1
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Tanaka M, Arima K, Ide H, Koshi M, Ohno N, Imamura M, Matsui T. Application of graphite carbon black assisted-laser desorption ionization-mass spectrometry for soy sauce product discrimination. Biosci Biotechnol Biochem 2024; 88:656-664. [PMID: 38533648 DOI: 10.1093/bbb/zbae034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 03/08/2024] [Indexed: 03/28/2024]
Abstract
In a previous study, we developed a novel analytical method to directly and simultaneously detect taste- and odor-active compounds using graphite carbon black (GCB)-assisted laser desorption ionization mass spectrometry (LDI-MS). In this study, we aimed to evaluate food quality using a variety of soy sauces using the method to discriminate each product. Graphite carbon black-laser desorption ionization-mass spectrometry allowed the provision of hundreds of MS peaks derived from soy sauces in both positive and negative modes without any tedious sample pretreatments. Principal component analysis using the obtained MS peaks clearly distinguished three soy sauce products based on the manufacturing countries (Japan, China, and India). Moreover, this method identified distinct MS peaks for discrimination, which significantly correlated with their quantitative amounts in the products. Thus, GCB-LDI-MS analysis was established as a simple and rapid technique for food analysis, illustrating the chemical patterns of food products.
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Affiliation(s)
- Mitsuru Tanaka
- Faculty of Agriculture, Graduate School of Kyushu University, Fukuoka, Japan
- Research and Development Center for Five-Sense Devices, Kyushu University, Fukuoka, Japan
| | - Keishiro Arima
- Faculty of Agriculture, Graduate School of Kyushu University, Fukuoka, Japan
| | - Haruna Ide
- Faculty of Agriculture, Graduate School of Kyushu University, Fukuoka, Japan
| | - Mariko Koshi
- Faculty of Agriculture, Graduate School of Kyushu University, Fukuoka, Japan
| | - Naoto Ohno
- Research & Development Division, Kikkoman Co., Chiba, Japan
| | - Miho Imamura
- Research & Development Division, Kikkoman Co., Chiba, Japan
| | - Toshiro Matsui
- Faculty of Agriculture, Graduate School of Kyushu University, Fukuoka, Japan
- Research and Development Center for Five-Sense Devices, Kyushu University, Fukuoka, Japan
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2
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Scoggins TR, Specker JT, Prentice BM. Multiple ion isolation and accumulation events for selective chemical noise reduction and dynamic range enhancement in MALDI imaging mass spectrometry. Analyst 2024; 149:2459-2468. [PMID: 38525787 PMCID: PMC11149414 DOI: 10.1039/d4an00160e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
Abundant chemical noise in MALDI imaging mass spectrometry experiments can impede the detection of less abundant compounds of interest. This chemical noise commonly originates from the MALDI matrix as well as other endogenous compounds present in high concentrations and/or with high ionization efficiencies. MALDI imaging mass spectrometry of biological tissues measures numerous biomolecular compounds that exist in a wide range of concentrations in vivo. When ion trapping instruments are used, highly abundant ions can dominate the charge capacity and lead to space charge effects that hinder the dynamic range and detection of lowly abundant compounds of interest. Gas-phase fractionation has been previously utilized in mass spectrometry to isolate and enrich target analytes. Herein, we have characterized the use of multiple continuous accumulations of selected ions (Multi CASI) to reduce the abundance of chemical noise and diminish the effects of space charge in MALDI imaging mass spectrometry experiments. Multi CASI utilizes the mass-resolving capability of a quadrupole mass filter to perform multiple sequential ion isolation events prior to a single mass analysis of the combined ion population. Multi CASI was used to improve metabolite and lipid detection in the MALDI imaging mass spectrometry analysis of rat brain tissue.
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Affiliation(s)
- Troy R Scoggins
- Department of Chemistry, University of Florida, Gainesville, FL, USA.
| | | | - Boone M Prentice
- Department of Chemistry, University of Florida, Gainesville, FL, USA.
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3
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Macdonald JK, Clift CL, Saunders J, Zambrzycki SC, Mehta AS, Drake RR, Angel PM. Differential Protease Specificity by Collagenase as a Novel Approach to Serum Proteomics That Includes Identification of Extracellular Matrix Proteins without Enrichment. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:487-497. [PMID: 38329320 PMCID: PMC10921462 DOI: 10.1021/jasms.3c00366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/18/2023] [Accepted: 01/10/2024] [Indexed: 02/09/2024]
Abstract
Circulating extracellular matrix (ECM) proteins are serological biomarkers of interest due to their association with pathologies involving disease processes such as fibrosis and cancers. In this study, we investigate the potential for serum biomarker research using differential protease specificity (DPS), leveraging alternate protease specificity as a targeting mechanism to selectively digest circulating ECM protein serum proteins. A proof-of-concept study is presented using serum from patients with cirrhotic liver or hepatocellular carcinoma. The approach uses collagenase DPS for digestion of deglycosylated serum and liquid-chromatography-trapped ion mobility-tandem mass spectrometry (LC-TIMS-MS/MS) to enhance the detection of ECM proteins in serum. It requires no sample enrichment and minimizes the albumin average precursor intensity readout to less than 1.2%. We further demonstrate the capabilities for using the method as a high-throughput matrix-assisted laser/desorption ionization mass spectrometry (MALDI-MS) assay coupled with reference library searching. A goal is to improve the depth and breadth of biofluid proteomics for noninvasive assays.
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Affiliation(s)
- Jade K. Macdonald
- Department of Cell and Molecular
Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | | | | | - Stephen C. Zambrzycki
- Department of Cell and Molecular
Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Anand S. Mehta
- Department of Cell and Molecular
Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Richard R. Drake
- Department of Cell and Molecular
Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Peggi M. Angel
- Department of Cell and Molecular
Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina 29425, United States
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4
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Lellman S, Reynolds CK, Jones AB, Taylor N, Cramer R. LAP-MALDI MS Profiling and Identification of Potential Biomarkers for the Detection of Bovine Tuberculosis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:13899-13905. [PMID: 37677086 PMCID: PMC10515614 DOI: 10.1021/acs.jafc.3c01879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 08/14/2023] [Accepted: 08/22/2023] [Indexed: 09/09/2023]
Abstract
Detecting bovine tuberculosis (bTB) primarily relies on the tuberculin skin test, requiring two separate animal handling events with a period of incubation time (normally 3 days) between them. Here, we present the use of liquid atmospheric pressure (LAP)-MALDI for the identification of bTB infection, employing a three-class prediction model that was obtained by supervised linear discriminant analysis (LDA) and tested with bovine mastitis samples as disease-positive controls. Noninvasive collection of nasal swabs was used to collect samples, which were subsequently subjected to a short (<4 h) sample preparation method. Cross-validation of the three-class LDA model from the processed nasal swabs provided a sensitivity of 75.0% and specificity of 90.1%, with an overall classification accuracy of 85.7%. These values are comparable to those for the skin test, showing that LAP-MALDI MS has the potential to provide an alternative single-visit diagnostic platform that can detect bTB within the same day of sampling.
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Affiliation(s)
- Sophie
E. Lellman
- Department
of Chemistry, University of Reading, Whiteknights, Reading RG6 6DX, United Kingdom
| | - Christopher K. Reynolds
- School
of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading RG6 6EU, United Kingdom
| | - A.K. Barney Jones
- School
of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading RG6 6EU, United Kingdom
| | - Nick Taylor
- Veterinary
Epidemiology and Economics Research Unit (VEERU), PAN Livestock Services
Ltd, School of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading RG6 6EU, United Kingdom
| | - Rainer Cramer
- Department
of Chemistry, University of Reading, Whiteknights, Reading RG6 6DX, United Kingdom
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5
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Calabrese V, Schmitz-Afonso I, Riah-Anglet W, Trinsoutrot-Gattin I, Pawlak B, Afonso C. Direct introduction MALDI FTICR MS based on dried droplet deposition applied to non-targeted metabolomics on Pisum Sativum root exudates. Talanta 2023; 253:123901. [PMID: 36088848 DOI: 10.1016/j.talanta.2022.123901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 12/13/2022]
Abstract
Non-targeted metabolomic approaches based on direct introduction (DI) through a soft ionization source are nowadays used for large-scale analysis and wide cover-up of metabolites in complex matrices. When coupled with ultra-high-resolution Fourier-Transform ion cyclotron resonance (FTICR MS), DI is generally performed through electrospray (ESI), which, despite the great analytical throughput, can suffer of matrix effects due to residual salts or charge competitors. In alternative, matrix assisted laser desorption ionization (MALDI) coupled with FTICR MS offers relatively high salt tolerance but it is mainly used for imaging of small molecule within biological tissues. In this study, we report a systematic evaluation on the performance of direct introduction ESI and MALDI coupled with FTICR MS applied to the analysis of root exudates (RE), a complex mixture of metabolites released from plant root tips and containing a relatively high salt concentration. Classic dried droplet deposition followed by screening of best matrices and ratio allowed the selection of high ranked conditions for non-targeted metabolomics on RE. Optimization of MALDI parameters led to improved reproducibility and precision. A RE desalted sample was used for comparison on ionization efficiency of the two sources and ion enhancement at high salinity was highlighted in MALDI by spiking desalted solution with inorganic salts. Application of a true lyophilized RE sample exhibited the complementarity of the two sources and the ability of MALDI in the detection of undisclosed metabolites suffering of matrix effects in ESI mode.
