1
|
Le MT, Holden DT, Manheim JM, Dziekonski ET, Iyer K, Graham Cooks R. Two-Dimensional Tandem Mass Spectrometry for Biopolymer Structural Analysis. Angew Chem Int Ed Engl 2024; 63:e202315904. [PMID: 38117612 DOI: 10.1002/anie.202315904] [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: 11/10/2023] [Revised: 12/15/2023] [Accepted: 12/19/2023] [Indexed: 12/22/2023]
Abstract
Biopolymer analysis, including proteomics and glycomics, relies heavily on the use of mass spectrometry for structural elucidation, including sequence determination. Novel methods to improve sample workup, instrument performance, and data analysis continue to be developed to address shortcomings associated with sample preparation, analysis time, data quality, and data interpretation. Here, we present a new method that couples in-source collision-induced dissociation (IS-CID) with two-dimensional tandem mass spectrometry (2D MS/MS) as a way to simplify proteomics and glycomics workflows while also providing additional insight into analyte structures over traditional MS/MS experiments. Specifically, IS-CID is employed as a gas-phase digestion method, i.e., to break down intact full-length polysaccharide or peptide ions prior to mass analysis. The resulting mixtures of oligomeric ions are analyzed by 2D-MS/MS, a technique that allows association of product ions with their precursor ions without isolation of the latter. A novel data analysis strategy is introduced to leverage the second dimension of 2D MS/MS spectra, in which stairstep patterns, representing outputs of a molecule's MSn scans, are extracted for structural interconnectivity information on the oligomer. The results demonstrate the potential applicability of 2D MS/MS strategies to the modern omics workflow and structural analysis of various classes of biopolymers.
Collapse
Affiliation(s)
- MyPhuong T Le
- Purdue University, Department of Chemistry, West Lafayette, IN 47907, USA
| | - Dylan T Holden
- Purdue University, Department of Chemistry, West Lafayette, IN 47907, USA
| | - Jeremy M Manheim
- Merck & Co., Inc., Analytical Research and Development, Rahway, NJ 07065, USA
| | - Eric T Dziekonski
- Purdue University, Department of Chemistry, West Lafayette, IN 47907, USA
| | - Kiran Iyer
- Merck & Co., Inc., Analytical Research and Development, Rahway, NJ 07065, USA
| | - R Graham Cooks
- Purdue University, Department of Chemistry, West Lafayette, IN 47907, USA
| |
Collapse
|
2
|
Wu Q, Yu J, Zhang M, Xiong Y, Zhu L, Wei B, Wu T, Du Y. Serum lipidomic profiling for liver cancer screening using surface-assisted laser desorption ionization MS and machine learning. Talanta 2024; 268:125371. [PMID: 37931569 DOI: 10.1016/j.talanta.2023.125371] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/26/2023] [Accepted: 10/28/2023] [Indexed: 11/08/2023]
Abstract
The liver is a major organ in metabolism, and alterations in serum lipids are associated with liver disorders. Here, a rapid, easy, and reliable screening technique based on lipidomic profiling was developed using machine learning and surface-assisted laser desorption ionization mass spectrometry (SALDI MS) for liver cancer diagnosis. A graphitized carbon matrix (GCM) was created for serum lipid profiling in SALDI MS and demonstrated a better performance for neutral lipids analysis than conventional organic matrices. The fingerprint of serum lipids, including triacylglycerols (TGs), diacylglycerols (DGs), cholesteryl esters (CEs), glycerophospholipids (GPs), and other components, could be directly obtained by GCM-assisted LDI MS without extraction. Five machine learning methods were applied to distinguish liver cancer (LC) patients from healthy controls (HC) and chronic hepatitis B (CHB) patients. The best diagnostic performance was attained by linear discriminant analysis (LDA), which has a confusion matrix accuracy of 98.3 %. The receiver operating characteristic (ROC) curve for liver cancer exhibited an area under the curve (AUC) of 0.99, indicating a high degree of prediction accuracy. One-way ANOVA analysis revealed that numerous TGs were down-regulated in LC group. The results demonstrated the viability of GCM-assisted LDI MS as a valuable diagnostic tool for liver cancer.
Collapse
Affiliation(s)
- Qiong Wu
- School of Chemistry and Molecular Engineering and Shanghai Key Laboratory of Functional Materials Chemistry, and Research Centre of Analysis and Test, East China University of Science and Technology, Shanghai, 200237, China
| | - Jing Yu
- School of Chemistry and Molecular Engineering and Shanghai Key Laboratory of Functional Materials Chemistry, and Research Centre of Analysis and Test, East China University of Science and Technology, Shanghai, 200237, China
| | - Mingjin Zhang
- School of Chemistry and Chemical Engineering, Qinghai Normal University, Xining, Qinghai, 810016, China
| | - Yinran Xiong
- School of Chemistry and Molecular Engineering and Shanghai Key Laboratory of Functional Materials Chemistry, and Research Centre of Analysis and Test, East China University of Science and Technology, Shanghai, 200237, China
| | - Lijia Zhu
- School of Chemistry and Molecular Engineering and Shanghai Key Laboratory of Functional Materials Chemistry, and Research Centre of Analysis and Test, East China University of Science and Technology, Shanghai, 200237, China
| | - Bo Wei
- Department of Infectious Diseases, Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
| | - Ting Wu
- School of Chemistry and Molecular Engineering and Shanghai Key Laboratory of Functional Materials Chemistry, and Research Centre of Analysis and Test, East China University of Science and Technology, Shanghai, 200237, China.
| | - Yiping Du
- School of Chemistry and Molecular Engineering and Shanghai Key Laboratory of Functional Materials Chemistry, and Research Centre of Analysis and Test, East China University of Science and Technology, Shanghai, 200237, China.
| |
Collapse
|
3
|
Urine-Based Antigen (Protein) Detection Test for the Diagnosis of Visceral Leishmaniasis. Microorganisms 2020; 8:microorganisms8111676. [PMID: 33126760 PMCID: PMC7693408 DOI: 10.3390/microorganisms8111676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 11/29/2022] Open
Abstract
This review describes and appraises a novel protein-based antigen detection test for visceral leishmaniasis (VL). The test detects in patient’s urine six proteins from Leishmania infantum (chagasi) and Leishmania donovani, the etiological agents of VL. The gold standard test for VL is microscopic observation of the parasites in aspirates from spleen, liver, or bone marrow (and lymph node for dogs). Culture of the parasites or detection of their DNA in these aspirates are also commonly used. Serological tests are available but they cannot distinguish patients with active VL from either healthy subjects exposed to the parasites or from subjects who had a successful VL treatment. An antigen detection test based on the agglutination of anti-leishmania carbohydrates antibody coated latex beads has been described. However, the results obtained with this carbohydrate-based test have been conflicting. Using mass spectrometry, we discovered six L. infantum/L. donovani proteins excreted in the urine of VL patients and used them as markers for the development of a robust mAb-based antigen (protein) detection test. The test is assembled in a multiplexed format to simultaneously detect all six markers. Its initial clinical validation showed a sensitivity of 93% and specificity of 100% for VL diagnosis.
Collapse
|
4
|
Chen G, Fan M, Liu Y, Sun B, Liu M, Wu J, Li N, Guo M. Advances in MS Based Strategies for Probing Ligand-Target Interactions: Focus on Soft Ionization Mass Spectrometric Techniques. Front Chem 2019; 7:703. [PMID: 31709232 PMCID: PMC6819514 DOI: 10.3389/fchem.2019.00703] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 10/08/2019] [Indexed: 12/12/2022] Open
Abstract
The non-covalent interactions between small drug molecules and disease-related proteins (ligand-target interactions) mediate various pharmacological processes in the treatment of different diseases. The development of the analytical methods to assess those interactions, including binding sites, binding energies, stoichiometry and association-dissociation constants, could assist in clarifying the mechanisms of action, precise treatment of targeted diseases as well as the targeted drug discovery. For the last decades, mass spectrometry (MS) has been recognized as a powerful tool to study the non-covalent interactions of the ligand-target complexes with the characteristics of high sensitivity, high-resolution, and high-throughput. Soft ionization mass spectrometry, especially the electrospray mass spectrometry (ESI-MS) and matrix assisted laser desorption ionization mass spectrometry (MALDI-MS), could achieve the complete transformation of the target analytes into the gas phase, and subsequent detection of the small drug molecules and disease-related protein complexes, and has exerted great advantages for studying the drug ligands-protein targets interactions, even in case of identifying active components as drug ligands from crude extracts of medicinal plants. Despite of other analytical techniques for this purpose, such as the NMR and X-ray crystallography, this review highlights the principles, research hotspots and recent applications of the soft ionization mass spectrometry and its hyphenated techniques, including hydrogen-deuterium exchange mass spectrometry (HDX-MS), chemical cross-linking mass spectrometry (CX-MS), and ion mobility spectrometry mass spectrometry (IMS-MS), in the study of the non-covalent interactions between small drug molecules and disease-related proteins.
