 2016; 409:421-429. [DOI: 10.1007/s00216-016-9690-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 05/15/2016] [Accepted: 06/03/2016] [Indexed: 11/24/2022]
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18
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Marsico ALM, Elci GS, Moyano DF, Yesilbag Tonga G, Duncan B, Landis RF, Rotello VM, Vachet RW. Enhanced Laser Desorption/Ionization Mass Spectrometric Detection of Gold Nanoparticles in Biological Samples Using the Synergy between Added Matrix and the Gold Core. Anal Chem 2015; 87:12145-50. [DOI: 10.1021/acs.analchem.5b02985] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Alyssa L. M. Marsico
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Gokhan S. Elci
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Daniel F. Moyano
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Gulen Yesilbag Tonga
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Bradley Duncan
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Ryan F. Landis
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Vincent M. Rotello
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Richard W. Vachet
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
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19
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Marsico ALM, Creran B, Duncan B, Elci SG, Jiang Y, Onasch TB, Wormhoudt J, Rotello VM, Vachet RW. Inkjet-printed gold nanoparticle surfaces for the detection of low molecular weight biomolecules by laser desorption/ionization mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1931-1937. [PMID: 26202457 DOI: 10.1007/s13361-015-1223-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 06/22/2015] [Accepted: 06/26/2015] [Indexed: 05/24/2023]
Abstract
Effective detection of low molecular weight compounds in matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is often hindered by matrix interferences in the low m/z region of the mass spectrum. Here, we show that monolayer-protected gold nanoparticles (AuNPs) can serve as alternate matrices for the very sensitive detection of low molecular weight compounds such as amino acids. Amino acids can be detected at low fmol levels with minimal interferences by properly choosing the AuNP deposition method, density, size, and monolayer surface chemistry. By inkjet-printing AuNPs at various densities, we find that AuNP clusters are essential for obtaining the greatest sensitivity. Graphical Abstract ᅟ.
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Affiliation(s)
- Alyssa L M Marsico
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, 01003, USA
| | - Brian Creran
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, 01003, USA
| | - Bradley Duncan
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, 01003, USA
| | - S Gokhan Elci
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, 01003, USA
| | - Ying Jiang
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, 01003, USA
| | | | | | - Vincent M Rotello
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, 01003, USA
| | - Richard W Vachet
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, 01003, USA.
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20
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Bernier MC, Wysocki VH, Dagan S. Laser desorption ionization of small molecules assisted by tungsten oxide and rhenium oxide particles. JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:891-8. [PMID: 26349643 PMCID: PMC4566159 DOI: 10.1002/jms.3597] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 03/04/2015] [Accepted: 03/25/2015] [Indexed: 05/11/2023]
Abstract
Inorganic metal oxides have shown potential as matrices for assisting in laser desorption ionization with advantages over the aromatic acids typically used. Rhenium and tungsten oxides are attractive options due to their high work functions and relative chemical inertness. In this work, it is shown that ReO3 and WO3 , in microparticle (μP) powder forms, can efficiently facilitate ionization of various types of small molecules and provide minimized background contamination at analyte concentrations below 1 ng/µL. This study shows that untreated inorganic WO3 and ReO3 particles are valid matrix options for detection of protonatable, radical, and precharged species under laser desorption ionization. Qualitatively, the WO3 μP showed improved detection of apigenin, sodiated glucose, and precharged analyte choline, while the ReO3 μP allowed better detection of protonated cocaine, quinuclidine, ametryn, and radical ions of polyaromatic hydrocarbons at detection levels as low as 50 pg/µL. For thermometer ion survival yield experiments, it was also shown that the ReO3 powder was significantly softer than α-cyano-4-hydroxycinnaminic acid. Furthermore, it provided higher intensities of cocaine and polyaromatic hydrocarbons, at laser flux values equal to those used with α-cyano-4-hydroxycinnaminic acid.