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Affiliation(s)
- Valentina Calabrese
- Normandie Univ, COBRA, UMR 6014 and FR 3038, Université de Rouen, INSA de Rouen, CNRS, IRCOF, 1 Rue Tesnières, 76821, Mont-Saint-Aignan, Cedex, France
| | - Isabelle Schmitz-Afonso
- Normandie Univ, COBRA, UMR 6014 and FR 3038, Université de Rouen, INSA de Rouen, CNRS, IRCOF, 1 Rue Tesnières, 76821, Mont-Saint-Aignan, Cedex, France.
| | - Wassila Riah-Anglet
- UniLaSalle, AGHYLE Research Unit UP 2018.C101, Rouen Team, 76134 Mont-Saint Aignan, SFR Normandie Végétal FED 4277, 76000, Rouen, France
| | - Isabelle Trinsoutrot-Gattin
- UniLaSalle, AGHYLE Research Unit UP 2018.C101, Rouen Team, 76134 Mont-Saint Aignan, SFR Normandie Végétal FED 4277, 76000, Rouen, France
| | - Barbara Pawlak
- Laboratoire GlycoMEV UR 4358, Université de Rouen Normandie, SFR Normandie Végétal FED 4277, 76000, Rouen, France
| | - Carlos Afonso
- Normandie Univ, COBRA, UMR 6014 and FR 3038, Université de Rouen, INSA de Rouen, CNRS, IRCOF, 1 Rue Tesnières, 76821, Mont-Saint-Aignan, Cedex, France
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6
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Liu H, Pan Y, Xiong C, Han J, Wang X, Chen J, Nie Z. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) for in situ analysis of endogenous small molecules in biological samples. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116809] [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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7
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Zegarra-Urquia CL, Santiago J, Bumgardner JD, Goroncy AK, Vega-Baudrit J, Hernández-Escobar CA, Zaragoza-Contreras EA. Characterization of isoniazid incorporation into chitosan-poly(aspartic acid) nanoparticles. INT J POLYM MATER PO 2022. [DOI: 10.1080/00914037.2022.2145287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
| | - Julio Santiago
- Departamento de Química Orgánica, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Joel D. Bumgardner
- Biomedical Engineering, The University of Memphis, Memphis, Tennessee, USA
| | | | - José Vega-Baudrit
- Centro Nacional de Alta Tecnología “Dr. Franklin Chang Díaz”, Laboratorio Nacional de Nanotecnología (LANOTEC), San José, Costa Rica
- POLIUNA, Escuela de Química, Universidad Nacional, Heredia, Costa Rica
| | - Claudia A. Hernández-Escobar
- Department of Engineering and Materials Chemistry, Centro de Investigación en Materiales Avanzados, Complejo Industrial Chihuahua, Chihuahua, Mexico
| | - E. Armando Zaragoza-Contreras
- Department of Engineering and Materials Chemistry, Centro de Investigación en Materiales Avanzados, Complejo Industrial Chihuahua, Chihuahua, Mexico
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8
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Kobylis P, Kasprzyk M, Nowacki A, Caban M. An investigation of the ionicity of selected ionic liquid matrices used for matrix-assisted laser desorption/ionization. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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9
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Hou Y, Gao Y, Guo S, Zhang Z, Chen R, Zhang X. Applications of spatially resolved omics in the field of endocrine tumors. Front Endocrinol (Lausanne) 2022; 13:993081. [PMID: 36704039 PMCID: PMC9873308 DOI: 10.3389/fendo.2022.993081] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 12/15/2022] [Indexed: 01/11/2023] Open
Abstract
Endocrine tumors derive from endocrine cells with high heterogeneity in function, structure and embryology, and are characteristic of a marked diversity and tissue heterogeneity. There are still challenges in analyzing the molecular alternations within the heterogeneous microenvironment for endocrine tumors. Recently, several proteomic, lipidomic and metabolomic platforms have been applied to the analysis of endocrine tumors to explore the cellular and molecular mechanisms of tumor genesis, progression and metastasis. In this review, we provide a comprehensive overview of spatially resolved proteomics, lipidomics and metabolomics guided by mass spectrometry imaging and spatially resolved microproteomics directed by microextraction and tandem mass spectrometry. In this regard, we will discuss different mass spectrometry imaging techniques, including secondary ion mass spectrometry, matrix-assisted laser desorption/ionization and desorption electrospray ionization. Additionally, we will highlight microextraction approaches such as laser capture microdissection and liquid microjunction extraction. With these methods, proteins can be extracted precisely from specific regions of the endocrine tumor. Finally, we compare applications of proteomic, lipidomic and metabolomic platforms in the field of endocrine tumors and outline their potentials in elucidating cellular and molecular processes involved in endocrine tumors.
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Affiliation(s)
- Yinuo Hou
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Yan Gao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Shudi Guo
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Zhibin Zhang
- General Surgery, Tianjin First Center Hospital, Tianjin, China
- *Correspondence: Zhibin Zhang, ; Ruibing Chen, ; Xiangyang Zhang,
| | - Ruibing Chen
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- *Correspondence: Zhibin Zhang, ; Ruibing Chen, ; Xiangyang Zhang,
| | - Xiangyang Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- *Correspondence: Zhibin Zhang, ; Ruibing Chen, ; Xiangyang Zhang,
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10
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Treu A, Römpp A. Matrix ions as internal standard for high mass accuracy matrix-assisted laser desorption/ionization mass spectrometry imaging. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021; 35:e9110. [PMID: 33880828 DOI: 10.1002/rcm.9110] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/16/2021] [Accepted: 04/18/2021] [Indexed: 06/12/2023]
Abstract
RATIONALE High mass accuracy is indispensable for reliable identification in matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) imaging. Ubiquitous matrix ions can serve as reference masses for mass calibration if their sum formula is known. Here we report an overview of ions generated on tissue by 11 common MALDI matrices for use in internal or external mass calibration. METHODS Matrices covered in this study were applied onto coronal mouse brain sections using a pneumatic sprayer setup. MALDI imaging was performed on a Q Exactive HF orbital trapping mass spectrometer coupled to an AP-SMALDI 10 source. Measurements were conducted with high mass resolution (240 k full width at half maximum at m/z 200) and high mass accuracy with a root mean square mass error of better than 1.5 ppm achieved via internal mass calibration using matrix ions. RESULTS MALDI MS imaging was used to investigate ions generated on tissue by 11 common MALDI matrices. An example of using matrix ions for internal mass calibration in MALDI imaging of drug substances and lipids in murine lung sections is presented. Tables containing the cluster composition, sum formulae, and the measured and theoretical m/z ratios of the identified ions were compiled for each matrix. CONCLUSION Using matrix ions as reference masses for internal and external mass calibration in MALDI MS imaging is an effective and elegant way to achieve sub-ppm mass accuracy as it makes use of ubiquitous signals present in every MALDI MS spectrum without the need for an additional calibration standard.
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Affiliation(s)
- Axel Treu
- Bioanalytical Sciences and Food Analysis, University of Bayreuth, Bayreuth, Germany
| | - Andreas Römpp
- Bioanalytical Sciences and Food Analysis, University of Bayreuth, Bayreuth, Germany
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11
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Blaschke CRK, McDowell CT, Black AP, Mehta AS, Angel PM, Drake RR. Glycan Imaging Mass Spectrometry: Progress in Developing Clinical Diagnostic Assays for Tissues, Biofluids, and Cells. Clin Lab Med 2021; 41:247-266. [PMID: 34020762 PMCID: PMC8862151 DOI: 10.1016/j.cll.2021.03.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
N-glycan imaging mass spectrometry (IMS) can rapidly and reproducibly identify changes in disease-associated N-linked glycosylation that are linked with histopathology features in standard formalin-fixed paraffin-embedded tissue samples. It can detect multiple N-glycans simultaneously and has been used to identify specific N-glycans and carbohydrate structural motifs as possible cancer biomarkers. Recent advancements in instrumentation and sample preparation are also discussed. The tissue N-glycan IMS workflow has been adapted to new glass slide-based assays for effective and rapid analysis of clinical biofluids, cultured cells, and immunoarray-captured glycoproteins for detection of changes in glycosylation associated with disease.
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Affiliation(s)
- Calvin R K Blaschke
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, 173 Ashley Avenue, BSB 358, Charleston, SC 29425, USA
| | - Colin T McDowell
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, 173 Ashley Avenue, BSB 358, Charleston, SC 29425, USA
| | - Alyson P Black
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, 173 Ashley Avenue, BSB 358, Charleston, SC 29425, USA
| | - Anand S Mehta
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, 173 Ashley Avenue, BSB 358, Charleston, SC 29425, USA
| | - Peggi M Angel
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, 173 Ashley Avenue, BSB 358, Charleston, SC 29425, USA
| | - Richard R Drake
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, 173 Ashley Avenue, BSB 358, Charleston, SC 29425, USA.
