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Prims S, Van Ginneken C, Van Ostade X, Casteleyn C. Welfare Assessment in Pigs Using the Salivary Proteome. Animals (Basel) 2024; 14:1703. [PMID: 38891749 PMCID: PMC11171187 DOI: 10.3390/ani14111703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 06/21/2024] Open
Abstract
Identifying the potential presence of stress at the pig farm is fundamental since it affects pig welfare. As a result, a reliable and straightforward tool to monitor stress could record the welfare status of the animals. Although numerous methods to assess the welfare of pigs have been developed in the past, no gold standard has been established yet. Recently, the value of saliva as a tool to identify chronic stress in piglets was explored, as it can be collected fast and non-invasively. Since the protein composition, i.e., the proteome of porcine saliva, responds to stress, the affected proteins could be used as salivary stress biomarkers. The present review first defines stress and its relationship with welfare. Next, the porcine gland-specific salivary proteome is characterized. Finally, six potential salivary biomarkers for stress are proposed, i.e., odorant-binding protein, vomeromodulin-like protein, chitinase, lipocalin-1, long palate lung and nasal epithelium protein, and alpha-2-HS-glycoprotein.
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Affiliation(s)
- Sara Prims
- Comparative Perinatal Development, Department of Veterinary Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium; (S.P.); (C.V.G.)
| | - Chris Van Ginneken
- Comparative Perinatal Development, Department of Veterinary Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium; (S.P.); (C.V.G.)
| | - Xaveer Van Ostade
- Laboratory of Protein Science, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium;
| | - Christophe Casteleyn
- Comparative Perinatal Development, Department of Veterinary Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium; (S.P.); (C.V.G.)
- Department of Morphology, Medical Imaging, Orthopedics, Physiotherapy and Nutrition, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
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Wang H, Jin H, Chai R, Li H, Fan J, Wang Y, Wei F, Ma S. An Analysis of Polysaccharides from Eight Plants by a Novel Heart-Cutting Two-Dimensional Liquid Chromatography Method. Foods 2024; 13:1173. [PMID: 38672845 PMCID: PMC11049114 DOI: 10.3390/foods13081173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/07/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Natural polysaccharides are important active biomolecules. However, the analysis and structural characterization of polysaccharides are challenging tasks that often require multiple techniques and maps to reflect their structural features. This study aimed to propose a new heart-cutting two-dimensional liquid chromatography (2D-LC) method for separating and analyzing polysaccharides to explore the multidimensional information of polysaccharide structure in a single map. That is, the first-dimension liquid chromatography (1D-LC) presents molecular-weight information, and the second-dimension liquid chromatography (2D-LC) shows the fingerprints of polysaccharides. In this 2D-LC system, the size-exclusion chromatography-hydrophilic interaction chromatography (SEC-HILIC) model was established. Coupling with a charged aerosol detector (CAD) eliminated the need for the derivatization of the polysaccharide sample, allowing the whole process to be completed within 80 min. The methods were all validated in terms of precision, linearity, stability, and repeatability. The capability of the new 2D-LC method was demonstrated in determining various species of natural polysaccharides. Our experimental data demonstrated the feasibility of the whole systematic approach, opening the door for further applications in the field of natural polysaccharide analysis.