Collapse
Affiliation(s)
- Guilin Chen
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Minxia Fan
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Ye Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Baoqing Sun
- State Key Laboratory of Respiratory Disease, National Clinical Center for Respiratory Diseases, Guangzhou Institute of Respiratory Diseases, First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Meixian Liu
- State Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Taipa, Macau
| | - Jianlin Wu
- State Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Taipa, Macau
| | - Na Li
- State Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Taipa, Macau
| | - Mingquan Guo
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| |
Collapse
|
5
|
Tang Y, Zhang JL. Recent developments in DNA adduct analysis using liquid chromatography coupled with mass spectrometry. J Sep Sci 2019; 43:31-55. [PMID: 31573133 DOI: 10.1002/jssc.201900737] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 09/04/2019] [Accepted: 09/27/2019] [Indexed: 12/15/2022]
Abstract
The formation of DNA adducts by genotoxic agents is an early event in cancer development, and it may lead to gene mutations, thereby initiating tumor development. The measurement of DNA adducts can provide critical information about the genotoxic potential of a chemical and its mechanism of carcinogenesis. In recent decades, liquid chromatography coupled with mass spectrometry has become the most important technique for analyzing DNA adducts. The improvements in resolution achievable with new chromatographic separation techniques coupled with the high specificity and sensitivity and wide dynamic range of new mass spectrometry systems have been used for both qualitative and quantitative analyses of DNA adducts. This review discusses the challenges in qualitative and quantitative analyses of DNA adducts by liquid chromatography coupled with mass spectrometry and highlights recent developments towards overcoming the limitations of liquid chromatography coupled with mass spectrometry methods. The key steps and new solutions, such as sample preparation, mass spectrometry fragmentation, and method validation, are summarized. In addition, the fundamental principles and latest advances in DNA adductomic approaches are reviewed.
Collapse
Affiliation(s)
- Yu Tang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, P. R. China
| | - Jin-Lan Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, P. R. China
| |
Collapse
|
6
|
Buczkowski A, Palecz B, Schroeder G. Stoichiometry and thermodynamics of gemcitabine and cucurbituril Q7 supramolecular complexes in high acidic aqueous solution. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.10.077] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
7
|
Rinschen MM, Limbutara K, Knepper MA, Payne DM, Pisitkun T. From Molecules to Mechanisms: Functional Proteomics and Its Application to Renal Tubule Physiology. Physiol Rev 2019; 98:2571-2606. [PMID: 30182799 DOI: 10.1152/physrev.00057.2017] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Classical physiological studies using electrophysiological, biophysical, biochemical, and molecular techniques have created a detailed picture of molecular transport, bioenergetics, contractility and movement, and growth, as well as the regulation of these processes by external stimuli in cells and organisms. Newer systems biology approaches are beginning to provide deeper and broader understanding of these complex biological processes and their dynamic responses to a variety of environmental cues. In the past decade, advances in mass spectrometry-based proteomic technologies have provided invaluable tools to further elucidate these complex cellular processes, thereby confirming, complementing, and advancing common views of physiology. As one notable example, the application of proteomics to study the regulation of kidney function has yielded novel insights into the chemical and physical processes that tightly control body fluids, electrolytes, and metabolites to provide optimal microenvironments for various cellular and organ functions. Here, we systematically review, summarize, and discuss the most significant key findings from functional proteomic studies in renal epithelial physiology. We also identify further improvements in technological and bioinformatics methods that will be essential to advance precision medicine in nephrology.
Collapse
Affiliation(s)
- Markus M Rinschen
- Department II of Internal Medicine, University Hospital Cologne , Cologne , Germany ; Center for Molecular Medicine Cologne, University of Cologne , Cologne , Germany ; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne , Cologne , Germany ; Division of Nephrology, Faculty of Medicine, Chulalongkorn University , Bangkok , Thailand ; Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland ; and Center of Excellence in Systems Biology, Research Affairs, Faculty of Medicine, Chulalongkorn University , Bangkok , Thailand
| | - Kavee Limbutara
- Department II of Internal Medicine, University Hospital Cologne , Cologne , Germany ; Center for Molecular Medicine Cologne, University of Cologne , Cologne , Germany ; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne , Cologne , Germany ; Division of Nephrology, Faculty of Medicine, Chulalongkorn University , Bangkok , Thailand ; Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland ; and Center of Excellence in Systems Biology, Research Affairs, Faculty of Medicine, Chulalongkorn University , Bangkok , Thailand
| | - Mark A Knepper
- Department II of Internal Medicine, University Hospital Cologne , Cologne , Germany ; Center for Molecular Medicine Cologne, University of Cologne , Cologne , Germany ; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne , Cologne , Germany ; Division of Nephrology, Faculty of Medicine, Chulalongkorn University , Bangkok , Thailand ; Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland ; and Center of Excellence in Systems Biology, Research Affairs, Faculty of Medicine, Chulalongkorn University , Bangkok , Thailand
| | - D Michael Payne
- Department II of Internal Medicine, University Hospital Cologne , Cologne , Germany ; Center for Molecular Medicine Cologne, University of Cologne , Cologne , Germany ; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne , Cologne , Germany ; Division of Nephrology, Faculty of Medicine, Chulalongkorn University , Bangkok , Thailand ; Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland ; and Center of Excellence in Systems Biology, Research Affairs, Faculty of Medicine, Chulalongkorn University , Bangkok , Thailand
| | - Trairak Pisitkun
- Department II of Internal Medicine, University Hospital Cologne , Cologne , Germany ; Center for Molecular Medicine Cologne, University of Cologne , Cologne , Germany ; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne , Cologne , Germany ; Division of Nephrology, Faculty of Medicine, Chulalongkorn University , Bangkok , Thailand ; Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland ; and Center of Excellence in Systems Biology, Research Affairs, Faculty of Medicine, Chulalongkorn University , Bangkok , Thailand
| |
Collapse
|
8
|
Affiliation(s)
- Hope A. Flaxman
- Department of Chemistry and
Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Christina M. Woo
- Department of Chemistry and
Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| |
Collapse
|
9
|
Ishii K, Zhou M, Uchiyama S. Native mass spectrometry for understanding dynamic protein complex. Biochim Biophys Acta Gen Subj 2017; 1862:275-286. [PMID: 28965879 DOI: 10.1016/j.bbagen.2017.09.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/17/2017] [Accepted: 09/19/2017] [Indexed: 12/13/2022]
Abstract
Biomolecules have evolved to perform specific and sophisticated activities in a highly coordinated manner organizing into multi-component complexes consisting of proteins, nucleic acids, cofactors or ligands. Understanding such complexes represents a task in earnest for modern bioscience. Traditional structural techniques when extrapolating to macromolecules of ever increasing sizes are confronted with limitations posed by the difficulty in enrichment, solubility, stability as well as lack of homogeneity of these complexes. Alternative approaches are therefore prompted to bridge the gap, one of which is native mass spectrometry. Here we demonstrate the strength of native mass spectrometry, used alone or in combination with other biophysical methods such as analytical ultracentrifugation, small-angle neutron scattering, and small-angle X-ray scattering etc., in addressing dynamic aspects of protein complexes including structural reorganization, subunit exchange, as well as the assembly/disassembly processes in solution that are dictated by transient non-covalent interactions. We review recent studies from our laboratories and others applying native mass spectrometry to both soluble and membrane-embedded assemblies. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.