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12
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Kobylis P, Stepnowski P, Caban M. Review of the applicability of ionic liquid matrices for the quantification of small molecules by MALDI MS. Microchem J 2021. [DOI: 10.1016/j.microc.2021.105983] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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13
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Chen C, Laviolette SR, Whitehead SN, Renaud JB, Yeung KKC. Imaging of Neurotransmitters and Small Molecules in Brain Tissues Using Laser Desorption/Ionization Mass Spectrometry Assisted with Zinc Oxide Nanoparticles. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1065-1079. [PMID: 33783203 DOI: 10.1021/jasms.1c00021] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Inorganic nanostructured materials such as silicon, carbon, metals, and metal oxides have been explored as matrices of low-background signals to assist the laser desorption/ionization (LDI) mass spectrometric (MS) analysis of small molecules, but their applications for imaging of small molecules in biological tissues remain limited in the literature. Titanium dioxide is one of the known nanoparticles (NP) that can effectively assist LDI MS imaging of low molecular weight molecules (LMWM). TiO2 NP is commercially available as dispersions, which can be applied using a chemical solution sprayer. However, aggregation of NP can occur in the dispersions, and the aggregated NP can slowly clog the sprayer nozzle. In this work, the use of zinc oxide (ZnO) NP for LDI MS imaging is investigated as a superior alternative due to its dissolution in acidic pH. ZnO NP was found to deliver similar or better results in the imaging of LMWM in comparison to TiO2 NP. The regular acid washes were effective in minimizing clogging and maintaining high reproducibility. High-quality images of mouse sagittal and rat coronal tissue sections were obtained. Ions were detected predominately as Na+ or K+ adducts in the positive ion mode. The number of LMWM detected with ZnO NP was similar to that obtained with TiO2 NP, and only a small degree of specificity was observed.
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Affiliation(s)
| | | | | | - Justin B Renaud
- London Research and Development Center, Agriculture and Agri-Food Canada, London, ON N5 V 4T3, Canada
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14
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Clift CL, Drake RR, Mehta A, Angel PM. Multiplexed imaging mass spectrometry of the extracellular matrix using serial enzyme digests from formalin-fixed paraffin-embedded tissue sections. Anal Bioanal Chem 2021; 413:2709-2719. [PMID: 33206215 PMCID: PMC8012227 DOI: 10.1007/s00216-020-03047-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/08/2020] [Accepted: 11/04/2020] [Indexed: 12/14/2022]
Abstract
We report a multiplexed imaging mass spectrometry method which spatially localizes and selectively accesses the extracellular matrix on formalin-fixed paraffin-embedded tissue sections. The extracellular matrix (ECM) consists of (1) fibrous proteins, post-translationally modified (PTM) via N- and O-linked glycosylation, as well as hydroxylation on prolines and lysines, and (2) glycosaminoglycan-decorated proteoglycans. Accessing all these components poses a unique analytical challenge. Conventional peptide analysis via trypsin inefficiently captures ECM peptides due to their low abundance, intra- and intermolecular cross-linking, and PTMs. In previous studies, we have developed matrix-assisted laser desorption ionization imaging mass spectrometry (MALDI-IMS) techniques to capture collagen peptides via collagenase type III digestion, both alone and after N-glycan removal via PNGaseF digest. However, in fibrotic tissues, the buildup of ECM components other than collagen-type proteins, including elastin and glycosaminoglycans, limits efficacy of any single enzyme to access the complex ECM. Here, we have developed a novel serial enzyme strategy to define the extracellular matrix, including PTMs, from a single tissue section for MALDI-IMS applications. Graphical Abstract.
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Affiliation(s)
- Cassandra L Clift
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, 173 Ashley Avenue, Charleston, SC, 29425, USA
| | - Richard R Drake
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, 173 Ashley Avenue, Charleston, SC, 29425, USA
| | - Anand Mehta
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, 173 Ashley Avenue, Charleston, SC, 29425, USA
| | - Peggi M Angel
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, 173 Ashley Avenue, Charleston, SC, 29425, USA.
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15
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Amiri R, Farrokhpour H, Tabrizchi M. Sodium salts effect on the time of flight mass spectra of some amino acids in the
direct‐
laser desorption ionization and matrix‐assisted laser desorption/ionization. J CHIN CHEM SOC-TAIP 2021. [DOI: 10.1002/jccs.202000400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Razieh Amiri
- Department of Chemistry Isfahan University of Technology Isfahan Iran
| | | | - Mahmoud Tabrizchi
- Department of Chemistry Isfahan University of Technology Isfahan Iran
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16
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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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17
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Qu H, Jackson MA, Yap K, Harvey PJ, Gilding EK, Craik DJ. Production of a structurally validated cyclotide in rice suspension cells is enabled by a supporting biosynthetic enzyme. PLANTA 2020; 252:97. [PMID: 33155076 DOI: 10.1007/s00425-020-03505-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/26/2020] [Indexed: 05/22/2023]
Abstract
We demonstrate the production of a structurally correct cyclotide in rice suspension cells with co-expression of a ligase-type AEP, which unlocks monocotyledons as production platforms to produce cyclotides. Cyclotides are a class of backbone-cyclic plant peptides that harbor a cystine knot composed of three disulfide bonds. These structural features make cyclotides particularly stable, and thus they have attracted significant attention for their use in biotechnological applications such as drug design. Currently, chemical synthesis is the predominant strategy to produce cyclotides for research purposes. However, synthetic production becomes costly both economically and environmentally at large scale. Plants offer an attractive alternative to chemical synthesis because of their lower cost and environmental footprint. In this study, rice suspension cells were engineered to produce the prototypical cyclotide, kalata B1 (kB1), a cyclotide with insecticidal properties from the African plant Oldenlandia affinis. Engineered rice cells produced structurally validated kB1 at yields of 64.21 µg/g (DW), which was dependent on the co-expression of a peptide ligase-competent asparaginyl endopeptidase OaAEP1b from O. affinis. Without co-expression, kB1 was predominantly produced as linear peptide. Through HPLC-MS co-elution, reduction, alkylation, enzymatic digestion, and proton NMR analysis, kB1 produced in rice was shown to be structurally identical to native kB1. This study reports the first example of an engineered plant suspension cell culture with the required molecular machinery for efficient production and cyclisation of a heterologous cyclotide.
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Affiliation(s)
- Haiou Qu
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Mark A Jackson
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Kuok Yap
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Peta J Harvey
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Edward K Gilding
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, 4072, Australia.
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18
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Angel PM, Spruill L, Jefferson M, Bethard JR, Ball LE, Hughes-Halbert C, Drake RR. Zonal regulation of collagen-type proteins and posttranslational modifications in prostatic benign and cancer tissues by imaging mass spectrometry. Prostate 2020; 80:1071-1086. [PMID: 32687633 PMCID: PMC7857723 DOI: 10.1002/pros.24031] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 06/01/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND The emergence of reactive stroma is a hallmark of prostate cancer (PCa) progression and a potential source for prognostic and diagnostic markers of PCa. Collagen is a main component of reactive stroma and changes systematically and quantitatively to reflect the course of PCa, yet has remained undefined due to a lack of tools that can define collagen protein structure. Here we use a novel collagen-targeting proteomics approach to investigate zonal regulation of collagen-type proteins in PCa prostatectomies. METHODS Prostatectomies from nine patients were divided into zones containing 0%, 5%, 20%, 70% to 80% glandular tissue and 0%, 5%, 25%, 70% by mass of PCa tumor following the McNeal model. Tissue sections from zones were graded by a pathologist for Gleason score, percent tumor present, percent prostatic intraepithelial neoplasia and/or inflammation (INF). High-resolution accurate mass collagen targeting proteomics was done on a select subset of tissue sections from patient-matched tumor or nontumor zones. Imaging mass spectrometry was used to investigate collagen-type regulation corresponding to pathologist-defined regions. RESULTS Complex collagen proteomes were detected from all zones. COL17A and COL27A increased in zones of INF compared with zones with tumor present. COL3A1, COL4A5, and COL8A2 consistently increased in zones with tumor content, independent of tumor size. Collagen hydroxylation of proline (HYP) was altered in tumor zones compared with zones with INF and no tumor. COL3A1 and COL5A1 showed significant changes in HYP peptide ratios within tumor compared with zones of INF (2.59 ± 0.29, P value: .015; 3.75 ± 0.96 P value .036, respectively). By imaging mass spectrometry COL3A1 showed defined localization and regulation to tumor pathology. COL1A1 and COL1A2 showed gradient regulation corresponding to PCa pathology across zones. Pathologist-defined tumor regions showed significant increases in COL1A1 HYP modifications compared with COL1A2 HYP modifications. Certain COL1A1 and COL1A2 peptides could discriminate between pathologist-defined tumor and inflammatory regions. CONCLUSIONS Site-specific posttranslational regulation of collagen structure by proline hydroxylation may be involved in reactive stroma associated with PCa progression. Translational and posttranslational regulation of collagen protein structure has potential for new markers to understand PCa progression and outcomes.