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Affiliation(s)
| | | | - Shai Dagan
- Permanent address: Israel Institute for Biological Research, Ness Ziona, Israel
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21
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Cho YT, Su H, Wu WJ, Wu DC, Hou MF, Kuo CH, Shiea J. Biomarker Characterization by MALDI-TOF/MS. Adv Clin Chem 2015; 69:209-54. [PMID: 25934363 DOI: 10.1016/bs.acc.2015.01.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mass spectrometric techniques frequently used in clinical diagnosis, such as gas chromatography-mass spectrometry, liquid chromatography-mass spectrometry, ambient ionization mass spectrometry, and matrix-assisted laser desorption ionization/time-of-flight mass spectrometry (MALDI-TOF/MS), are discussed. Due to its ability to rapidly detect large biomolecules in trace amounts, MALDI-TOF/MS is an ideal tool for characterizing disease biomarkers in biologic samples. Clinical applications of MS for the identification and characterization of microorganisms, DNA fragments, tissues, and biofluids are introduced. Approaches for using MALDI-TOF/MS to detect various disease biomarkers including peptides, proteins, and lipids in biological fluids are further discussed. Finally, various sample pretreatment methods which improve the detection efficiency of disease biomarkers are introduced.
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Affiliation(s)
- Yi-Tzu Cho
- Department of Cosmetic Applications and Management, Yuh-Ing Junior College of Health Care & Management, Kaohsiung, Taiwan
| | - Hung Su
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Wen-Jeng Wu
- Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Deng-Chyang Wu
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Center for Stem Cell Research, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ming-Feng Hou
- Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Chao-Hung Kuo
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Center for Stem Cell Research, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Jentaie Shiea
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung, Taiwan; Center for Stem Cell Research, Kaohsiung Medical University, Kaohsiung, Taiwan; Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung, Taiwan.
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22
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Ding Y, Weng LT, Yang M, Yang Z, Lu X, Huang N, Leng Y. Insights into the aggregation/deposition and structure of a polydopamine film. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:12258-12269. [PMID: 25262750 DOI: 10.1021/la5026608] [Citation(s) in RCA: 161] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Surface-adherent polydopamine (PDA) films as multifunctional coatings can be easily deposited onto a wide range of materials through dopamine self-polymerization. However, a lack of in-depth understanding of PDA aggregation and deposition processes and definite structure elucidation of PDA make it challenging to tailor the surface characteristic and functionality of the PDA films. Herein, we demonstrate that the surface characteristics of the PDA films can be readily tuned by controlling the competitive interplay between PDA aggregation in solution and deposition on the substrate. Moreover, a structural investigation of the PDA films using analytical tools such as X-ray photoelectron spectroscopy (XPS), time-of-flight secondary ion mass spectrometry (ToF-SIMS), and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) allows us to propose a new structure model for the PDA building block. The (DHI)2/PCA trimer complex, which consists of two 5,6-dihydroxyindole (DHI) units and one pyrrolecarboxylic acid (PCA) moiety, is definitely identified as a primary building block of PDA, and its formation is steered by covalent interactions in the initial stages of polymerization. In latter stages, the (DHI)2/PCA trimer complexes are further linked primarily through noncovalent interactions to build up the supramolecular structure of PDA. This study provides new insights into the mechanisms of PDA buildup.
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Affiliation(s)
- Yonghui Ding
- Department of Mechanical and Aerospace Engineering, ‡Materials Characterization and Preparation Facility, and §Department of Chemical and Biomolecular Engineering, The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon, Hong Kong
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23
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Ágoston K, Gyémánt G, Kalmár L, Kerékgyártó J, Szurmai Z, Döncző B, Guttman A. Synthesis and MALDI-TOF MS Analysis of Protected Oligosaccharide Components ofN-Glycoproteins. J Carbohydr Chem 2014. [DOI: 10.1080/07328303.2014.950737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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24
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Sandoval W. Matrix‐Assisted Laser Desorption/Ionization Time‐of‐Flight Mass Analysis of Peptides. ACTA ACUST UNITED AC 2014; 77:16.2.1-16.2.11. [DOI: 10.1002/0471140864.ps1602s77] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Wendy Sandoval
- Department of Protein Chemistry, Genentech South San Francisco California
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25
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van Gool AJ, Hendrickson RC. The proteomic toolbox for studying cerebrospinal fluid. Expert Rev Proteomics 2014; 9:165-79. [DOI: 10.1586/epr.12.6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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27