Collapse
Affiliation(s)
- Kentaro Ishii
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
| | - Min Zhou
- Institute of Bio-analytical Chemistry, School of Chemical Engineering, Nanjing University of Science and Technology, No. 200 Xiaolingwei Street, Nanjing 210094, China.
| | - Susumu Uchiyama
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan; Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| |
Collapse
|
10
|
Meher AK, Chen YC. Electrospray Modifications for Advancing Mass Spectrometric Analysis. ACTA ACUST UNITED AC 2017; 6:S0057. [PMID: 28573082 DOI: 10.5702/massspectrometry.s0057] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 12/30/2016] [Indexed: 11/23/2022]
Abstract
Generation of analyte ions in gas phase is a primary requirement for mass spectrometric analysis. One of the ionization techniques that can be used to generate gas phase ions is electrospray ionization (ESI). ESI is a soft ionization method that can be used to analyze analytes ranging from small organics to large biomolecules. Numerous ionization techniques derived from ESI have been reported in the past two decades. These ion sources are aimed to achieve simplicity and ease of operation. Many of these ionization methods allow the flexibility for elimination or minimization of sample preparation steps prior to mass spectrometric analysis. Such ion sources have opened up new possibilities for taking scientific challenges, which might be limited by the conventional ESI technique. Thus, the number of ESI variants continues to increase. This review provides an overview of ionization techniques based on the use of electrospray reported in recent years. Also, a brief discussion on the instrumentation, underlying processes, and selected applications is also presented.
Collapse
Affiliation(s)
| | - Yu-Chie Chen
- Department of Applied Chemistry, National Chiao Tung University
| |
Collapse
|
11
|
Ruhaak LR, van der Burgt YE, Cobbaert CM. Prospective applications of ultrahigh resolution proteomics in clinical mass spectrometry. Expert Rev Proteomics 2016; 13:1063-1071. [DOI: 10.1080/14789450.2016.1253477] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- L. Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Yuri E.M. van der Burgt
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, the Netherlands
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Christa M. Cobbaert
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, the Netherlands
| |
Collapse
|
12
|
Bernier MC, Wysocki VH, Dagan S. Laser desorption ionization of small molecules assisted by tungsten oxide and rhenium oxide particles. JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:891-8. [PMID: 26349643 PMCID: PMC4566159 DOI: 10.1002/jms.3597] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 03/04/2015] [Accepted: 03/25/2015] [Indexed: 05/11/2023]
Abstract
Inorganic metal oxides have shown potential as matrices for assisting in laser desorption ionization with advantages over the aromatic acids typically used. Rhenium and tungsten oxides are attractive options due to their high work functions and relative chemical inertness. In this work, it is shown that ReO3 and WO3 , in microparticle (μP) powder forms, can efficiently facilitate ionization of various types of small molecules and provide minimized background contamination at analyte concentrations below 1 ng/µL. This study shows that untreated inorganic WO3 and ReO3 particles are valid matrix options for detection of protonatable, radical, and precharged species under laser desorption ionization. Qualitatively, the WO3 μP showed improved detection of apigenin, sodiated glucose, and precharged analyte choline, while the ReO3 μP allowed better detection of protonated cocaine, quinuclidine, ametryn, and radical ions of polyaromatic hydrocarbons at detection levels as low as 50 pg/µL. For thermometer ion survival yield experiments, it was also shown that the ReO3 powder was significantly softer than α-cyano-4-hydroxycinnaminic acid. Furthermore, it provided higher intensities of cocaine and polyaromatic hydrocarbons, at laser flux values equal to those used with α-cyano-4-hydroxycinnaminic acid.
Collapse
Affiliation(s)
| | | | - Shai Dagan
- Permanent address: Israel Institute for Biological Research, Ness Ziona, Israel
| |
Collapse
|
13
|
Nagy E, Ábrók M, Bartha N, Bereczki L, Juhász E, Kardos G, Kristóf K, Miszti C, Urbán E. Special application of matrix-assisted laser desorption ionization time-of-flight mass spectrometry in clinical microbiological diagnostics. Orv Hetil 2014; 155:1495-503. [DOI: 10.1556/oh.2014.29985] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Matrix-assisted laser desorption ionization time-of-flight mass spectrometry as a new possibility for rapid identification of bacteria and fungi revolutionized the clinical microbiological diagnostics. It has an extreme importance in the routine microbiological laboratories, as identification of the pathogenic species rapidly will influence antibiotic selection before the final determination of antibiotic resistance of the isolate. The classical methods for identification of bacteria or fungi, based on biochemical tests, are influenced by many environmental factors. The matrix-assisted laser desorption ionization time-of-flight mass spectrometry is a rapid method which is able to identify a great variety of the isolated bacteria and fungi based on the composition of conserved ribosomal proteins. Recently several other applications of the method have also been investigated such as direct identification of pathogens from the positive blood cultures. There are possibilities to identify bacteria from the urine samples in urinary tract infection or from other sterile body fluids. Using selective enrichment broth Salmonella sp from the stool samples can be identified more rapidly, too. The extended spectrum beta-lactamase or carbapenemase production of the isolated bacteria can be also detected by this method helping the antibiotic selection in some cases. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry based methods are suitable to investigate changes in deoxyribonucleic acid or ribonucleic acid, to carry out rapid antibiotic resistance determination or other proteomic analysis. The aim of this paper is to give an overview about present possibilities of using this technique in the clinical microbiological routine procedures. Orv. Hetil., 2014, 155(38), 1495–1503.
Collapse
Affiliation(s)
- Erzsébet Nagy
- Szegedi Tudományegyetem, Általános Orvostudományi Kar Klinikai Mikrobiológiai Diagnosztikai Intézet Szeged Pf. 427 6701
| | - Marianna Ábrók
- Szegedi Tudományegyetem, Általános Orvostudományi Kar Klinikai Mikrobiológiai Diagnosztikai Intézet Szeged Pf. 427 6701
| | - Noémi Bartha
- Szegedi Tudományegyetem, Általános Orvostudományi Kar Klinikai Mikrobiológiai Diagnosztikai Intézet Szeged Pf. 427 6701
| | - László Bereczki
- Szegedi Tudományegyetem, Általános Orvostudományi Kar Klinikai Mikrobiológiai Diagnosztikai Intézet Szeged Pf. 427 6701
| | - Emese Juhász
- Semmelweis Egyetem, Általános Orvostudományi Kar Laboratóriumi Medicina Intézet, Klinikai Mikrobiológiai Diagnosztikai Laboratórium Budapest
| | - Gábor Kardos
- Debreceni Egyetem, Általános Orvostudományi Kar Orvosi Mikrobiológiai Intézet Debrecen
| | - Katalin Kristóf
- Semmelweis Egyetem, Általános Orvostudományi Kar Laboratóriumi Medicina Intézet, Klinikai Mikrobiológiai Diagnosztikai Laboratórium Budapest
| | - Cecilia Miszti
- Debreceni Egyetem, Általános Orvostudományi Kar Orvosi Mikrobiológiai Intézet Debrecen
| | - Edit Urbán
- Szegedi Tudományegyetem, Általános Orvostudományi Kar Klinikai Mikrobiológiai Diagnosztikai Intézet Szeged Pf. 427 6701
| |
Collapse
|
14
|
Gavina JMA, Yao C, Feng YL. Recent developments in DNA adduct analysis by mass spectrometry: a tool for exposure biomonitoring and identification of hazard for environmental pollutants. Talanta 2014; 130:475-94. [PMID: 25159438 DOI: 10.1016/j.talanta.2014.06.050] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 06/19/2014] [Accepted: 06/22/2014] [Indexed: 02/08/2023]
Abstract
DNA adducts represent an important category of biomarkers for detection and exposure surveillance of potential carcinogenic and genotoxic chemicals in the environment. Sensitive and specific analytical methods are required to detect and differentiate low levels of adducts from native DNA from in vivo exposure. In addition to biomonitoring of environmental pollutants, analytical methods have been developed for structural identification of adducts which provides fundamental information for determining the toxic pathway of hazardous chemicals. In order to achieve the required sensitivity, mass spectrometry has been increasingly utilized to quantify adducts at low levels as well as to obtain structural information. Furthermore, separation techniques such as chromatography and capillary electrophoresis can be coupled to mass spectrometry to increase the selectivity. This review will provide an overview of advances in detection of adducted and modified DNA by mass spectrometry with a focus on the analysis of nucleosides since 2007. Instrument advances, sample and instrument considerations, and recent applications will be summarized in the context of hazard assessment. Finally, advances in biomonitoring applying mass spectrometry will be highlighted. Most importantly, the usefulness of DNA adducts measurement and detection will be comprehensively discussed as a tool for assessment of in vitro and in vivo exposure to environmental pollutants.