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Affiliation(s)
- Peggi M. Angel
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Proteomics Center, Medical University of South Carolina, Charleston, SC
| | - Laura Spruill
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC
| | - Melanie Jefferson
- Department of Psychiatry & Behavioral Sciences, Medical University of South Carolina, Charleston, SC
| | - Jennifer R. Bethard
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Proteomics Center, Medical University of South Carolina, Charleston, SC
| | - Lauren E. Ball
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Proteomics Center, Medical University of South Carolina, Charleston, SC
| | - Chanita Hughes-Halbert
- Department of Psychiatry & Behavioral Sciences, Medical University of South Carolina, Charleston, SC
| | - Richard R. Drake
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Proteomics Center, Medical University of South Carolina, Charleston, SC
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19
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Denti V, Piga I, Guarnerio S, Clerici F, Ivanova M, Chinello C, Paglia G, Magni F, Smith A. Antigen Retrieval and Its Effect on the MALDI-MSI of Lipids in Formalin-Fixed Paraffin-Embedded Tissue. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1619-1624. [PMID: 32678590 PMCID: PMC8009503 DOI: 10.1021/jasms.0c00208] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissue represents the primary source of clinical tissue and is routinely used in MALDI-MSI studies. However, it is not particularly suitable for lipidomics imaging given that many species are depleted during tissue processing. Irrespective, a number of solvent-resistant lipids remain, but their extraction may be hindered by the cross-link between proteins. Therefore, an antigen retrieval step could enable the extraction of a greater number of lipids and may provide information that is complementary to that which can be obtained from other biomolecules, such as proteins. In this short communication, we aim to address the effect of performing antigen retrieval prior to MALDI-MSI of lipids in FFPE tissue. As a result, an increased number of lipid signals could be detected and may have derived from lipid species that are known to be implicated in the lipid-protein cross-linking that is formed as a result of formalin fixation. Human renal cancer tissue was used as a proof of concept to determine whether using these detected lipid signals were also able to highlight the histopathological regions that were present. These preliminary findings may highlight the potential to enhance the clinical relevance of the lipidomic information obtained from FFPE tissue.
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Affiliation(s)
- Vanna Denti
- Clinical
Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, Vedano al Lambro 20854, Italy
| | - Isabella Piga
- Clinical
Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, Vedano al Lambro 20854, Italy
| | - Sonia Guarnerio
- Biomolecular
Sciences Research Centre, Sheffield-Hallam
University, City Campus, Howard Street, Sheffield S1 1WB, United Kingdom
| | - Francesca Clerici
- Clinical
Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, Vedano al Lambro 20854, Italy
| | - Mariia Ivanova
- Clinical
Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, Vedano al Lambro 20854, Italy
| | - Clizia Chinello
- Clinical
Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, Vedano al Lambro 20854, Italy
| | - Giuseppe Paglia
- Clinical
Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, Vedano al Lambro 20854, Italy
| | - Fulvio Magni
- Clinical
Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, Vedano al Lambro 20854, Italy
| | - Andrew Smith
- Clinical
Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, Vedano al Lambro 20854, Italy
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20
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Lellman SE, Cramer R. Bacterial identification by lipid profiling using liquid atmospheric pressure matrix-assisted laser desorption/ionization mass spectrometry. ACTA ACUST UNITED AC 2019; 58:930-938. [DOI: 10.1515/cclm-2019-0908] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/25/2019] [Indexed: 12/16/2022]
Abstract
Abstract
Background
In recent years, mass spectrometry (MS) has been applied to clinical microbial biotyping, exploiting the speed of matrix-assisted laser desorption/ionization (MALDI) in recording microbe-specific MS profiles. More recently, liquid atmospheric pressure (AP) MALDI has been shown to produce extremely stable ion flux from homogenous samples and ‘electrospray ionization (ESI)-like’ multiply charged ions for larger biomolecules, whilst maintaining the benefits of traditional MALDI including high tolerance to contaminants, low analyte consumption and rapid analysis. These and other advantages of liquid AP-MALDI MS have been explored in this study to investigate its potential in microbial biotyping.
Methods
Genetically diverse bacterial strains were analyzed using liquid AP-MALDI MS, including clinically relevant species such as Escherichia coli, Staphylococcus aureus and Klebsiella pneumoniae. Bacterial cultures were subjected to a simple and fast extraction protocol using ethanol and formic acid. Extracts were spotted with a liquid support matrix (LSM) and analyzed using a Synapt G2-Si mass spectrometer with an in-house built AP-MALDI source.
Results
Each species produces a unique lipid profile in the m/z range of 400–1100, allowing species discrimination. Traditional (solid) MALDI MS produced spectra containing a high abundance of matrix-related clusters and an absence of lipid peaks. The MS profiles of the bacterial species tested form distinct clusters using principle component analysis (PCA) with a classification accuracy of 98.63% using a PCA-based prediction model.
Conclusions
Liquid AP-MALDI MS profiles can be sufficient to distinguish clinically relevant bacterial pathogens and other bacteria, based on their unique lipid profiles. The analysis of the lipid MS profiles is typically excluded from commercial instruments approved for clinical diagnostics.
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Affiliation(s)
- Sophie E. Lellman
- Department of Chemistry , University of Reading , Whiteknights, Reading , UK
| | - Rainer Cramer
- Department of Chemistry , University of Reading , Whiteknights, Reading , UK
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21
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Self-assembling peptides imaged by correlated liquid cell transmission electron microscopy and MALDI-imaging mass spectrometry. Nat Commun 2019; 10:4837. [PMID: 31645558 PMCID: PMC6811541 DOI: 10.1038/s41467-019-12660-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 09/12/2019] [Indexed: 01/12/2023] Open
Abstract
We describe the observation of stimuli-induced peptide-based nanoscale assemblies by liquid cell transmission electron microscopy (LCTEM). LCTEM offers the opportunity to directly image nanoscale materials in liquid. Despite broad interest in characterizing biological phenomena, electron beam-induced damage remains a significant problem. Concurrently, methods for verifying chemical structure during or following an LCTEM experiment have been few, with key examples limited to electron diffraction or elemental analysis of crystalline materials; this strategy is not translatable to biopolymers observed in nature. In this proof-of-concept study, oligomeric peptides are biologically or chemically stimulated within the liquid cell in a TEM to assemble into nanostructures. The resulting materials are analyzed by MALDI-imaging mass spectrometry (MALDI-IMS) to verify their identity. This approach confirms whether higher-order assemblies observed by LCTEM consist of intact peptides, verifying that observations made during the in situ experiment are because of those same peptides and not aberrant electron beam damage effects.
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22
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Angel PM, Saunders J, Clift CL, White-Gilbertson S, Voelkel-Johnson C, Yeh E, Mehta A, Drake RR. A Rapid Array-Based Approach to N-Glycan Profiling of Cultured Cells. J Proteome Res 2019; 18:3630-3639. [PMID: 31535553 DOI: 10.1021/acs.jproteome.9b00303] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Typically, N-glycosylation studies done on cultured cells require up to millions of cells followed by lengthy preparation to release, isolate, and profile N-glycans. To overcome these limitations, we report a rapid array-based workflow for profiling N-glycan signatures from cells, adapted from imaging mass spectrometry used for on-tissue N-glycan profiling. Using this approach, N-glycan profiles from a low-density array of eight cell chambers could be reported within 4 h of completing cell culture. Approaches are demonstrated that account for background N-glycans due to serum media. Normalization procedures are shown. The method is robust and reproducible, requiring as few as 3000 cells per replicate with a 3-20% coefficient of variation to capture label-free profiles of N-glycans. Quantification by stable isotopic labeling of N-glycans in cell culture is demonstrated and adds no additional time to preparation. Utility of the method is demonstrated by measurement of N-glycan turnover rates due to induction of oxidative stress in human primary aortic endothelial cells. The developed method and ancillary tools serve as a foundational launching point for rapid profiling of N-glycans ranging from high-density arrays down to single cells in culture.
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23
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Bader TK, Rappe TM, Veglia G, Distefano MD. Synthesis and NMR Characterization of the Prenylated Peptide, a-Factor. Methods Enzymol 2019; 614:207-238. [PMID: 30611425 DOI: 10.1016/bs.mie.2018.09.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Protein and peptide prenylation is an essential biological process involved in many signal transduction pathways. Hence, it plays a critical role in establishing many major human ailments, including Alzheimer's disease, amyotrophic lateral sclerosis (ALS), malaria, and Ras-related cancers. Yeast mating pheromone a-factor is a small dodecameric peptide that undergoes prenylation and subsequent processing in a manner identical to larger proteins. Due to its small size in addition to its well-characterized behavior in yeast, a-factor is an attractive model system to study the prenylation pathway. Traditionally, chemical synthesis and characterization of a-factor have been challenging, which has limited its use in prenylation studies. In this chapter, a robust method for the synthesis of a-factor is presented along with a description of the characterization of the peptide using MALDI and NMR. Finally, complete assignments of resonances from the isoprenoid moiety and a-factor from COSY, TOCSY, HSQC, and long-range HMBC NMR spectra are presented. This methodology should be useful for the synthesis and characterization of other mature prenylated peptides and proteins.
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Affiliation(s)
- Taysir K Bader
- University of Minnesota, Twin Cities, Minneapolis, MN, United States
| | - Todd M Rappe
- University of Minnesota, Twin Cities, Minneapolis, MN, United States
| | - Gianlugi Veglia
- University of Minnesota, Twin Cities, Minneapolis, MN, United States
| | - Mark D Distefano
- University of Minnesota, Twin Cities, Minneapolis, MN, United States.