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Doster ME, Johnson SA. Carbon–Hydrogen Bond Stannylation and Alkylation Catalyzed by Nitrogen-Donor-Supported Nickel Complexes: Intermediates with Ni–Sn Bonds and Catalytic Carbostannylation of Ethylene with Organostannanes. Organometallics 2013. [DOI: 10.1021/om4003889] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Meghan E. Doster
- Department of Chemistry & Biochemistry, University of Windsor, Windsor, Ontario, Canada N9B 3P4
| | - Samuel A. Johnson
- Department of Chemistry & Biochemistry, University of Windsor, Windsor, Ontario, Canada N9B 3P4
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28
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Cho YT, Su H, Huang TL, Chen HC, Wu WJ, Wu PC, Wu DC, Shiea J. Matrix-assisted laser desorption ionization/time-of-flight mass spectrometry for clinical diagnosis. Clin Chim Acta 2013; 415:266-75. [DOI: 10.1016/j.cca.2012.10.032] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2012] [Accepted: 10/16/2012] [Indexed: 01/01/2023]
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29
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Hines HB. Microbial proteomics using mass spectrometry. Methods Mol Biol 2012; 881:159-86. [PMID: 22639214 DOI: 10.1007/978-1-61779-827-6_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Proteomic analyses involve a series of intricate, interdependent steps involving approaches and technical issues that must be fully coordinated to obtain the optimal amount of required information about the test subject. Fortunately, many of these steps are common to most test subjects, requiring only modifications to or, in some cases, substitution of some of the steps to ensure they are relevant to the desired objective of a study. This fortunate occurrence creates an essential core of proteomic approaches and techniques that are consistently available for most studies, regardless of test subject. In this chapter, an overview of some of these core approaches, techniques, and mass spectrometric instrumentation is given, while indicating how such steps are useful for and applied to bacterial investigations. To exemplify how such proteomic concepts and techniques are applicable to bacterial investigations, a practical, quantitative method useful for bacterial proteomic analysis is presented with a discussion of possibilities, pitfalls, and some emerging technology to provide a compilation of information from the diverse literature that is intermingled with experimental experience.
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Affiliation(s)
- Harry B Hines
- Integrated Toxicology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA.
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30
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Liu H, Dai L, Hao Z, Huang W, Yang Q. Hydrophobic cavity in C-terminus is essential for hTNF-α trimer conformation. Biochimie 2012; 94:1001-8. [DOI: 10.1016/j.biochi.2011.12.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 12/19/2011] [Indexed: 10/14/2022]
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[Urinary peptides and calcium oxalate nephrolithiasis, a combined approach: MALDI-TOF mass spectrometry and MicroBCA Protein Assay]. Urologia 2011; 78:227-32. [PMID: 21965035 DOI: 10.5301/ru.2011.8692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2011] [Indexed: 11/20/2022]
Abstract
BACKGROUND Urinary lithiasis is one of the most common benign urological diseases. There is growing evidence that a delicate equilibrium regulated by the function of proteins, soluble peptides, membrane proteins and intracellular mechanisms actually exists. We have studied the urinary protein composition of patients affected by calcium oxalate nephrolithiasis in order to discover a biomarker or any predisposing factors. METHODS The urinary protein composition of 17 patients (11 males, 6 females; mean age 45yrs ± 14SD), affected by calcium oxalate nephrolithiasis, was assessed in comparison with 17 healthy subjects. A qualitative assay was performed using MALDI-TOF mass spectrometry in a spectrum between 1 and 5kDa (medium size peptides), and a numerical (quantitative) assay using specific filters and MicroBCA Protein Assay. RESULTS No differences were detected in the mass spectrums between patients and control subjects: all peaks overlapped perfectly. The results of the numerical assay suggest that concentrations of protein species <5kDa in control samples were actually higher than those which were found in patients. The differences are statistically significant. CONCLUSIONS The study detected neither a biomarker nor any predisposing factors in "stone former" patients. The assessment of the results obtained, in terms of quantitative differences, indicate the need for further research.
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Abstract
A novel analytical method, called Liquid Phase Ion Mobility Spectrometry (LiPIMS) was demonstrated, where aqueous phase analytes were ionized and introduced into non-aqueous liquids, transported by an external electric field from the point of generation to a collection electrode. Ions were produced from a unique liquid phase ionization process, called Electrodispersion Ionization. Spectra of analyte ions illustrated the potential of LiPIMS as a new separation technique. Experimental data showed that electrodispersion ionization was effective in generating nanoampere level of ion current in hexane and benzene from aqueous samples. By controlling the ionization voltage in relation to the sample flow rate, it was possible to operate the electrodispersion ionization source in both continuous and pulsed ionization modes. Unique LiPIMS spectra of aqueous samples of tetramethylammonium bromide, tetrabutylammonium bromide and bradykinin were presented and their respected liquid phase ion mobility values were determined.