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Affiliation(s)
- Haonan Wang
- National Institutes for Food and Drug Control, National Medical Products Administration, Beijing 102629, China
- National Institutes for Food and Drug Control, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Hongyu Jin
- National Institutes for Food and Drug Control, National Medical Products Administration, Beijing 102629, China
| | - Ruiping Chai
- Thermo Fisher Scientific (China) Co., Ltd., Shanghai 201206, China
| | - Hailiang Li
- National Institutes for Food and Drug Control, National Medical Products Administration, Beijing 102629, China
| | - Jing Fan
- National Institutes for Food and Drug Control, National Medical Products Administration, Beijing 102629, China
| | - Ying Wang
- National Institutes for Food and Drug Control, National Medical Products Administration, Beijing 102629, China
| | - Feng Wei
- National Institutes for Food and Drug Control, National Medical Products Administration, Beijing 102629, China
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3
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Castillo J, de la Iglesia A, Leiva M, Jodar M, Oliva R. Proteomics of human spermatozoa. Hum Reprod 2023; 38:2312-2320. [PMID: 37632247 DOI: 10.1093/humrep/dead170] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 07/12/2023] [Indexed: 08/27/2023] Open
Abstract
Proteomic methodologies offer a robust approach to identify and quantify thousands of proteins from semen components in both fertile donors and infertile patients. These strategies provide an unprecedented discovery potential, which many research teams are currently exploiting. However, it is essential to follow a suitable experimental design to generate robust data, including proper purification of samples, appropriate technical procedures to increase identification throughput, and data analysis following quality criteria. More than 6000 proteins have been described so far through proteomic analyses in the mature sperm cell, increasing our knowledge on processes involved in sperm function, intercommunication between spermatozoa and seminal fluid, and the transcriptional origin of the proteins. These data have been complemented with comparative studies to ascertain the potential role of the identified proteins on sperm maturation and functionality, and its impact on infertility. By comparing sperm protein profiles, many proteins involved in the acquisition of fertilizing ability have been identified. Furthermore, altered abundance of specific protein groups has been observed in a wide range of infertile phenotypes, including asthenozoospermia, oligozoospermia, and normozoospermia with unsuccessful assisted reproductive techniques outcomes, leading to the identification of potential clinically useful protein biomarkers. Finally, proteomics has been used to evaluate alterations derived from semen sample processing, which might have an impact on fertility treatments. However, the intrinsic heterogeneity and inter-individual variability of the semen samples have resulted in a relatively low overlap among proteomic reports, highlighting the relevance of combining strategies for data validation and applying strict criteria for proteomic data analysis to obtain reliable results. This mini-review provides an overview of the most critical steps to conduct robust sperm proteomic studies, the most relevant results obtained so far, and potential next steps to increase the impact of sperm proteomic data.
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Affiliation(s)
- Judit Castillo
- Molecular Biology of Reproduction and Development Research Group, Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Fundació Clínic per a la Recerca Biomèdica, Universitat de Barcelona (UB), Barcelona, Spain
| | - Alberto de la Iglesia
- Molecular Biology of Reproduction and Development Research Group, Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Fundació Clínic per a la Recerca Biomèdica, Universitat de Barcelona (UB), Barcelona, Spain
| | - Marina Leiva
- Molecular Biology of Reproduction and Development Research Group, Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Fundació Clínic per a la Recerca Biomèdica, Universitat de Barcelona (UB), Barcelona, Spain
| | - Meritxell Jodar
- Molecular Biology of Reproduction and Development Research Group, Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Fundació Clínic per a la Recerca Biomèdica, Universitat de Barcelona (UB), Barcelona, Spain
- Biochemistry and Molecular Genetics Service, Biomedical Diagnostic Center (CDB), Hospital Clínic de Barcelona, Barcelona, Spain
| | - Rafael Oliva
- Molecular Biology of Reproduction and Development Research Group, Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Fundació Clínic per a la Recerca Biomèdica, Universitat de Barcelona (UB), Barcelona, Spain
- Biochemistry and Molecular Genetics Service, Biomedical Diagnostic Center (CDB), Hospital Clínic de Barcelona, Barcelona, Spain
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Molenaar SRA, Bos TS, Boelrijk J, Dahlseid TA, Stoll DR, Pirok BWJ. Computer-driven optimization of complex gradients in comprehensive two-dimensional liquid chromatography. J Chromatogr A 2023; 1707:464306. [PMID: 37639847 DOI: 10.1016/j.chroma.2023.464306] [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: 05/30/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 08/31/2023]
Abstract
Method development in comprehensive two-dimensional liquid chromatography (LC × LC) is a complicated endeavor. The dependency between the two dimensions and the possibility of incorporating complex gradient profiles, such as multi-segmented gradients or shifting gradients, renders method development by "trial-and-error" time-consuming and highly dependent on user experience. In this work, an open-source algorithm for the automated and interpretive method development of complex gradients in LC × LC-mass spectrometry (MS) was developed. A workflow was designed to operate within a closed-loop that allowed direct interaction between the LC × LC-MS system and a data-processing computer which ran in an unsupervised and automated fashion. Obtaining accurate retention models in LC × LC is difficult due to the challenges associated with the exact determination of retention times, curve fitting because of the use of gradient elution, and gradient deformation. Thus, retention models were compared in terms of repeatability of determination. Additionally, the design of shifting gradients in the second dimension and the prediction of peak widths were investigated. The algorithm was tested on separations of a tryptic digest of a monoclonal antibody using an objective function that included the sum of resolutions and analysis time as quality descriptors. The algorithm was able to improve the separation relative to a generic starting method using these complex gradient profiles after only four method-development iterations (i.e., sets of chromatographic conditions). Further iterations improved retention time and peak width predictions and thus the accuracy in the separations predicted by the algorithm.