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24
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Wu E, Feng K, Shi R, Lv R, Ouyang F, Li SSC, Zhong J, Liu J. Hybrid CuCoO-GO enables ultrasensitive detection of antibiotics with enhanced laser desorption/ionization at nano-interfaces. Chem Sci 2018; 10:257-267. [PMID: 30713636 PMCID: PMC6333240 DOI: 10.1039/c8sc03692f] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 10/05/2018] [Indexed: 01/21/2023] Open
Abstract
The soaring concerns globally on antibiotic overuse have made calls for the development of rapid and sensitive detection methods urgent. Here we report that the hybrid CuCoO-GO matrix allows for sensitive detection of various antibiotics in combination with MALDI TOF MS. The new matrix is composed of few-layered GO nanosheets decorated with CuCoO nanoparticles with an average size of 10 nm, and exhibits excellent aqueous suspensibility. Accurate quantitation of the sulfonamide antibiotics in milk samples have been demonstrated using a CuCoO-GO matrix and a stable isotope (C13)-labeled analyte as the internal standard. Our experiments have achieved lower limits of detection (LOD) by several hundred fold for the detection of a panel of representative antibiotics, in comparison with the literature reports. Both intrabacterial and extrabacterial residual antibiotics can be sensitively detected with our method. We have further investigated the molecular mechanism of the enhanced desorption/ionization efficiency by the CuCoO-GO matrix with synchrotron radiation techniques for the first time. This work provides a sensitive matrix enabling MALDI-TOF MS to be applied in small molecular analysis, but also presents a distinct perspective on the mechanism behind the material functions.
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Affiliation(s)
- Enhui Wu
- Institute of Functional Nano and Soft Materials (FUNSOM) , Jiangsu Key Laboratory for Carbon-based Functional Materials and Devices , Joint International Research Laboratory of Carbon-based Functional Materials and Devices , Soochow University , Suzhou , Jiangsu Province 215123 , China . ;
| | - Kun Feng
- Institute of Functional Nano and Soft Materials (FUNSOM) , Jiangsu Key Laboratory for Carbon-based Functional Materials and Devices , Joint International Research Laboratory of Carbon-based Functional Materials and Devices , Soochow University , Suzhou , Jiangsu Province 215123 , China . ;
| | - Rui Shi
- Institute of Functional Nano and Soft Materials (FUNSOM) , Jiangsu Key Laboratory for Carbon-based Functional Materials and Devices , Joint International Research Laboratory of Carbon-based Functional Materials and Devices , Soochow University , Suzhou , Jiangsu Province 215123 , China . ;
| | - Rui Lv
- Institute of Functional Nano and Soft Materials (FUNSOM) , Jiangsu Key Laboratory for Carbon-based Functional Materials and Devices , Joint International Research Laboratory of Carbon-based Functional Materials and Devices , Soochow University , Suzhou , Jiangsu Province 215123 , China . ;
| | - Fuzhong Ouyang
- Institute of Functional Nano and Soft Materials (FUNSOM) , Jiangsu Key Laboratory for Carbon-based Functional Materials and Devices , Joint International Research Laboratory of Carbon-based Functional Materials and Devices , Soochow University , Suzhou , Jiangsu Province 215123 , China . ;
| | - Shawn S C Li
- Department of Biochemistry , Western University , London , Ontario N6A 5C1 , Canada
| | - Jun Zhong
- Institute of Functional Nano and Soft Materials (FUNSOM) , Jiangsu Key Laboratory for Carbon-based Functional Materials and Devices , Joint International Research Laboratory of Carbon-based Functional Materials and Devices , Soochow University , Suzhou , Jiangsu Province 215123 , China . ;
| | - Jian Liu
- Institute of Functional Nano and Soft Materials (FUNSOM) , Jiangsu Key Laboratory for Carbon-based Functional Materials and Devices , Joint International Research Laboratory of Carbon-based Functional Materials and Devices , Soochow University , Suzhou , Jiangsu Province 215123 , China . ;
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25
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Zhong J, Banazadeh A, Peng W, Mechref Y. A carbon nanoparticles-based solid-phase purification method facilitating sensitive MALDI-MS analysis of permethylated N-glycans. Electrophoresis 2018; 39:3087-3095. [PMID: 30086189 DOI: 10.1002/elps.201800254] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/01/2018] [Accepted: 08/01/2018] [Indexed: 12/29/2022]
Abstract
In recent decades, MALDI-MS has been extensively used for the analysis of glycans. However, native glycans usually have low ionization efficiency in MS, which hinders the direct analysis. Permethylation of glycans is a solution for this issue, but a significant amount of salt is introduced during this process, which can further suppress the MS signals. Thus, it is necessary to purify the glycans prior to MALDI-MS analysis. In this study, we developed a carbon nanoparticles-based solid-phase purification method to enable direct MALDI-MS analysis of permethylated glycans. Two carbon nanomaterials, carbon nanoparticles (CNPs) and graphene nanosheets (GNs), and two conventional carbon materials, activated charcoal and porous graphitic carbon (PGC), were investigated as sorbents to purify permethylated N-glycans derived from ribonuclease B and fetuin. The results confirmed the superior performance of CNPs over the other carbon materials. Additionally, our method was also employed to purify glycans released from human sera in different esophageal disease stages. The obtained data confirmed 16 and 18 structures in adenocarcinoma and Barret's sera with significantly different relative intensities versus disease-free sera. Comparing the performance of CNPs-based solid-phase purification method employed in this study to online purification suggested more than 97% recovery rate. The results of this study demonstrate that CNPs have the potential to be a better alternative to existing solid-phase purification sorbents.
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Affiliation(s)
- Jieqiang Zhong
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Alireza Banazadeh
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
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26
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Ucal Y, Ozpinar A. Improved spectra for MALDI MSI of peptides using ammonium phosphate monobasic in MALDI matrix. JOURNAL OF MASS SPECTROMETRY : JMS 2018; 53:635-648. [PMID: 29745432 DOI: 10.1002/jms.4198] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 04/19/2018] [Accepted: 04/25/2018] [Indexed: 05/03/2023]
Abstract
MALDI mass spectrometry imaging (MSI) enables analysis of peptides along with histology. However, there are several critical steps in MALDI MSI of peptides, 1 of which is spectral quality. Suppression of MALDI matrix clusters by the aid of ammonium salts in MALDI experiments is well known. It is asserted that addition of ammonium salts dissociates potential matrix adducts and thereafter decreases matrix cluster formation. Consequently, MALDI MS sensitivity and mass accuracy increase. Up to our knowledge, a limited number of MALDI MSI studies used ammonium salts as matrix additives to suppress matrix clusters and enhance peptide signals. In this work, we investigated the effect of ammonium phosphate monobasic (AmP) as alpha-cyano-4-hydroxycinnamic acid (α-CHCA) matrix additive in MALDI MSI of peptides. Prior to MALDI MSI, the effect of varying concentrations of AmP in α-CHCA was assessed in bovine serum albumin tryptic digests and compared with the control (α-CHCA without AmP). Based on our data, the addition of AmP as matrix additive decreased matrix cluster formation regardless of its concentration, and specifically, 8 mM AmP and 10 mM AmP increased bovine serum albumin peptide signal intensities. In MALDI MSI of peptides, both 8 and 10 mM AmP in α-CHCA improved peptide signals especially in the mass range of m/z 2000 to 3000. In particular, 9 peptide signals were found to have differential intensities within the tissues deposited with AmP in α-CHCA (AUC > 0.60). To the best of our knowledge, this is the first MALDI MSI of peptides work investigating different concentrations of AmP as α-CHCA matrix additive to enhance peptide signals in formalin-fixed paraffin-embedded (FFPE) tissues. Further, AmP as part of α-CHCA matrix could enhance protein identifications and support MALDI MSI-based proteomic approaches.
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Affiliation(s)
- Yasemin Ucal
- School of Medicine, Department of Medical Biochemistry, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Aysel Ozpinar
- School of Medicine, Department of Medical Biochemistry, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
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27
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Calvano CD, Monopoli A, Cataldi TRI, Palmisano F. MALDI matrices for low molecular weight compounds: an endless story? Anal Bioanal Chem 2018; 410:4015-4038. [DOI: 10.1007/s00216-018-1014-x] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 02/27/2018] [Accepted: 03/08/2018] [Indexed: 10/17/2022]
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28
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Dong J, Ning W, Mans DJ, Mans JD. A binary matrix for the rapid detection and characterization of small-molecule cardiovascular drugs by MALDI-MS and MS/MS. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2018; 10:572-578. [PMID: 30319716 PMCID: PMC6178826 DOI: 10.1039/c7ay02583a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A mixture of α-cyano-4-hydroxycinnamic acid and 1,5-diaminonaphthalene was discovered as a novel binary matrix for the qualitative analysis of 14 small-molecule (~250-550 Da) cardiovascular drugs by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) and MS/MS in either positive or negative ion mode.