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Affiliation(s)
- Maggie Tam
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA
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33
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Porta T, Grivet C, Knochenmuss R, Varesio E, Hopfgartner G. Alternative CHCA-based matrices for the analysis of low molecular weight compounds by UV-MALDI-tandem mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2011; 46:144-152. [PMID: 21259393 DOI: 10.1002/jms.1875] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2010] [Accepted: 11/24/2010] [Indexed: 05/30/2023]
Abstract
Analysis of low molecular weight compounds (LMWC) in complex matrices by vacuum matrix-assisted laser desorption/ionization (MALDI) often suffers from matrix interferences, which can severely degrade limits of quantitation. It is, therefore, useful to have available a range of suitable matrices, which exhibit complementary regions of interference. Two newly synthesized α-cyanocinnamic acid derivatives are reported here; (E)-2-cyano-3-(naphthalen-2-yl)acrylic acid (NpCCA) and (2E)-3-(anthracen-9-yl)-2-cyanoprop-2enoic acid (AnCCA). Along with the commonly used α-cyano-4-hydroxycinnamic acid (CHCA), and the recently developed 4-chloro-α-cyanocinnamic acid (Cl-CCA) matrices, these constitute a chemically similar series of matrices covering a range of molecular weights, and with correspondingly differing ranges of spectral interference. Their performance was compared by measuring the signal-to-noise ratios (S/N) of 47 analytes, mostly pharmaceuticals, with the different matrices using the selected reaction monitoring (SRM) mode on a triple quadrupole instrument equipped with a vacuum MALDI source. AnCCA, NpCCA and Cl-CCA were found to offer better signal-to-noise ratios in SRM mode than CHCA, but Cl-CCA yielded the best results for 60% of the compounds tested. To better understand the relative performance of this matrix series, the proton affinities (PAs) were measured using the kinetic method. Their relative values were: AnCCA > CHCA > NpCCA > Cl-CCA. This ordering is consistent with the performance data. The synthesis of the new matrices is straightforward and they provide (1) tunability of matrix background interfering ions and (2) enhanced analyte response for certain classes of compounds.
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Affiliation(s)
- Tiffany Porta
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Life Sciences Mass Spectrometry, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
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Messelhäusser U, Kämpf P, Colditz J, Bauer H, Schreiner H, Höller C, Busch U. Qualitative and Quantitative Detection of Human Pathogenic Yersinia enterocolitica in Different Food Matrices at Retail Level in Bavaria. Foodborne Pathog Dis 2011; 8:39-44. [DOI: 10.1089/fpd.2010.0589] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Ute Messelhäusser
- Laboratory of Food Microbiology, Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Peter Kämpf
- Laboratory of Food Microbiology, Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Janine Colditz
- Laboratory of Food Microbiology, Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Hans Bauer
- Laboratory of Food Microbiology, Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Hermann Schreiner
- Laboratory of Food Microbiology, Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Christiane Höller
- Laboratory of Food Microbiology, Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Ulrich Busch
- Laboratory of Food Microbiology, Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
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35
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Street JM, Dear JW. The application of mass-spectrometry-based protein biomarker discovery to theragnostics. Br J Clin Pharmacol 2010; 69:367-78. [PMID: 20406221 DOI: 10.1111/j.1365-2125.2009.03610.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Over the last decade rapid developments in mass spectrometry have allowed the identification of multiple proteins in complex biological samples. This proteomic approach has been applied to biomarker discovery in the context of clinical pharmacology (the combination of biomarker and drug now being termed 'theragnostics'). In this review we provide a roadmap for early protein biomarker discovery studies, focusing on some key questions that regularly confront researchers.