Collapse
Affiliation(s)
- Jennilee M A Gavina
- Exposure and Biomonitoring Division, Environmental Health Science and Research Bureau, Environmental and Radiation Health Sciences Directorate, Healthy Environments and Consumer Safety Branch, Health Canada, 50 Columbine Driveway, AL: 0800C, Ottawa, Ontario, Canada K1A 0K9
| | - Chunhe Yao
- Exposure and Biomonitoring Division, Environmental Health Science and Research Bureau, Environmental and Radiation Health Sciences Directorate, Healthy Environments and Consumer Safety Branch, Health Canada, 50 Columbine Driveway, AL: 0800C, Ottawa, Ontario, Canada K1A 0K9
| | - Yong-Lai Feng
- Exposure and Biomonitoring Division, Environmental Health Science and Research Bureau, Environmental and Radiation Health Sciences Directorate, Healthy Environments and Consumer Safety Branch, Health Canada, 50 Columbine Driveway, AL: 0800C, Ottawa, Ontario, Canada K1A 0K9.
| |
Collapse
|
15
|
Ankrah NYD, May AL, Middleton JL, Jones DR, Hadden MK, Gooding JR, LeCleir GR, Wilhelm SW, Campagna SR, Buchan A. Phage infection of an environmentally relevant marine bacterium alters host metabolism and lysate composition. ISME JOURNAL 2013; 8:1089-100. [PMID: 24304672 DOI: 10.1038/ismej.2013.216] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 10/27/2013] [Accepted: 10/31/2013] [Indexed: 11/09/2022]
Abstract
Viruses contribute to the mortality of marine microbes, consequentially altering biological species composition and system biogeochemistry. Although it is well established that host cells provide metabolic resources for virus replication, the extent to which infection reshapes host metabolism at a global level and the effect of this alteration on the cellular material released following viral lysis is less understood. To address this knowledge gap, the growth dynamics, metabolism and extracellular lysate of roseophage-infected Sulfitobacter sp. 2047 was studied using a variety of techniques, including liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based metabolomics. Quantitative estimates of the total amount of carbon and nitrogen sequestered into particulate biomass indicate that phage infection redirects ∼75% of nutrients into virions. Intracellular concentrations for 82 metabolites were measured at seven time points over the infection cycle. By the end of this period, 71% of the detected metabolites were significantly elevated in infected populations, and stable isotope-based flux measurements showed that these cells had elevated metabolic activity. In contrast to simple hypothetical models that assume that extracellular compounds increase because of lysis, a profile of metabolites from infected cultures showed that >70% of the 56 quantified compounds had decreased concentrations in the lysate relative to uninfected controls, suggesting that these small, labile nutrients were being utilized by surviving cells. These results indicate that virus-infected cells are physiologically distinct from their uninfected counterparts, which has implications for microbial community ecology and biogeochemistry.
Collapse
Affiliation(s)
- Nana Yaw D Ankrah
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Amanda L May
- Department of Chemistry, University of TN, Knoxville, TN, USA
| | | | - Daniel R Jones
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Mary K Hadden
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | | | - Gary R LeCleir
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Steven W Wilhelm
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | | | - Alison Buchan
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| |
Collapse
|
16
|
Li Z, Jiang A, Yue T, Wang J, Wang Y, Su J. Purification and identification of five novel antioxidant peptides from goat milk casein hydrolysates. J Dairy Sci 2013; 96:4242-51. [PMID: 23684032 DOI: 10.3168/jds.2012-6511] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 02/23/2013] [Indexed: 11/19/2022]
Abstract
The present research described the preparation, purification, and identification of antioxidant peptides from goat milk casein (GMC). Goat milk casein was hydrolyzed by using a combination of neutral and alkaline proteases to obtain goat milk casein hydrolysates (GMCH) with high antioxidant activity. After desalting by nonpolar macroporous absorption resin, GMCH was isolated and purified by gel filtration chromatography and reversed-phase HPLC, respectively, and further identified by nanoliter electrospray ionization-tandem mass spectrometry. Antioxidant activities of GMC, GMCH, and pure peptides were evaluated and compared using free radical scavenging activity, metal ion chelating ability, and anti-lipid peroxidation ability. Compared with GMC, the free radical-scavenging ability and ferrous ion-chelating ability of GMCH increased significantly. The inhibition effect of lipid peroxidation of GMCH was much stronger than that of tert-butylhydroquinone and phytogermine and a little lower than that of ascorbic acid. The antioxidant activity of GMCH could be attributed to the high antioxidant activity of oligopeptides, especially 5 novel oligopeptides: Val-Tyr-Pro-Phe, Phe-Gly-Gly-Met-Ala-His, Phe-Pro-Tyr-Cys-Ala-Pro, Tyr-Val-Pro-Glu-Pro-Phe, and Tyr-Pro-Pro-Tyr-Glu-Thr-Tyr, which were first observed in GMCH. The antioxidant activity of these 5 novel oligopeptides and GMCH increased 3.59 to 380 times compared with GMC, combining anti-lipid peroxidation ability of GMCH, which indicated that GMCH and its purified fractions in different stages could be used as functional food ingredients, food additives, and pharmaceutical agents in the future.
Collapse
Affiliation(s)
- Z Li
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China.
| | | | | | | | | | | |
Collapse
|
17
|
Hsu YF, Lin JL, Chu ML, Wang YS, Chen CH. Macromolecular ion accelerator mass spectrometer. Analyst 2013; 138:7384-91. [DOI: 10.1039/c3an01534c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
18
|
Aquino PF, Fischer JSG, Neves-Ferreira AGC, Perales J, Domont GB, Araujo GDT, Barbosa VC, Viana J, Chalub SRS, Lima de Souza AQ, Carvalho MGC, Leão de Souza AD, Carvalho PC. Are Gastric Cancer Resection Margin Proteomic Profiles More Similar to Those from Controls or Tumors? J Proteome Res 2012; 11:5836-42. [DOI: 10.1021/pr300612x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Priscila F. Aquino
- Departamento de Química, Universidade Federal do Amazonas, Amazonas, Brazil
| | | | | | - Jonas Perales
- Laboratório de Toxinologia, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Gilberto B. Domont
- Proteomics Unit, Rio de Janeiro Proteomics Network,
Departamento de Bioquímica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gabriel D. T. Araujo
- Proteomics Unit, Rio de Janeiro Proteomics Network,
Departamento de Bioquímica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Valmir C. Barbosa
- Programa de Engenharia de Sistemas
e Computação, COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jucilana Viana
- Escola Superior de Ciências
da Saúde, Universidade do Estado do Amazonas, Amazonas, Brazil
| | - Sidney R. S. Chalub
- Departamento
de Cirurgia Digestiva, Universidade Federal do Amazonas, Amazonas, Brazil
| | | | - Maria G. C. Carvalho
- Departamento
de Patologia, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | |
Collapse
|
19
|
Mandal MK, Yoshimura K, Chen LC, Yu Z, Nakazawa T, Katoh R, Fujii H, Takeda S, Nonami H, Hiraoka K. Application of probe electrospray ionization mass spectrometry (PESI-MS) to clinical diagnosis: solvent effect on lipid analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:2043-2047. [PMID: 22923015 DOI: 10.1007/s13361-012-0462-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Revised: 07/27/2012] [Accepted: 07/29/2012] [Indexed: 06/01/2023]
Abstract
We have examined several combinations of solvents with the aim of optimizing the ionization conditions for molecular diagnosis of malignant tumours by PESI-MS. Although the best conditions may depend on the actual species in the sample, the optimal conditions for renal cell carcinoma (RCC) were achieved by using alcohols. PESI-MS successfully delineated the differential expression of phospholipids (PCs) and triacylglycerols (TAGs) in noncancerous and RCC tissues by using these solvent systems. This study paves the way for the application of PESI-MS in medical samples.