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Affiliation(s)
- Jinlan Dong
- Division of Pharmaceutical Analysis, Center for Drug Evaluation and Research, Food and Drug Administration, St. Louis, MO, 63110, USA
| | - Wenjing Ning
- Division of Pharmaceutical Analysis, Center for Drug Evaluation and Research, Food and Drug Administration, St. Louis, MO, 63110, USA
| | - Daniel J Mans
- Division of Pharmaceutical Analysis, Center for Drug Evaluation and Research, Food and Drug Administration, St. Louis, MO, 63110, USA
| | - Jamie D Mans
- Division of Pharmaceutical Analysis, Center for Drug Evaluation and Research, Food and Drug Administration, St. Louis, MO, 63110, USA
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29
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Angel PM, Comte-Walters S, Ball LE, Talbot K, Mehta A, Brockbank KGM, Drake RR. Mapping Extracellular Matrix Proteins in Formalin-Fixed, Paraffin-Embedded Tissues by MALDI Imaging Mass Spectrometry. J Proteome Res 2017; 17:635-646. [PMID: 29161047 DOI: 10.1021/acs.jproteome.7b00713] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Collagens and elastin form the fundamental framework of all tissues and organs, and their expression and post-translational processing are tightly regulated in disease and health. Because of their unique structural composition and properties, it is a recognized challenge to access these protein structures within the complex tissue microenvironment to understand how localized changes modulate tissue health. We describe a new workflow using a combination of matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) with matrix metalloproteinase (MMP) enzymes to access and report on spatial localization of collagen and elastin sequences in formalin-fixed, paraffin-embedded (FFPE) tissues. The developed technology provides new access to collagens and elastin sequences localized to tissue features that were previously unattainable. This high-throughput technological advance should be applicable to any tissue regardless of disease type, tissue origin, or disease status and is thus relevant to all research: basic, translational, or clinical.
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Affiliation(s)
| | | | | | | | | | - Kelvin G M Brockbank
- Tissue Testing Technologies LLC , North Charleston, South Carolina 29406, United States.,Department of Bioengineering, Clemson University , Clemson, South Carolina 29634, United States
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30
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Dilillo M, Pellegrini D, Ait-Belkacem R, de Graaf EL, Caleo M, McDonnell LA. Mass Spectrometry Imaging, Laser Capture Microdissection, and LC-MS/MS of the Same Tissue Section. J Proteome Res 2017. [DOI: 10.1021/acs.jproteome.7b00284] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Marialaura Dilillo
- Fondazione Pisana per la Scienza ONLUS, 56121 Pisa, Italy
- Department of Chemistry
and Industrial Chemistry, University of Pisa, 56126 Pisa, Italy
| | - Davide Pellegrini
- Fondazione Pisana per la Scienza ONLUS, 56121 Pisa, Italy
- NEST, Scuola Normale Superiore di Pisa, 56127 Pisa, Italy
| | | | | | | | - Liam A. McDonnell
- Fondazione Pisana per la Scienza ONLUS, 56121 Pisa, Italy
- Center for Proteomics
and Metabolomics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
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31
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Kaya I, Michno W, Brinet D, Iacone Y, Zanni G, Blennow K, Zetterberg H, Hanrieder J. Histology-Compatible MALDI Mass Spectrometry Based Imaging of Neuronal Lipids for Subsequent Immunofluorescent Staining. Anal Chem 2017; 89:4685-4694. [PMID: 28318232 DOI: 10.1021/acs.analchem.7b00313] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS) enables acquisition of spatial distribution maps for molecular species in situ. This can provide comprehensive insights on the pathophysiology of different diseases. However, current sample preparation and MALDI-IMS acquisition methods have limitations in preserving molecular and histological tissue morphology, resulting in interfered correspondence of MALDI-IMS data with subsequently acquired immunofluorescent staining results. We here investigated the histology compatibility of MALDI-IMS to image neuronal lipids in rodent brain tissue with subsequent immunohistochemistry and fluorescent staining of histological features. This was achieved by sublimation of a low ionization energy matrix compound, 1,5-diaminonapthalene (1,5-DAN), minimizing the number of low-energy laser shots. This yielded improved lipid spectral quality and speed of data acquisition and reduced matrix cluster formation along with preservation of specific histological information at cellular levels. This gentle, histology-compatible MALDI-IMS protocol also diminished thermal effects and mechanical stress created during nanosecond laser ablation processes that were prominent in subsequent immunofluorescent staining images but not with classical hematoxylin and eosin (H&E) staining on the same tissue section. Furthermore, this methodology proved to be a powerful strategy for investigating β-amyloid (Aβ) plaque-associated neuronal lipids as exemplified by performing high-resolution MALDI-IMS with subsequent fluorescent amyloid staining in a transgenic mouse model of Alzheimer's disease (tgSwe).
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Affiliation(s)
- Ibrahim Kaya
- Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg , 431 80 Mölndal, Sweden
| | - Wojciech Michno
- Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg , 431 80 Mölndal, Sweden
| | - Dimitri Brinet
- Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg , 431 80 Mölndal, Sweden.,Department of Chemistry and Molecular Biology, University of Gothenburg , 412 96 Gothenburg, Sweden
| | - Yasmine Iacone
- Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg , 431 80 Mölndal, Sweden
| | - Giulia Zanni
- Karolinska Institute, Department of Women's and Children's Health, Karolinska University Hospital , 171 76 Stockholm, Sweden
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg , 431 80 Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital , 431 80 Mölndal, Sweden
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg , 431 80 Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital , 431 80 Mölndal, Sweden.,Department of Molecular Neuroscience, UCL Institute of Neurology, University College London , London, WC1N 3BG, United Kingdom
| | - Jörg Hanrieder
- Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg , 431 80 Mölndal, Sweden.,Department of Molecular Neuroscience, UCL Institute of Neurology, University College London , London, WC1N 3BG, United Kingdom
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32
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Organic matrices, ionic liquids, and organic matrices@nanoparticles assisted laser desorption/ionization mass spectrometry. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.01.012] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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33
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Antisecretory Factor (AF) egg-yolk peptides reflects the intake of AF-activating feed in hens. CLINICAL NUTRITION EXPERIMENTAL 2017. [DOI: 10.1016/j.yclnex.2017.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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34
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Liu X, Ding W, Wu Y, Zeng C, Luo Z, Fu H. Penicillamine-protected Ag 20 nanoclusters and fluorescence chemosensing for trace detection of copper ions. NANOSCALE 2017; 9:3986-3994. [PMID: 28267164 DOI: 10.1039/c6nr09818e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We report the synthesis of penicillamine-protected Ag20 nanoclusters (NCs), with properties of high monodispersity, red fluorescence and water solubility. Full characterization of the Ag20 NCs is addressed, along with first-principles optimization calculations, revealing the chemical composition and structure of the as-prepared Ag NCs within a molecular formula [Ag20(DPA)18-H]-. Moreover, natural bond orbital (NBO) analysis demonstrates the charge-transfer interactions between the ligand and Ag atoms, and helps in understanding the origins of fluorescence of Ag20 NCs related to the ligand-to-metal charge transfer (LMCT) mechanism. Further, fluorescence chemosensing of the Ag20 NCs is demonstrated for tracing copper ions with high sensitivity and selectivity in aqueous solution.
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Affiliation(s)
- Xianhu Liu
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China. and Department of Chemistry, Huaibei Normal University, Huaibei, Anhui 235000, P. R. China
| | - Weihua Ding
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.
| | - Yishi Wu
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.
| | - Chenghui Zeng
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.
| | - Zhixun Luo
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.
| | - Hongbing Fu
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.
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35
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Wang P, Giese RW. Recommendations for quantitative analysis of small molecules by matrix-assisted laser desorption ionization mass spectrometry. J Chromatogr A 2017; 1486:35-41. [PMID: 28118972 DOI: 10.1016/j.chroma.2017.01.040] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 12/21/2016] [Accepted: 01/16/2017] [Indexed: 12/15/2022]
Abstract
Matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) has been used for quantitative analysis of small molecules for many years. It is usually preceded by an LC separation step when complex samples are tested. With the development several years ago of "modern MALDI" (automation, high repetition laser, high resolution peaks), the ease of use and performance of MALDI as a quantitative technique greatly increased. This review focuses on practical aspects of modern MALDI for quantitation of small molecules conducted in an ordinary way (no special reagents, devices or techniques for the spotting step of MALDI), and includes our ordinary, preferred methods The review is organized as 18 recommendations with accompanying explanations, criticisms and exceptions.
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Affiliation(s)
- Poguang Wang
- Department of Pharmaceutical Sciences and Barnett Institute, Bouve College, Northeastern University, Boston, MA 02115, USA
| | - Roger W Giese
- Department of Pharmaceutical Sciences and Barnett Institute, Bouve College, Northeastern University, Boston, MA 02115, USA.