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Affiliation(s)
- Jonathan M Street
- Centre for Cardiovascular Science, Edinburgh University, Queen's Medical Research Institute, UK
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36
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Lesur A, Varesio E, Hopfgartner G. Protein Quantification by MALDI-Selected Reaction Monitoring Mass Spectrometry Using Sulfonate Derivatized Peptides. Anal Chem 2010; 82:5227-37. [DOI: 10.1021/ac100602d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Antoine Lesur
- Life Sciences Mass Spectrometry, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Emmanuel Varesio
- Life Sciences Mass Spectrometry, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Gérard Hopfgartner
- Life Sciences Mass Spectrometry, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
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37
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Analysis of lysozyme in cheese by immunocapture mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2010; 878:201-6. [DOI: 10.1016/j.jchromb.2009.07.040] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Revised: 07/28/2009] [Accepted: 07/30/2009] [Indexed: 10/20/2022]
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38
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Zagorski D, Bedin S, Oleinikov V, Polyakov N, Rybalko O, Mchedlishvili B. Metallic microwires obtained as replicas of etched ion tracks in polymer matrixes: Microscopy and emission properties. RADIAT MEAS 2009. [DOI: 10.1016/j.radmeas.2009.10.049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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39
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Oleinikov V, Zagorski D, Bedin S, Volosnikov A, Emelyanov P, Kozmin Y, Mchedlishvili B. The study of the desorption/ionization from the replicas of etched ion tracks. RADIAT MEAS 2008. [DOI: 10.1016/j.radmeas.2008.04.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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40
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Conrotto P, Hellman U. Lys Tag: an easy and robust chemical modification for improved de novo sequencing with a matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometer. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2008; 22:1823-1833. [PMID: 18470875 DOI: 10.1002/rcm.3555] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Mass spectrometry using a matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) instrument is a widespread technique for various types of proteomic analysis. Along with an expanding interest in proteomics, there is a strong requirement for the identification of proteins with high confidence from biological samples. Peptide modification by a wide variety of post-translational modifications (PTMs), the existence of different protein isoforms and the presence of uncharacterized genomes of many species, make protein identification through peptide mass fingerprinting (PMF) often unachievable. Peptide de novo sequencing has been proven to be a useful approach to overcome these variables, and efficient derivatization processes are important tools to achieve this goal. In the present work we describe the methodology and experimental applications of a fast, efficient and cheap lysine derivatization. This chemical modification improves the signals from lysine-terminated peptides and can be efficiently used as a lysine-blocking agent in combination with other derivatization techniques. Most importantly, upon peptide fragmentation it generates a neat series of predominantly y-ions, allowing the determination of unambiguous amino acid sequences. Moreover, this chemical compound was used with target-eluted samples, enabling a second, alternative analysis of the same sample in the MALDI mass spectrometer.
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Affiliation(s)
- Paolo Conrotto
- Ludwig Institute for Cancer Research, Uppsala University, Box 595, SE-751 24 Uppsala, Sweden
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41
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Sook BR, Block DR, Sumithran S, Montañez GE, Rodgers KR, Dawson JH, Eichenbaum Z, Dixon DW. Characterization of SiaA, a Streptococcal Heme-Binding Protein Associated with a Heme ABC Transport System. Biochemistry 2008; 47:2678-88. [DOI: 10.1021/bi701604y] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Brian R. Sook
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302-4098, Department of Chemistry, Biochemistry, and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105-5516, Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, and Department of Biology, Georgia State University, Atlanta, Georgia 30303
| | - Darci R. Block
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302-4098, Department of Chemistry, Biochemistry, and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105-5516, Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, and Department of Biology, Georgia State University, Atlanta, Georgia 30303
| | - Suganya Sumithran
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302-4098, Department of Chemistry, Biochemistry, and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105-5516, Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, and Department of Biology, Georgia State University, Atlanta, Georgia 30303
| | - Griselle E. Montañez
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302-4098, Department of Chemistry, Biochemistry, and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105-5516, Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, and Department of Biology, Georgia State University, Atlanta, Georgia 30303
| | - Kenton R. Rodgers
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302-4098, Department of Chemistry, Biochemistry, and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105-5516, Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, and Department of Biology, Georgia State University, Atlanta, Georgia 30303
| | - John H. Dawson
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302-4098, Department of Chemistry, Biochemistry, and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105-5516, Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, and Department of Biology, Georgia State University, Atlanta, Georgia 30303
| | - Zehava Eichenbaum
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302-4098, Department of Chemistry, Biochemistry, and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105-5516, Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, and Department of Biology, Georgia State University, Atlanta, Georgia 30303
| | - Dabney W. Dixon
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302-4098, Department of Chemistry, Biochemistry, and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105-5516, Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, and Department of Biology, Georgia State University, Atlanta, Georgia 30303
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42
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Wu J, Feng M, Ruan KH. Assembling NMR structures for the intracellular loops of the human thromboxane A2 receptor: implication of the G protein-coupling pocket. Arch Biochem Biophys 2007; 470:73-82. [PMID: 18073117 DOI: 10.1016/j.abb.2007.11.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2007] [Revised: 11/14/2007] [Accepted: 11/15/2007] [Indexed: 11/28/2022]
Abstract
It has been reported that the multiple intracellular loops (iLPs) of the thromboxane A(2) receptor (TP) are involved in the receptor G protein coupling. In this study, a high-resolution 2D NMR technique was used to determine the 3D structures of the first, second, and third iLPs of the TP using synthetic peptides constrained into the loop structures. 2D (1)H NMR spectra, TOCSY and NOESY were obtained for the two peptides from proton NMR experiments. The NMR data was processed and assigned through the Felix 2000 program. Standard methods were used to acquire sequence-specific assignments. Structure calculations were processed through DGII and NMR refinement programs within the Insight II program. We were able to calculate and use the NOE constraints to obtain the superimposed structure of 10 structures for each iLP peptide. The NMR-determined structures of the iLP peptides were used to refine a homology model of the TP. A 3D G-protein-binding cavity, formed by the three intracellular loops, was predicted by the docking of the C-terminal domain of the Galphaq. Based on the structural model and the previous mutagenesis studies, the residues, R130, R60, C223, F138, L360, V361, E358 and Y359, which are important for interaction with the G protein, were further highlighted. These results reveal the possibly important molecular mechanisms in TP signaling and provide structural information to characterize other prostanoid receptor signalings.