Collapse
Affiliation(s)
- Mridul Kanti Mandal
- Clean Energy Research Center, University of Yamanashi, Kofu, Yamanashi, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Sospedra I, Soler C, Mañes J, Soriano JM. Rapid whole protein quantitation of staphylococcal enterotoxins A and B by liquid chromatography/mass spectrometry. J Chromatogr A 2012; 1238:54-9. [DOI: 10.1016/j.chroma.2012.03.022] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Revised: 02/17/2012] [Accepted: 03/06/2012] [Indexed: 11/24/2022]
|
21
|
Grzetic J, Oomens J. Spectroscopic evidence for an oxazolone structure in anionic b-type peptide fragments. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:290-300. [PMID: 22170467 PMCID: PMC3264858 DOI: 10.1007/s13361-011-0297-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2011] [Revised: 10/31/2011] [Accepted: 11/02/2011] [Indexed: 05/31/2023]
Abstract
Infrared spectra of anionic b-type fragments generated by collision induced dissociation (CID) from deprotonated peptides are reported. Spectra of the b(2) fragments of deprotonated AlaAlaAla and AlaTyrAla have been recorded over the 800-1800 cm(-1) spectral range by multiple-photon dissociation (MPD) spectroscopy using an FTICR mass spectrometer in combination with the free electron laser FELIX. Structural characterization of the b-type fragments is accomplished by comparison with density functional theory calculated spectra at the B3LYP/6-31++G(d,p) level for different isomeric structures. Although diketopiperazine structures represent the energetically lowest isomers, the IR spectra suggest an oxazolone structure for the b(2) fragments of both peptides. Deprotonation is shown to occur on the oxazolone α-carbon, which leads to a conjugated structure in which the negative charge is practically delocalized over the entire oxazolone ring, providing enhanced gas-phase stability.
Collapse
Affiliation(s)
- Josipa Grzetic
- FOM Institute for Plasma Physics Rijnhuizen, Edisonbaan 14, 3439MN Nieuwegein, The Netherlands
| | - Jos Oomens
- FOM Institute for Plasma Physics Rijnhuizen, Edisonbaan 14, 3439MN Nieuwegein, The Netherlands
- van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| |
Collapse
|
22
|
Pacholarz KJ, Garlish RA, Taylor RJ, Barran PE. Mass spectrometry based tools to investigate protein–ligand interactions for drug discovery. Chem Soc Rev 2012; 41:4335-55. [DOI: 10.1039/c2cs35035a] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
|
23
|
Stewart KW, Phillips ARJ, Whiting L, Jüllig M, Middleditch MJ, Cooper GJS. A simple and rapid method for identifying and semi-quantifying peptide hormones in isolated pancreatic islets by direct-tissue matrix-assisted laser desorption ionization time-of-flight mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2011; 25:3387-3395. [PMID: 22002691 DOI: 10.1002/rcm.5239] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We describe a new, simple, robust and efficient method based on direct-tissue matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry that enables consistent semi-quantitation of peptide hormones in isolated pancreatic islets from normal and diabetic rodents. Prominent signals were measured that corresponded to all the main peptide hormones present in islet-endocrine cells: (α-cells) glucagon, glicentin-related polypeptide/GRPP; (β-cells) insulin I, insulin II, C-peptide I, C-peptide II, amylin; (δ-cells) somatostatin-14; and (PP-cells), and pancreatic polypeptide. The signal ratios coincided with known relative hormone abundances. The method demonstrated that severe insulin deficiency is accompanied by elevated levels of all non-β-cell-hormones in diabetic rat islets, consistent with alleviation of paracrine suppression of hormone production by non-β-cells. It was also effective in characterizing hormonal phenotype in hemizygous human-amylin transgenic mice that express human and mouse amylin in approx. equimolar quantities. Finally, the method demonstrated utility in basic peptide-hormone discovery by identifying a prominent new Gcg-gene-derived peptide (theoretical monoisotopic molecular weight 3263.5 Da), closely related to but distinct from GRPP, in diabetic islets. This peptide, whose sequence is HAPQDTEENARSFPASQTEPLEDPNQINE in Rattus norvegicus, could be a peptide hormone whose roles in physiology and metabolic disease warrant further investigation. This method provides a powerful new approach that could provide important new insights into the physiology and regulation of peptide hormones in islets and other endocrine tissues. It has potentially wide-ranging applications that encompass endocrinology, pharmacology, phenotypic analysis in genetic models of metabolic disease, and hormone discovery, and could also effectively limit the numbers of animals required for such studies.
Collapse
|
24
|
Tunable fragmentation of organic molecules in laser ablation glow discharge time-of-flight mass spectrometry. Anal Bioanal Chem 2011; 402:2565-76. [DOI: 10.1007/s00216-011-5498-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Revised: 10/07/2011] [Accepted: 10/11/2011] [Indexed: 10/15/2022]
|
25
|
Fernandes RMT, Gomes GC, Porcari AM, Pimentel JRV, Porciúncula PM, Martins-Júnior HA, Miguez PHP, da Costa JL, Amaral PH, Perecin F, Meurer EC, Furtado PV, Simas RC, Eberlin MN, Ferreira CR, Madureira EH. LC-MS/MS quantitation of plasma progesterone in cattle. Theriogenology 2011; 76:1266-74.e1-2. [PMID: 21798587 DOI: 10.1016/j.theriogenology.2011.05.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Revised: 05/11/2011] [Accepted: 05/12/2011] [Indexed: 10/17/2022]
Abstract
Quantitation of progesterone (P(4)) in biological fluids is often performed by radioimmunoassay (RIA), whereas liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) has been used much less often. Due to its autoconfirmatory nature, LC-MS/MS greatly minimizes false positives and interference. Herein we report and compare with RIA an optimized LC-MS/MS method for rapid, efficient, and cost-effective quantitation of P(4) in plasma of cattle with no sample derivatization. The quantitation of plasma P(4) released from three nonbiodegradable, commercial, intravaginal P(4)-releasing devices (IPRD) over 192 h in six ovariectomized cows was compared in a pairwise study as a test case. Both techniques showed similar P(4) kinetics (P > 0.05) whereas results of P(4) quantitation by RIA were consistently higher compared with LC-MS/MS (P < 0.05) due to interference and matrix effects. The LC-MS/MS method was validated according to the recommended analytical standards and displayed P(4) limits of detection (LOD) and quantitation (LOQ) of 0.08 and a 0.25 ng/mL, respectively. The high selective LC-MS/MS method proposed herein for P(4) quantitation eliminates the risks associated with radioactive handling; it also requires no sample derivatization, which is a common requirement for LC-MS/MS quantitation of steroid hormones. Its application to multisteroid assays is also viable, and it is envisaged that it may provide a gold standard technique for hormone quantitation in animal reproductive science studies.
Collapse
Affiliation(s)
- R M T Fernandes
- ThoMSon Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas-UNICAMP, Campinas, SP, Brazil
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Kanie O, Kanie Y, Daikoku S, Shioiri Y, Kurimoto A, Mutsuga S, Goto S, Ito Y, Suzuki K. Multi-stage mass spectrometric information obtained by deconvolution of energy-resolved spectra acquired by triple-quadrupole mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2011; 25:1617-1624. [PMID: 21594937 DOI: 10.1002/rcm.5031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Triple-quadrupole mass spectrometry (TQ-MS) provides the capability to carry out collision-induced dissociation (CID) and it offers advantages in quantification when connected with high-performance liquid chromatography through an electrospray ionization interface. However, although TQ-MS provides information on partial structures through the analysis of product ions obtained by CID experiments, the method only provides single-stage CID experiments, which limits the detailed structural information that can be obtained. Herein, a method of overcoming this limitation of TQ-MS is described. A spectrum obtained by energy-resolved mass spectrometry (ERMS) was used to deconvolute the fragmentation process, with a Galili-antigenic trisaccharide derivative being used as an example. A replot of the ERMS data showing the ratios of the product ions to the precursor ion resulted in a descriptive graph. Analysis of the sum of the ratios of individual product ions to the precursor ion at specific CID energies revealed that the members of a series of product ions were related to each other. The obtained relationships and the m/z values of the product ions provided information on the fragmentation process taking place during the dissociation, indicating that the ERMS spectrum obtained by TQ-MS contained equivalent information to that obtainable by multi-stage MS/MS (MS(n); n≥2). This method may allow users of triple-quadrupole mass spectrometers to obtain MS(n)-type information by performing a single ERMS experiment, which is even advantageous over quadrupole ion trap (QIT)-MS/MS because CID experiments on individual first-generation product ions are not required.