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36
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Tanaka M. Study on the Physiological Benefits of Food Compounds on Vascular Health and Their Underlying Mechanisms. J JPN SOC FOOD SCI 2017. [DOI: 10.3136/nskkk.64.285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Mitsuru Tanaka
- Faculty of Agriculture, Graduate School of Kyushu University
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37
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SALDI-TOF-MS analyses of small molecules (citric acid, dexasone, vitamins E and A) using TiO2 nanocrystals as substrates. Anal Bioanal Chem 2016; 408:7481-90. [DOI: 10.1007/s00216-016-9846-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 06/28/2016] [Accepted: 07/28/2016] [Indexed: 11/25/2022]
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38
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An evaluation of the impact of urban air pollution on paint dosimeters by tracking changes in the lipid MALDI-TOF mass spectra profile. Talanta 2016; 155:53-61. [DOI: 10.1016/j.talanta.2016.04.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 04/02/2016] [Accepted: 04/04/2016] [Indexed: 11/24/2022]
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39
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Wiangnon K, Cramer R. Liquid MALDI MS Analysis of Complex Peptide and Proteome Samples. J Proteome Res 2016; 15:2998-3008. [DOI: 10.1021/acs.jproteome.6b00148] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Kanjana Wiangnon
- Department
of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, United Kingdom
| | - Rainer Cramer
- Department
of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, United Kingdom
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40
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Abdelhamid HN. Ionic liquids for mass spectrometry: Matrices, separation and microextraction. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2015.12.007] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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41
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Škrášková K, Claude E, Jones EA, Towers M, Ellis SR, Heeren RMA. Enhanced capabilities for imaging gangliosides in murine brain with matrix-assisted laser desorption/ionization and desorption electrospray ionization mass spectrometry coupled to ion mobility separation. Methods 2016; 104:69-78. [PMID: 26922843 DOI: 10.1016/j.ymeth.2016.02.014] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 02/03/2016] [Accepted: 02/22/2016] [Indexed: 12/17/2022] Open
Abstract
The increased interest in lipidomics calls for improved yet simplified methods of lipid analysis. Over the past two decades, mass spectrometry imaging (MSI) has been established as a powerful technique for the analysis of molecular distribution of a variety of compounds across tissue surfaces. Matrix-assisted laser desorption/ionization (MALDI) MSI is widely used to study the spatial distribution of common lipids. However, a thorough sample preparation and necessity of vacuum for efficient ionization might hamper its use for high-throughput lipid analysis. Desorption electrospray ionization (DESI) is a relatively young MS technique. In DESI, ionization of molecules occurs under ambient conditions, which alleviates sample preparation. Moreover, DESI does not require the application of an external matrix, making the detection of low mass species more feasible due to the lack of chemical matrix background. However, irrespective of the ionization method, the final information obtained during an MSI experiment is very complex and its analysis becomes challenging. It was shown that coupling MSI to ion mobility separation (IMS) simplifies imaging data interpretation. Here we employed DESI and MALDI MSI for a lipidomic analysis of the murine brain using the same IMS-enabled instrument. We report for the first time on the DESI IMS-MSI of multiply sialylated ganglioside species, as well as their acetylated versions, which we detected directly from the murine brain tissue. We show that poly-sialylated gangliosides can be imaged as multiply charged ions using DESI, while they are clearly separated from the rest of the lipid classes based on their charge state using ion mobility. This represents a major improvement in MSI of intact fragile lipid species. We additionally show that complementary lipid information is reached under particular conditions when DESI is compared to MALDI MSI.
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Affiliation(s)
- Karolina Škrášková
- M4I, The Maastricht MultiModal Molecular Imaging Institute, University of Maastricht, Maastricht, The Netherlands; FOM-Institute AMOLF, Amsterdam, The Netherlands; TI-COAST, Amsterdam, The Netherlands
| | | | - Emrys A Jones
- Waters Corporation, Wilmslow, UK; Imperial College London, London, UK
| | | | - Shane R Ellis
- M4I, The Maastricht MultiModal Molecular Imaging Institute, University of Maastricht, Maastricht, The Netherlands; FOM-Institute AMOLF, Amsterdam, The Netherlands
| | - Ron M A Heeren
- M4I, The Maastricht MultiModal Molecular Imaging Institute, University of Maastricht, Maastricht, The Netherlands; FOM-Institute AMOLF, Amsterdam, The Netherlands; TI-COAST, Amsterdam, The Netherlands.
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42
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Duncan MW, Nedelkov D, Walsh R, Hattan SJ. Applications of MALDI Mass Spectrometry in Clinical Chemistry. Clin Chem 2015; 62:134-43. [PMID: 26585930 DOI: 10.1373/clinchem.2015.239491] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 11/02/2015] [Indexed: 02/02/2023]
Abstract
BACKGROUND MALDI-TOF mass spectrometry (MS) is set to make inroads into clinical chemistry because it offers advantages over other analytical platforms. These advantages include low acquisition and operating costs, ease of use, ruggedness, and high throughput. When coupled with innovative front-end strategies and applied to important clinical problems, it can deliver rapid, sensitive, and cost-effective assays. CONTENT This review describes the general principles of MALDI-TOF MS, highlights the unique features of the platform, and discusses some practical methods based upon it. There is substantial potential for MALDI-TOF MS to make further inroads into clinical chemistry because of the selectivity of mass detection and its ability to independently quantify proteoforms. SUMMARY MALDI-TOF MS has already transformed the practice of clinical microbiology and this review illustrates how and why it is now set to play an increasingly important role in in vitro diagnostics in particular, and clinical chemistry in general.
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Affiliation(s)
- Mark W Duncan
- Division of Endocrinology, Diabetes & Metabolism, Department of Medicine, School of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO; Obesity Research Center, College of Medicine, King Saud University, Riyadh 11461, Saudi Arabia;
| | - Dobrin Nedelkov
- Molecular Biomarkers Laboratory, Biodesign Institute, Arizona State University, Tempe, AZ
| | - Ryan Walsh
- Division of Endocrinology, Diabetes & Metabolism, Department of Medicine, School of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO
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43
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Sugiyama E, Masaki N, Matsushita S, Setou M. Ammonium Sulfate Improves Detection of Hydrophilic Quaternary Ammonium Compounds through Decreased Ion Suppression in Matrix-Assisted Laser Desorption/Ionization Imaging Mass Spectrometry. Anal Chem 2015; 87:11176-81. [DOI: 10.1021/acs.analchem.5b02672] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Eiji Sugiyama
- Department
of Cell Biology
and Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku Hamamatsu, Shizuoka, 431-3192, Japan
| | - Noritaka Masaki
- Department
of Cell Biology
and Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku Hamamatsu, Shizuoka, 431-3192, Japan
| | - Shoko Matsushita
- Department
of Cell Biology
and Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku Hamamatsu, Shizuoka, 431-3192, Japan
| | - Mitsutoshi Setou
- Department
of Cell Biology
and Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku Hamamatsu, Shizuoka, 431-3192, Japan
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44
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Richardson SL, Hanjra P, Zhang G, Mackie BD, Peterson DL, Huang R. A direct, ratiometric, and quantitative MALDI-MS assay for protein methyltransferases and acetyltransferases. Anal Biochem 2015; 478:59-64. [PMID: 25778392 DOI: 10.1016/j.ab.2015.03.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 02/18/2015] [Accepted: 03/04/2015] [Indexed: 01/22/2023]
Abstract
Protein methylation and acetylation play important roles in biological processes, and misregulation of these modifications is involved in various diseases. Therefore, it is critical to understand the activities of the enzymes responsible for these modifications. Herein we describe a sensitive method for ratiometric quantification of methylated and acetylated peptides via MALDI-MS by direct spotting of enzymatic methylation and acetylation reaction mixtures without tedious purification procedures. The quantifiable detection limit for peptides with our method is approximately 10 fmol. This is achieved by increasing the signal-to-noise ratio through the addition of NH4H2PO4 to the matrix solution and reduction of the matrix α-cyanohydroxycinnamic acid concentration to 2 mg/ml. We have demonstrated the application of this method in enzyme kinetic analysis and inhibition studies. The unique feature of this method is the simultaneous quantification of multiple peptide species for investigation of processivity mechanisms. Its wide buffer compatibility makes it possible to be adapted to investigate the activity of any protein methyltransferase or acetyltransferase.
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Affiliation(s)
- Stacie L Richardson
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA; Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Pahul Hanjra
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA; Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Gang Zhang
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA; Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Brianna D Mackie
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA; Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Darrell L Peterson
- Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23219, USA; Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Rong Huang
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA; Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23219, USA.
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45
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Palmer AD, Bunch J, Styles IB. The use of random projections for the analysis of mass spectrometry imaging data. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:315-22. [PMID: 25522725 PMCID: PMC4320302 DOI: 10.1007/s13361-014-1024-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 08/28/2014] [Accepted: 10/08/2014] [Indexed: 05/04/2023]
Abstract
The 'curse of dimensionality' imposes fundamental limits on the analysis of the large, information rich datasets that are produced by mass spectrometry imaging. Additionally, such datasets are often too large to be analyzed as a whole and so dimensionality reduction is required before further analysis can be performed. We investigate the use of simple random projections for the dimensionality reduction of mass spectrometry imaging data and examine how they enable efficient and fast segmentation using k-means clustering. The method is computationally efficient and can be implemented such that only one spectrum is needed in memory at any time. We use this technique to reveal histologically significant regions within MALDI images of diseased human liver. Segmentation results achieved following a reduction in the dimensionality of the data by more than 99% (without peak picking) showed that histologic changes due to disease can be automatically visualized from molecular images.