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Affiliation(s)
- Jiaxin Wu
- The Center for Experimental Therapeutics and PharmacoInformatics, Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Room 521 Science & Research Building 2, Houston, TX 77204-5037, USA
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43
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Srebalus Barnes CA, Lim A. Applications of mass spectrometry for the structural characterization of recombinant protein pharmaceuticals. MASS SPECTROMETRY REVIEWS 2007; 26:370-88. [PMID: 17410555 DOI: 10.1002/mas.20129] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Therapeutic proteins produced using recombinant DNA technologies are generally complex, heterogeneous, and subject to a variety of enzymatic or chemical modifications during expression, purification, and long-term storage. The use of mass spectrometry (MS) for the evaluation of recombinant protein sequence and structure provides detailed information regarding amino acid modifications and sequence alterations that have the potential to affect the safety and activity of therapeutic protein products. General MS approaches for the characterization of recombinant therapeutic protein products will be reviewed with particular attention given to the standard MS tools available in most biotechnology laboratories. A number of recent examples will be used to illustrate the utility of MS strategies for evaluation of recombinant protein heterogeneity resulting from post-translational modifications (PTMs), sequence variations generated from proteolysis or transcriptional/translational errors, and degradation products which are formed during processing or final product storage. Specific attention will be given to the MS characterization of monoclonal antibodies as a model system for large, glycosylated, recombinant proteins. Detailed examples highlighting the use of MS for the analysis of monoclonal antibody glycosylation, deamidation, and disulfide mapping will be used to illustrate the application of these techniques to a wide variety of heterogeneous therapeutic protein products. The potential use of MS to support the selection of cell line/clone selection and formulation development for therapeutic antibody products will also be discussed.
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44
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Ottens AK, Kobeissy FH, Fuller BF, Liu MC, Oli MW, Hayes RL, Wang KKW. Novel neuroproteomic approaches to studying traumatic brain injury. PROGRESS IN BRAIN RESEARCH 2007; 161:401-18. [PMID: 17618994 DOI: 10.1016/s0079-6123(06)61029-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Neuroproteomics entails wide-scope study of the nervous system proteome in both its content and dynamics. The field employs high-end analytical mass spectrometry and novel high-throughput antibody approaches to characterize as many proteins as possible. The most common application has been differential analysis to identify a limited set of highly dynamic proteins associated with injury, disease, or other altered states of the nervous system. Traumatic brain injury (TBI) is an important neurological condition where neuroproteomics has revolutionized the characterization of protein dynamics, leading to a greater understanding of post-injury biochemistry. Further, proteins of altered abundance or post-translational modifications identified by neuroproteomic studies are candidate biochemical markers of TBI. This chapter explores the use of neuroproteomics in the study of TBI and the validation of identified putative biomarkers for subsequent clinical translation into novel injury diagnostics.
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Affiliation(s)
- Andrew K Ottens
- Department of Psychiatry, Center for Neuroproteomics and Biomarkers Research at the McKnight Brain Institute of the University of Florida, PO Box 100256, Gainesville, FL 32610, USA.