Collapse
Affiliation(s)
- Osamu Kanie
- Japan Science and Technology Agency (JST), ERATO, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.
| | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Colantonio S, Simpson JT, Fisher RJ, Yavlovich A, Belanger JM, Puri A, Blumenthal R. Quantitative analysis of phospholipids using nanostructured laser desorption ionization targets. Lipids 2011; 46:469-77. [PMID: 21327726 PMCID: PMC3238685 DOI: 10.1007/s11745-010-3493-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Accepted: 10/20/2010] [Indexed: 10/18/2022]
Abstract
Since its introduction as an ionization technique in mass spectrometry, matrix-assisted laser desorption ionization (MALDI) has been applied to a wide range of applications. Quantitative small molecule analysis by MALDI, however, is limited due to the presence of intense signals from the matrix coupled with non-homogeneous surfaces. The surface used in nano-structured laser desorption ionization (NALDI) eliminates the need for a matrix and the resulting interferences, and allows for quantitative analysis of small molecules. This study was designed to analyze and quantitate phospholipid components of liposomes. Here we have developed an assay to quantitate the DPPC and DC(8,9)PC in liposomes by NALDI following various treatments. To test our method we chose to analyze a liposome system composed of DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) and DC(8,9)PC (1,2-bis(tricosa-10,12-diynoyl)-sn-glycero-3-phosphocholine), as DC(8,9)PC is known to undergo cross-linking upon treatment with UV (254 nm) and this reaction converts the monomer into a polymer. First, calibration curves for pure lipids (DPPC and DC(8,9)PC) were created using DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) as an internal standard. The calibration curve for both DPPC and DC(8,9)PC showed an R(2) of 0.992, obtained using the intensity ratio of analyte and internal standard. Next, DPPC:DC(8,9)PC liposomes were treated with UV radiation (254 nm). Following this treatment, lipids were extracted from the liposomes and analyzed. The analysis of the lipids before and after UV exposure confirmed a decrease in the signal of DC(8,9)PC of about 90%. In contrast, there was no reduction in DPPC signal.
Collapse
Affiliation(s)
- Simona Colantonio
- Protein Chemistry Laboratory, Advanced Technology Program, SAIC-Frederick/NCI-Frederick, Frederick, MD 21702, USA.
| | | | | | | | | | | | | |
Collapse
|
28
|
Parikh N, Kumar D, Roy SR, Chakraborti AK. Surfactant mediated oxygen reuptake in water for green aerobic oxidation: mass-spectrometric determination of discrete intermediates to correlate oxygen uptake with oxidation efficiency. Chem Commun (Camb) 2011; 47:1797-9. [DOI: 10.1039/c0cc03166f] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
29
|
Merchant ML. Mass spectrometry in chronic kidney disease research. Adv Chronic Kidney Dis 2010; 17:455-68. [PMID: 21044768 DOI: 10.1053/j.ackd.2010.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Accepted: 09/21/2010] [Indexed: 01/14/2023]
Abstract
Proteomics has evolved into an invaluable tool for biomedical research and for research on renal diseases. A central player in the proteomic revolution is the mass spectrometer and its application in analyzing biological samples. Our need to understand both the identity of proteins and their abundance has led to improvements in the ability of mass spectrometers (such as with the use of the LTQ-Orbitrap mass spectrometer) to analyze complex (tryptic) peptide mixtures with high sensitivity and high mass accuracy in a high-throughput manner. Unsurprisingly, this occurred coincidentally with dramatic improvements in our understanding of CKD, the mechanisms through which CKD progresses, and the development of candidate CKD biomarkers. This review attempts to present a basic framework for the operational components of mass spectrometers, basic insight into how they are used in renal research, and a discussion on CKD research related to mass spectrometry.
Collapse
|
30
|
Abstract
Imaging mass spectrometry (IMS) using matrix-assisted laser desorption ionization (MALDI) is a new and effective tool for molecular studies of complex biological samples such as tissue sections. As histological features remain intact throughout the analysis of a section, distribution maps of multiple analytes can be correlated with histological and clinical features. Spatial molecular arrangements can be assessed without the need for target-specific reagents, allowing the discovery of diagnostic and prognostic markers of different cancer types and enabling the determination of effective therapies.
Collapse
Affiliation(s)
- Kristina Schwamborn
- Mass Spectrometry Research Center, Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232-2195, USA
| | | |
Collapse
|
31
|
Hart-Smith G, Barner-Kowollik C. Contemporary Mass Spectrometry and the Analysis of Synthetic Polymers: Trends, Techniques and Untapped Potential. MACROMOL CHEM PHYS 2010. [DOI: 10.1002/macp.201000107] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
32
|
Boxrud D. Advances in subtyping methods of foodborne disease pathogens. Curr Opin Biotechnol 2010; 21:137-41. [PMID: 20299203 DOI: 10.1016/j.copbio.2010.02.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2010] [Revised: 02/17/2010] [Accepted: 02/17/2010] [Indexed: 01/26/2023]
Abstract
Current subtyping methods for the detection of foodborne disease outbreaks have limitations that reduce their use by public health laboratories. Recent advances in subtyping of foodborne disease pathogens utilize techniques that identify nucleic acid polymorphisms. Recent methods of nucleic acid characterization such as microarrays and mass spectrometry (MS) may provide improvements such as increasing speed and data portability while decreasing labor compared to current methods. This article discusses multiple-locus variable-number tandem-repeat analysis, single-nucleotide polymorphisms, nucleic acid sequencing, whole genome sequencing, variable absent or present loci, microarrays and MS as potential subtyping methods to enhance our ability to detect foodborne disease outbreaks.
Collapse
|
33
|
Abstract
The ability to conduct validated analyses of biomarkers is critically important in order to establish the sensitivity and selectivity of the biomarker in identifying a particular disease. The use of stable-isotope dilution (SID) methodology in combination with LC–MS/MS provides the highest possible analytical specificity for quantitative determinations. This methodology is now widely used in the discovery and validation of putative exposure and disease biomarkers. This review will describe the application of SID LC–MS methodology for the analysis of small-molecule and protein biomarkers. It will also discuss potential future directions for the use of this methodology for rigorous biomarker analysis.
Collapse
Affiliation(s)
- Eugene Ciccimaro
- Thermo Fisher Scientific, 265 Davidson Avenue, Somerset, NJ 08873–4120, USA
| | - Ian A Blair
- Centers of Excellence in Environmental Toxicology and Cancer Pharmacology, Department of Pharmacology, University of Pennsylvania School of Medicine, 421 Curie Blvd, Philadelphia, PA 19104–6160, USA
| |
Collapse
|
34
|
Abstract
The microarraying of chemicals or biomolecules on a glass surface allows for dense storage and miniaturized screening experiments and can be deployed in chemical-biology research or drug discovery. Microarraying allows the production of scores of replicate slides. Small molecule libraries are typically stored as 10 mM DMSO stock solutions, whereas libraries of biomolecules are typically stored in high percentages of glycerol. Thus, a method is required to print such libraries on microarrays, and then assay them against biological targets. By printing either small molecule libraries or biomolecule libraries in an aqueous solvent containing glycerol, each adherent nanodroplet remains fixed at a position on the microarray by surface tension without the use of wells, without evaporating, and without the need for chemically linking the compound to the surface. Importantly, glycerol is a high boiling point solvent that is fully miscible with DMSO and water and has the additional property of stabilizing various enzymes. The nanoliter volume of the droplet forms the reaction compartment once additional reagents are metered onto the microarray, either by aerosol spray deposition or by addressable acoustic dispensing. Incubation of the nanodroplet microarray in a high humidity environment controls the final water content of the reaction. This platform has been validated for fluorescent HTS assays of protease and kinases as well as for fluorogenic substrate profiling of proteases. Label-free HTS is also possible by running nanoliter HTS reactions on a MALDI target for mass spectrometry (MS) analysis without the need for desalting of the samples. A method is described for running nanoliter-scale multicomponent homogeneous reactions followed by label-free MALDI MS spectrometry analysis of the reactions.