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Affiliation(s)
- Andrew D. Palmer
- PSIBS Doctoral Training Centre, University of Birmingham, Edgbaston B15 2TT Birmingham, UK
- Zentrum für Technomathematik, Fachbereich 3, Universität Bremen, Postfach 33 04 40, 28334 Bremen, Deutschland
| | - Josephine Bunch
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW Middlesex, UK
- School of Pharmacy, University of Nottingham, University Park NG7 2RD Nottingham, UK
| | - Iain B. Styles
- School of Computer Science, University of Birmingham, Edgbaston B15 2TT Birmingham, UK
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46
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Ohta Y, Iwamoto S, Kawabata SI, Tanimura R, Tanaka K. Salt Tolerance Enhancement of Liquid Chromatography-Matrix-Assisted Laser Desorption/Ionization-Mass Spectrometry Using Matrix Additive Methylenediphosphonic Acid. Mass Spectrom (Tokyo) 2014; 3:A0031. [PMID: 26819873 DOI: 10.5702/massspectrometry.a0031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 07/26/2014] [Indexed: 11/23/2022] Open
Abstract
Mass spectrometry (MS) is a highly sensitive analytical technique that is often coupled with liquid chromatography (LC). However, some buffering salts used in LC (e.g., phosphate and tris(hydroxymethyl)aminomethane (Tris)) are incompatible with MS since they cause ion-source contamination and signal suppression. In this study, we examined salt tolerance of MALDI and applied a matrix additive methylenediphosphonic acid (MDPNA) to reduce salt-induced signal suppression. MDPNA significantly improved the salt tolerance of MALDI-MS. Using ammonium formate buffer at pH 5.0, the effective range of buffering salt concentration in MALDI-MS using MDPNA was estimated up to 250 mM. MDPNA reduced signal suppression caused by buffering salts at pH 4.0 to 8.0. We observed that MDPNA effectively worked over a wide range of buffer conditions. MDPNA was further applied to hydrophilic interaction chromatography (HILIC) and chromatofocusing-MALDI-MS. As a result, the analytes in the eluent containing high-concentration salts were detected with high sensitivity. Thus, our study provides simple and fast LC-MALDI-MS analysis technique not having strict limitation of buffering condition in LC by using matrix additive MDPNA.
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Affiliation(s)
- Yuki Ohta
- Koichi Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation
| | - Shinichi Iwamoto
- Koichi Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation
| | | | - Ritsuko Tanimura
- Koichi Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation
| | - Koichi Tanaka
- Koichi Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation
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47
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Nelson KA, Daniels GJ, Fournie JW, Hemmer MJ. Optimization of whole-body zebrafish sectioning methods for mass spectrometry imaging. J Biomol Tech 2014; 24:119-27. [PMID: 23997659 DOI: 10.7171/jbt.13-2403-002] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Mass spectrometry imaging (MSI) methods and protocols have become widely adapted to a variety of tissues and species. However, the MSI literature contains minimal information on whole-body cryosection preparation for the zebrafish (ZF; Danio rerio), a model organism routinely used in developmental, toxicity, and carcinogenicity studies. The optimal medium for embedding and cryosectioning a whole organism or soft-tissue specimen for histological examination is a synthetic polymer mixture that is incompatible with MSI as a result of ion suppression. We describe the optimal methods and results for embedding and cryosectioning whole-body ZF for MALDI-MSI. We evaluated 13 distinct embedding media formulations and found a supportive hydrogel with the consistency of cartilage to be the optimal embedding medium. The hydrogel medium does not interfere with MSI data collection, aids in tissue stability, is readily available for purchase, and is easy to prepare and handle during cryosectioning. Additionally, we decreased the matrix cluster interference commonly caused by α-cyano-4-hydroxycinnamic acid by adding ammonium phosphate to the solvent spray solution. The optimized methods developed in our laboratory produced high-quality cryosections, as well as high-quality mass spectral images of sectioned ZF.
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Affiliation(s)
- Kimberly A Nelson
- United States Environmental Protection Agency, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Gulf Ecology Division, 1 Sabine Island Drive, Gulf Breeze, FL 32561, USA.
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48
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Touchard A, Dauvois M, Arguel MJ, Petitclerc F, Leblanc M, Dejean A, Orivel J, Nicholson GM, Escoubas P. Elucidation of the unexplored biodiversity of ant venom peptidomes via MALDI-TOF mass spectrometry and its application for chemotaxonomy. J Proteomics 2014; 105:217-31. [PMID: 24456813 DOI: 10.1016/j.jprot.2014.01.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 01/06/2014] [Accepted: 01/09/2014] [Indexed: 10/25/2022]
Abstract
UNLABELLED The rise of integrative taxonomy, a multi-criteria approach used in characterizing species, fosters the development of new tools facilitating species delimitation. Mass spectrometric (MS) analysis of venom peptides from venomous animals has previously been demonstrated to be a valid method for identifying species. Here we aimed to develop a rapid chemotaxonomic tool for identifying ants based on venom peptide mass fingerprinting. The study focused on the biodiversity of ponerine ants (Hymenoptera: Formicidae: Ponerinae) in French Guiana. Initial experiments optimized the use of automated matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to determine variations in the mass profiles of ant venoms using several MALDI matrices and additives. Data were then analyzed via a hierarchical cluster analysis to classify the venoms of 17 ant species. In addition, phylogenetic relationships were assessed and were highly correlated with methods using DNA sequencing of the mitochondrial gene cytochrome c oxidase subunit 1. By combining a molecular genetics approach with this chemotaxonomic approach, we were able to improve the accuracy of the taxonomic findings to reveal cryptic ant species within species complexes. This chemotaxonomic tool can therefore contribute to more rapid species identification and more accurate taxonomies. BIOLOGICAL SIGNIFICANCE This is the first extensive study concerning the peptide analysis of the venom of both Pachycondyla and Odontomachus ants. We studied the venoms of 17 ant species from French Guiana that permitted us to fine-tune the venom analysis of ponerine ants via MALDI-TOF mass spectrometry. We explored the peptidomes of crude ant venom and demonstrated that venom peptides can be used in the identification of ant species. In addition, the application of this novel chemotaxonomic method combined with a parallel genetic approach using COI sequencing permitted us to reveal the presence of cryptic ants within both the Pachycondyla apicalis and Pachycondyla stigma species complexes. This adds a new dimension to the search for means of exploiting the enormous biodiversity of venomous ants as a source for novel therapeutic drugs or biopesticides. This article is part of a Special Issue entitled: Proteomics of non-model organisms.
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Affiliation(s)
- Axel Touchard
- CNRS, UMR Ecologie des Forêts de Guyane (EcoFoG), Campus Agronomique, BP 316, 97379 Kourou Cedex, France.
| | - Mélodie Dauvois
- VenomeTech, 473 Route des Dolines - Villa 3, Valbonne 06560, France
| | | | - Frédéric Petitclerc
- CNRS, UMR Ecologie des Forêts de Guyane (EcoFoG), Campus Agronomique, BP 316, 97379 Kourou Cedex, France
| | - Mathieu Leblanc
- VenomeTech, 473 Route des Dolines - Villa 3, Valbonne 06560, France
| | - Alain Dejean
- CNRS, UMR Ecologie des Forêts de Guyane (EcoFoG), Campus Agronomique, BP 316, 97379 Kourou Cedex, France; Université de Toulouse, UPS, INP, Laboratoire Écologie Fonctionnelle et Environnement (ECOLAB), 118 route de Narbonne, 31062 Toulouse, France
| | - Jérôme Orivel
- CNRS, UMR Ecologie des Forêts de Guyane (EcoFoG), Campus Agronomique, BP 316, 97379 Kourou Cedex, France
| | - Graham M Nicholson
- Neurotoxin Research Group, School of Medical & Molecular Biosciences, University of Technology, Sydney, NSW, Australia
| | - Pierre Escoubas
- VenomeTech, 473 Route des Dolines - Villa 3, Valbonne 06560, France
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Usbeck JC, Kern CC, Vogel RF, Behr J. Optimization of experimental and modelling parameters for the differentiation of beverage spoiling yeasts by Matrix-Assisted-Laser-Desorption/Ionization–Time-of-Flight Mass Spectrometry (MALDI–TOF MS) in response to varying growth conditions. Food Microbiol 2013; 36:379-87. [DOI: 10.1016/j.fm.2013.07.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 04/30/2013] [Accepted: 07/12/2013] [Indexed: 01/24/2023]
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50
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Hong SM, Tanaka M, Yoshii S, Mine Y, Matsui T. Enhanced visualization of small peptides absorbed in rat small intestine by phytic-acid-aided matrix-assisted laser desorption/ionization-imaging mass spectrometry. Anal Chem 2013; 85:10033-9. [PMID: 24063774 DOI: 10.1021/ac402252j] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Enhanced visualization of small peptides absorbed through a rat intestinal membrane was achieved by matrix-assisted laser desorption/ionization time-of-flight imaging mass spectrometry (MALDI-IMS) with the aid of phytic acid as a matrix additive. Penetrants through intestinal peptide transporter 1, i.e., glycyl-sarcosine (Gly-Sar, 147.1 m/z) and antihypertensive dipeptide, Val-Tyr (281.2 m/z), were chosen for MALDI-IMS. The signal-to-noise (S/N) ratios of dipeptides Gly-Sar and Val-Tyr were seen to increase by 2.4- and 8.0-fold, respectively, when using a 2',4',6'-trihydroxyacetophenone (THAP) matrix containing 5.0 mM phytic acid, instead of the THAP matrix alone. Owing to the phytic-acid-aided MALDI-IMS method, Gly-Sar and Val-Tyr absorbed in the rat intestinal membrane were successfully visualized. The proposed imaging method also provided useful information on intestinal peptide absorption; to some extent, Val-Tyr was rapidly hydrolyzed to Tyr by peptidases located at the intestinal microvillus during the absorption process. In conclusion, the strongly acidic additive, phytic acid, is beneficial for enhancing the visualization of small peptides using MALDI-IMS, owing to the suppression of ionization-interfering salts in the tissue.
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Affiliation(s)
- Seong-Min Hong
- Division of Bioresources and Bioenvironmental Sciences, Faculty of Agriculture, Graduate School, Kyushu University , 6-10-1 Hakozaki, Fukuoka 812-8581, Japan
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