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45
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Moore SEM, Hemsley AR, French AN, Dudley E, Newton RP. New insights from MALDI-ToF MS, NMR, and GC-MS: mass spectrometry techniques applied to palynology. PROTOPLASMA 2006; 228:151-7. [PMID: 16937069 DOI: 10.1007/s00709-006-0168-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2005] [Accepted: 06/08/2005] [Indexed: 05/11/2023]
Abstract
The present study for the first time describes the application of matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-ToF MS) to palynology. With an accessible mass range of up to about 350,000 Da at subpicomolar range, this technique is ideal for the characterisation of bio-macromolecules, such as sporopollenin, found in fossil and extant pollen and spore walls, which often can only be isolated in very small quantities. At this stage, the limited solubility of sporopollenin allows for the identification of sections of this biopolymer, but with the optimisation of MALDI-ToF matrices, further structure elucidation will become possible. Furthermore, gas chromatography-mass spectrometry (GC-MS) and (1)H nuclear magnetic resonance ((1)H NMR) spectroscopy data obtained from a number of experiments revealed that some previously reported data were misinterpreted. These results add support to the hypothesis that common plasticizers were wrongly described as sporopollenin compounds.
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Affiliation(s)
- S E M Moore
- Laboratory for Experimental Palynology, School of Earth, Ocean and Planetary Sciences, Cardiff University, Cardiff, United Kingdom.
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46
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update covering the period 1999-2000. MASS SPECTROMETRY REVIEWS 2006; 25:595-662. [PMID: 16642463 DOI: 10.1002/mas.20080] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
This review describes the use of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry for the analysis of carbohydrates and glycoconjugates and continues coverage of the field from the previous review published in 1999 (D. J. Harvey, Matrix-assisted laser desorption/ionization mass spectrometry of carbohydrates, 1999, Mass Spectrom Rev, 18:349-451) for the period 1999-2000. As MALDI mass spectrometry is acquiring the status of a mature technique in this field, there has been a greater emphasis on applications rather than to method development as opposed to the previous review. The present review covers applications to plant-derived carbohydrates, N- and O-linked glycans from glycoproteins, glycated proteins, mucins, glycosaminoglycans, bacterial glycolipids, glycosphingolipids, glycoglycerolipids and related compounds, and glycosides. Applications of MALDI mass spectrometry to the study of enzymes acting on carbohydrates (glycosyltransferases and glycosidases) and to the synthesis of carbohydrates, are also covered.
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Affiliation(s)
- David J Harvey
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford OX1 3QU, United Kingdom.
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47
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Ottens AK, Kobeissy FH, Golden EC, Zhang Z, Haskins WE, Chen SS, Hayes RL, Wang KKW, Denslow ND. Neuroproteomics in neurotrauma. MASS SPECTROMETRY REVIEWS 2006; 25:380-408. [PMID: 16498609 DOI: 10.1002/mas.20073] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Neurotrauma in the form of traumatic brain injury (TBI) afflicts more Americans annually than Alzheimer's and Parkinson's disease combined, yet few researchers have used neuroproteomics to investigate the underlying complex molecular events that exacerbate TBI. Discussed in this review is the methodology needed to explore the neurotrauma proteome-from the types of samples used to the mass spectrometry identification and quantification techniques available. This neuroproteomics survey presents a framework for large-scale protein research in neurotrauma, as applied for immediate TBI biomarker discovery and the far-reaching systems biology understanding of how the brain responds to trauma. Ultimately, knowledge attained through neuroproteomics could lead to clinical diagnostics and therapeutics to lessen the burden of neurotrauma on society.
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Affiliation(s)
- Andrew K Ottens
- Center of Neuroproteomics and Biomarkers Research, McKnight Brain Institute, University of Florida, Gainesville, FL, USA.
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48
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Takinowaki H, Matsuda Y, Yoshida T, Kobayashi Y, Ohkubo T. The solution structure of the methylated form of the N-terminal 16-kDa domain of Escherichia coli Ada protein. Protein Sci 2006; 15:487-97. [PMID: 16452614 PMCID: PMC2249770 DOI: 10.1110/ps.051786306] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The N-terminal 16-kDa domain of Escherichia coli Ada protein (N-Ada16k) repairs DNA methyl phosphotriester lesions by an irreversible methyl transfer to its cysteine residue. Upon the methylation, the sequence-specific DNA binding affinity for the promoter region of the alkylation resistance genes is enhanced by 10(3)-fold. Then, it acts as a transcriptional regulator for the methylation damage. In this paper, we identified the methyl acceptor residue of N-Ada16k and determined the solution structure of the methylated form of N-Ada16k by using NMR and mass spectrometry. The results of a 13C-filtered 1H-13C HMBC experiment and MALDI-TOF MS and MS/MS experiments clearly showed that the methyl acceptor residue is Cys38. The solution structure revealed that it has two distinct subdomains connected by a flexible linker loop: the methyltransferase (MTase) subdomain with the zinc-thiolate center, and the helical subdomain with a helix-turn-helix motif. Interestingly, there is no potential hydrogen bond donor around Cys38, whereas the other three cysteine residues coordinated to a zinc ion have potential donors. Hence, Cys38 could retain its inherent nucleophilicity and react with a methyl phosphotriester. Furthermore, the structure comparison shows that there is no indication of a remarkable conformational change occurring upon the methylation. This implies that the electrostatic repulsion between the negatively charged DNA and the zinc-thiolate center may avoid the contact between the MTase subdomain and the DNA in the nonmethylated form. Thus, after the Cys38 methylation, the MTase subdomain can bind the cognate DNA because the negative charge of the zinc-thiolate center is reduced.