Collapse
Affiliation(s)
- Dhaval Gosalia
- Department of Chemical and Biomolecular Engineering, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA, USA
| | | |
Collapse
|
35
|
Deleuze C, De Pauw E, Quinton L. Selective reduction of C=C double bonds in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of microcystins. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2010; 16:91-99. [PMID: 20065523 DOI: 10.1255/ejms.1051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Cyanobacteria are photosynthetic bacteria encountered in various aquatic environments. Some of them are able to produce powerful toxins called cyanotoxins. Among cyanotoxins, microcystins (MCs) constitute a group of closely related cyclic heptapeptides. Their sequences are made up of classical amino acids as well as post- translational modified ones. Interestingly, in vivo metabolism of microcystins seems to be greatly dependent on various minor structural differences and particularly those of the seventh amino acid, which can be either dehydroalanine (or a derivative), dehydroaminobutyric acid (or a derivative), serine or alanine. As a consequence, microcystins have been classified on the basis of the nature of this singular amino acid. A major difficulty in the classification of such toxins is that some of them share the same molecular masses and the same molecular formulas. Consequently, a simple mass measurement is not sufficient to determine the structure and the class of a toxin of interest. Heavy and expensive techniques are used to classify them, such as multi-dimensional nuclear magnetic resonance and amino acid analysis. In this work, a new matrix-assisted laser desorption/ionization time-of-flight method leading to an easy classification of MCs is proposed. The methodology relies on the reductive properties of the matrix 1,5-diaminonaphtalene (1,5-DAN) which appears to be able to selectively reduce the double carbon-carbon bond belonging to the seventh amino acid. Moreover, the yield of reduction seems to be influenced by the degree of substitution of this double bond, allowing a discrimination between dehydroalanine and dehydroaminobutyric acid. This selective reduction was confirmed by the study of three synthetic peptides by mass spectrometry and tandem mass spectrometry. According to these results, the use of reductive matrices seems to be promising in the study of microcystins and in their classification. More generally, 1,5-DAN allows the selective reduction of double carbon-carbon bonds. This property could also be employed in the characterization of others types of compound displaying double bonds (petrochemistry, metabolomics....).
Collapse
Affiliation(s)
- Christelle Deleuze
- GIGA-R: Laboratoire de Spectrométrie de Masse (L.S.M.), Département de Chimie, Université de Liège, Liège, Belgium
| | | | | |
Collapse
|
36
|
Katona M, Kiss K, Angyal V, Kucsma N, Sarkadi B, Takáts Z, Szakács G. A mass spectrometry based functional assay for the quantitative assessment of ABC transporter activity. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2009; 23:3372-3376. [PMID: 19780062 DOI: 10.1002/rcm.4259] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
ATP-Binding Cassette (ABC) transporters are highly expressed in pharmacological barriers limiting the access of drugs to their targets. Since characterization of a compound as a transporter substrate or inhibitor bears significant consequences in drug development, there is a great need for reliable tools that enable the rapid analysis of the transport susceptibility of drugs. Here we describe a simple but very efficient high-performance liquid chromatography/mass spectrometry (HPLC/MS) assay for measuring the ABC transporter-dependent vesicular transport of compounds. In addition, we provide evidence that the requirement for sample preparation can be minimized using desorption electrospray ionization (DESI)-MS, paving the way for a direct, high-throughput investigation of drug-transporter interactions.
Collapse
Affiliation(s)
- Mária Katona
- Institute of Enzymology, Hungarian Academy of Sciences, H-1113 Budapest, Hungary
| | | | | | | | | | | | | |
Collapse
|
37
|
Vanderghem C, Blecker C, Danthine S, Deroanne C, Haubruge E, Guillonneau F, De Pauw E, Francis F. Proteome analysis of the bovine milk fat globule: Enhancement of membrane purification. Int Dairy J 2008. [DOI: 10.1016/j.idairyj.2008.02.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
38
|
Miyagi M, Nakazawa T. Determination of pKa Values of Individual Histidine Residues in Proteins Using Mass Spectrometry. Anal Chem 2008; 80:6481-7. [DOI: 10.1021/ac8009643] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Masaru Miyagi
- Case Center for Proteomics, Department of Pharmacology, Department of Ophthalmology and Visual Sciences, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106-4988, and Department of Chemistry, Nara Women’s University, Nara 630-8506, Japan
| | - Takashi Nakazawa
- Case Center for Proteomics, Department of Pharmacology, Department of Ophthalmology and Visual Sciences, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106-4988, and Department of Chemistry, Nara Women’s University, Nara 630-8506, Japan
| |
Collapse
|
39
|
Borges CR, Jarvis JW, Oran PE, Rogers SP, Nelson RW. Population studies of intact vitamin D binding protein by affinity capture ESI-TOF-MS. J Biomol Tech 2008; 19:167-176. [PMID: 19137103 PMCID: PMC2563926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Blood plasma proteins with molecular weights greater than approximately 30 kDa are refractory to comprehensive, high-throughput qualitative characterization of microheterogeneity across human populations. Analytical techniques for obtaining high mass resolution for targeted, intact protein characterization and, separately, high sample throughput exist, but efficient means of coupling these assay characteristics remain rather limited. This article discusses the impetus for analyzing intact proteins in a targeted manner across populations and describes the methodology required to couple mass spectrometric immunoassay with electrospray ionization mass spectrometry for the purpose of qualitatively characterizing a prototypical large plasma protein, vitamin D binding protein, across populations.
Collapse
Affiliation(s)
- Chad R Borges
- Molecular Biosignatures Analysis Unit, The Biodesign Institute at Arizona State University, Tempe, AZ 85287, USA.
| | | | | | | | | |
Collapse
|
40
|
Nemes P, Barton AA, Li Y, Vertes A. Ambient Molecular Imaging and Depth Profiling of Live Tissue by Infrared Laser Ablation Electrospray Ionization Mass Spectrometry. Anal Chem 2008; 80:4575-82. [DOI: 10.1021/ac8004082] [Citation(s) in RCA: 206] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Peter Nemes
- Department of Chemistry, W. M. Keck Institute for Proteomics Technology and Applications, George Washington University, Washington, D.C. 20052
| | - Alexis A. Barton
- Department of Chemistry, W. M. Keck Institute for Proteomics Technology and Applications, George Washington University, Washington, D.C. 20052
| | - Yue Li
- Department of Chemistry, W. M. Keck Institute for Proteomics Technology and Applications, George Washington University, Washington, D.C. 20052
| | - Akos Vertes
- Department of Chemistry, W. M. Keck Institute for Proteomics Technology and Applications, George Washington University, Washington, D.C. 20052
| |
Collapse
|
41
|
Tsao CW, Kumar P, Liu J, DeVoe DL. Dynamic Electrowetting on Nanofilament Silicon for Matrix-Free Laser Desorption/Ionization Mass Spectrometry. Anal Chem 2008; 80:2973-81. [DOI: 10.1021/ac7026029] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chia-Wen Tsao
- Department of Mechanical Engineering, University of Maryland, College Park Maryland 20742
| | - Parshant Kumar
- Department of Mechanical Engineering, University of Maryland, College Park Maryland 20742
| | - Jikun Liu
- Department of Mechanical Engineering, University of Maryland, College Park Maryland 20742
| | - Don L. DeVoe
- Department of Mechanical Engineering, University of Maryland, College Park Maryland 20742
| |
Collapse
|
42
|
Hyytiä-Trees EK, Cooper K, Ribot EM, Gerner-Smidt P. Recent developments and future prospects in subtyping of foodborne bacterial pathogens. Future Microbiol 2007; 2:175-85. [PMID: 17661654 DOI: 10.2217/17460913.2.2.175] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Infections caused by foodborne bacterial pathogens continue to be a major public health issue around the world. During the past decade, pulsed-field gel electrophoresis (PFGE) has become the gold standard for molecular subtyping and source tracking of most foodborne bacteria. Owing to problems inherent in PFGE technology, new methods have been developed focusing on DNA sequence-based subtyping. This review discusses the feasibility of using multilocus sequence typing, multiple-locus variable-number tandem repeat analysis, single nucleotide polymorphisms, microarrays, whole genome sequencing and mass spectrometry for subtyping foodborne bacterial pathogens.
Collapse
|
43
|
Veenstra TD. Electrospray ionization mass spectrometry in the study of biomolecular non-covalent interactions. Biophys Chem 2007; 79:63-79. [PMID: 17030314 DOI: 10.1016/s0301-4622(99)00037-x] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/1998] [Revised: 03/17/1999] [Accepted: 03/17/1999] [Indexed: 11/16/2022]
Abstract
In the past mass spectrometry has been limited to the study of small, stable molecules, however, with the emergence of electrospray ionization mass spectrometry (ESI-MS) large biomolecules as well as non-covalent biomolecular complexes can be studied. ESI-MS has been used to study non-covalent interactions involving proteins with metals, ligands, peptides, oligonucleotides, as well as other proteins. Although complementary to other well-established techniques such as circular dichroism and fluorescence spectroscopy, ESI-MS offers some advantages in speed, sensitivity, and directness particularly in the determination of the stoichiometry of the complex. One major advantage is the ability of ESI-MS to provide multiple signals each arising from a distinct population within the sample. In this review I will discuss some of the different types of non-covalent biomolecular interactions that have been studied using ESI-MS, highlighting examples which show the efficacy of using ESI-MS to probe the structure of biomolecular complexes.
Collapse
Affiliation(s)
- T D Veenstra
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratories, PO Box 999, MSIN K8-98, Richland, WA 99352, USA.
| |
Collapse
|
44
|
Lau CC, Yue PYK, Chui SH, Chui AKK, Yam WC, Wong RNS. Detection of single nucleotide polymorphisms in hepatitis B virus precore/basal core promoter region by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Anal Biochem 2007; 366:93-5. [PMID: 17498640 DOI: 10.1016/j.ab.2007.03.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2006] [Revised: 03/06/2007] [Accepted: 03/07/2007] [Indexed: 11/25/2022]
Affiliation(s)
- C C Lau
- Department of Biology, Science Faculty, Hong Kong Baptist University, Hong Kong
| | | | | | | | | | | |
Collapse
|
45
|
Zhu ZT, Li YM, Guo YT, Sun M, Zhao YF. Preliminary ESI-MS and MALDI-TOF Analysis on Phosphorylated Tetrapeptides with Xaa-Pro Motif. PHOSPHORUS SULFUR 2007. [DOI: 10.1080/10426500601059482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Zhen-Tai Zhu
- a The Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry , Tsinghua University , Beijing , P. R. China
| | - Yan-Mei Li
- a The Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry , Tsinghua University , Beijing , P. R. China
| | - Yan-Ting Guo
- a The Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry , Tsinghua University , Beijing , P. R. China
| | - Ming Sun
- a The Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry , Tsinghua University , Beijing , P. R. China
| | - Yu-Fen Zhao
- a The Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry , Tsinghua University , Beijing , P. R. China
| |
Collapse
|
46
|
Mathur S, Badertscher M, Scott M, Zenobi R. Critical evaluation of mass spectrometric measurement of dissociation constants: accuracy and cross-validation against surface plasmon resonance and circular dichroism for the calmodulin–melittin system. Phys Chem Chem Phys 2007; 9:6187-98. [DOI: 10.1039/b707946j] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
|
47
|
Li Z, Yalcin T, Cassady CJ. C-terminal amino acid residue loss for deprotonated peptide ions containing glutamic acid, aspartic acid, or serine residues at the C-terminus. JOURNAL OF MASS SPECTROMETRY : JMS 2006; 41:939-49. [PMID: 16810639 DOI: 10.1002/jms.1053] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Deprotonated peptides containing C-terminal glutamic acid, aspartic acid, or serine residues were studied by sustained off-resonance irradiation collision-induced dissociation (SORI-CID) in a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer with ion production by electrospray ionization (ESI). Additional studies were performed by post source decay (PSD) in a matrix-assisted laser desorption ionization/time-of-flight (MALDI/TOF) mass spectrometer. This work included both model peptides synthesized in our laboratory and bioactive peptides with more complex sequences. During SORI-CID and PSD, [M - H]- and [M - 2H]2- underwent an unusual cleavage corresponding to the elimination of the C-terminal residue. Two mechanisms are proposed to occur. They involve nucleophilic attack on the carbonyl carbon of the adjacent residue by either the carboxylate group of the C-terminus or the side chain carboxylate group of C-terminal glutamic acid and aspartic acid residues. To confirm the proposed mechanisms, AAAAAD was labelled by 18O specifically on the side chain of the aspartic acid residue. For peptides that contain multiple C-terminal glutamic acid residues, each of these residues can be sequentially eliminated from the deprotonated ions; a driving force may be the formation of a very stable pyroglutamatic acid neutral. For peptides with multiple aspartic acid residues at the C-terminus, aspartic acid residue loss is not sequential. For peptides with multiple serine residues at the C-terminus, C-terminal residue loss is sequential; however, abundant loss of other neutral molecules also occurs. In addition, the presence of basic residues (arginine or lysine) in the sequence has no effect on C-terminal residue elimination in the negative ion mode.
Collapse
Affiliation(s)
- Zhong Li
- Department of Chemistry, The University of Alabama, Tuscaloosa, AL 35487, USA
| | | | | |
Collapse
|
48
|
Su J, Rajapaksha TW, Peter ME, Mrksich M. Assays of Endogenous Caspase Activities: A Comparison of Mass Spectrometry and Fluorescence Formats. Anal Chem 2006; 78:4945-51. [PMID: 16841915 DOI: 10.1021/ac051974i] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This paper describes a label-free assay for measuring endogenous caspase protease activities in cell lysates. The assay format, termed SAMDI-MS (self-assembled monolayers for matrix assisted laser desorption ionization time-of-flight mass spectrometry), is based on the enzymatic modification of peptides immobilized to monolayer substrates, followed by direct detection of the products with mass spectrometry. Monolayers presenting peptide substrates for either caspase-3 or -8 were treated with lysates from Jurkat cells that were stimulated with staurosporine and SKW6.4 cells that were stimulated with LzCD95L. In both cases, the SAMDI assays reported on the activation of endogenous caspase enzymes with levels of detection that are similar to those observed using the commonly employed fluorogenic assays. The use of longer peptide substrates, which are not compatible with the fluorogenic assays, provided for a better resolution of the two caspase activities. This work is significant because it demonstrates that the SAMDI assay can be used to measure endogenous enzyme activities and because it avoids the loss of activity and specificity that often accompany label-dependent assay formats.
Collapse
Affiliation(s)
- Jing Su
- Howard Hughes Medical Institute and Department of Chemistry, University of Chicago, Chicago, Illinois 60637, USA
| | | | | | | |
Collapse
|
49
|
Fliegel D, Fuhrer K, Gonin M, Günther D. Evaluation of a pulsed glow discharge time-of-flight mass spectrometer as a detector for gas chromatography and the influence of the glow discharge source parameters on the information volume in chemical speciation analysis. Anal Bioanal Chem 2006; 386:169-79. [PMID: 16773303 DOI: 10.1007/s00216-006-0515-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2006] [Revised: 04/19/2006] [Accepted: 04/26/2006] [Indexed: 10/24/2022]
Abstract
The figures of merit of a pulsed glow discharge time-of-flight mass spectrometer (GD-TOFMS) as a detector for gas chromatography (GC) analysis were evaluated. The mass resolution for the GD-TOFMS was determined on FWHM in the high mass range (208Pb+) as high as 5,500. Precision of 400 subsequent analyses was calculated on 63Cu+ to be better than 1% RSD with no significant drift over the time of the analysis. Isotope precision based on the 63Cu+/65Cu+ ratio over 400 analyses was 1.5% RSD. The limits of detection for gaseous analytes (toluene in methanol as solvent) were determined to be as low as several hundred ppb or several hundred pg absolute without using any pre-concentration technique. Furthermore, the different GD source parameters like capillary distance, cathode-anode spacing, and GD source pressure with regards to the accessible elemental, structural, and molecular information were evaluated. It was demonstrated that each of these parameters has severe influence on the ratio of elemental, structural, and parent molecular information in chemical speciation analysis.
Collapse
Affiliation(s)
- Daniel Fliegel
- Laboratory of Inorganic Chemistry, ETH Zürich, 8093, Zürich, Switzerland,
| | | | | | | |
Collapse
|
50
|
Lelais G, Seebach D, Jaun B, Mathad R, Flögel O, Rossi F, Campo M, Wortmann A. β-Peptidic Secondary Structures Fortified and Enforced by Zn2+ Complexation – On the Way toβ-Peptidic Zinc Fingers? Helv Chim Acta 2006. [DOI: 10.1002/hlca.339] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|