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Affiliation(s)
- Hiroto Takinowaki
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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Li GH, Wan JZ, Le GW, Shi YH. Novel angiotensin I-converting enzyme inhibitory peptides isolated from Alcalase hydrolysate of mung bean protein. J Pept Sci 2006; 12:509-14. [PMID: 16680798 DOI: 10.1002/psc.758] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Mung bean protein isolates were hydrolyzed for 2 h by Alcalase. The generated hydrolysate showed angiotensin I-converting enzyme (ACE) inhibitory activity with the IC(50) value of 0.64 mg protein/ml. Three kinds of novel ACE inhibitory peptides were isolated from the hydrolysate by Sephadex G-15 and reverse-phase high performance liquid chromatography (RP-HPLC). These peptides were identified by amino acid composition analysis and matrix assisted-laser desorption/ionization time-of-flight tandem mass spectrometry (MALDI-TOF MS/MS), as Lys-Asp-Tyr-Arg-Leu, Val-Thr-Pro-Ala-Leu-Arg and Lys-Leu-Pro-Ala-Gly-Thr-Leu-Phe with the IC(50) values of 26.5 microM, 82.4 microM and 13.4 microM, respectively.
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Affiliation(s)
- Guan-Hong Li
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R. China.
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50
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Darie CC, Biniossek ML, Winter V, Mutschler B, Haehnel W. Isolation and structural characterization of the Ndh complex from mesophyll and bundle sheath chloroplasts of Zea mays. FEBS J 2005; 272:2705-16. [PMID: 15943805 DOI: 10.1111/j.1742-4658.2005.04685.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Complex I (NADH: ubiquinone oxidoreductase) is the first complex in the respiratory electron transport chain. Homologs of this complex exist in bacteria, mitochondria and chloroplasts. The minimal complex I from mitochondria and bacteria contains 14 different subunits grouped into three modules: membrane, connecting, and soluble subcomplexes. The complex I homolog (NADH dehydrogenase or Ndh complex) from chloroplasts from higher plants contains genes for two out of three modules: the membrane and connecting subcomplexes. However, there is not much information about the existence of the soluble subcomplex (which is the electron input device in bacterial complex I) in the composition of the Ndh complex. Furthermore, there are contrasting reports regarding the subunit composition of the Ndh complex and its molecular mass. By using blue native (BN)/PAGE and Tricine/PAGE or colorless-native (CN)/PAGE, BN/PAGE and Tricine/PAGE, combined with mass spectrometry, we attempted to obtain more information about the plastidal Ndh complex from maize (Zea mays). Using antibodies, we detected the expression of a new ndh gene (ndhE) in mesophyll (MS) and bundle sheath (BS) chloroplasts and in ethioplasts (ET). We determined the molecular mass of the Ndh complex (550 kDa) and observed that it splits into a 300 kDa membrane subcomplex (containing NdhE) and a 250 kDa subcomplex (containing NdhH, -J and -K). The Ndh complex forms dimers at 1000-1100 kDa in both MS and BS chloroplasts. Native/PAGE of the MS and BS chloroplasts allowed us to determine that the Ndh complex contains at least 14 different subunits. The native gel electrophoresis, western blotting and mass spectrometry allowed us to identify five of the Ndh subunits. We also provide a method that allows the purification of large amounts of Ndh complex for further structural, as well as functional studies.
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Affiliation(s)
- Costel C Darie
- Brookdale Department Molecular, Cell and Developmental Biology, Mount Sinai School of Medicine, New York, NY 10029-6574, USA.
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