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Affiliation(s)
- Stef R A Molenaar
- van 't Hoff Institute for Molecular Sciences, Analytical Chemistry Group, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; Centre for Analytical Sciences Amsterdam (CASA), Amsterdam, The Netherlands
| | - Tijmen S Bos
- Centre for Analytical Sciences Amsterdam (CASA), Amsterdam, The Netherlands; Division of Bioanalytical Chemistry, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Jim Boelrijk
- Centre for Analytical Sciences Amsterdam (CASA), Amsterdam, The Netherlands; AMLab, Informatics Institute, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; AI4Science Lab, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Tina A Dahlseid
- Department of Chemistry, Gustavus Adolphus College, Saint Peter, MN 56082, United States
| | - Dwight R Stoll
- Department of Chemistry, Gustavus Adolphus College, Saint Peter, MN 56082, United States
| | - Bob W J Pirok
- van 't Hoff Institute for Molecular Sciences, Analytical Chemistry Group, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; Centre for Analytical Sciences Amsterdam (CASA), Amsterdam, The Netherlands.
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5
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Zhang Q, Du H, Zhang Y. Recent progress on the detection of animal-derived food stimulants using mass spectrometry-based techniques. Front Nutr 2023; 10:1226530. [PMID: 37533577 PMCID: PMC10391635 DOI: 10.3389/fnut.2023.1226530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 06/28/2023] [Indexed: 08/04/2023] Open
Abstract
Background The misuse of animal-derived stimulants in food is becoming increasingly common, and mass spectrometry (MS) is used extensively for their detection and analysis. There is a growing demand for abused-substances detection, highlighting the need for systematic studies on the advantages of MS-based methods in detecting animal-derived stimulants. Objective We reviewed the application of chromatography-mass spectrometry to the screening and detection of food stimulants of animal origin. Specifically, we analyzed four common animal sources of synthetic steroids, β-receptor agonists, zearalenol (ZAL), and glucocorticoids. We also explored the potential of using chromatography-mass spectrometry to detect and analyze animal-derived foods. Methods We searched and screened the Web of Science and Google Scholar databases until April 2023. Our inclusion criteria included a publication year within the last 5 years, publication language of English, and the research fields of food analysis, environmental chemistry, and polymer science. Our keywords were "mass spectrometry," "anabolic androgenic steroids," "β-2agonists," "glucocorticoids," "zearalenone," and "doping." Results Although traditional techniques such as thin-layer chromatography and enzyme-linked immunoassays are simple, fast, and suitable for the initial screening of bulk products, they are limited by their relatively high detection limits. Among the methods based on MS, gas chromatography-mass spectrometry and liquid chromatography-tandem mass spectrometry are the most widely used for detecting food doping agents of animal origin. However, a sensitive method with high repeatability and a short analysis time for a large number of samples is still required. Advances in MS have enabled the detection of extremely low concentrations of these substances. Combining different techniques, such as high-resolution mass spectrometry, ultra-high performance liquid chromatography-tandem mass spectrometry, gas chromatography-combustion-isotope ratio mass spectrometry, ultra-high performance liquid chromatography-high resolution mass spectrometry, and two-dimensional chromatography, offers significant advantages for detecting trace illicit drugs in animal-derived foods. Due to advances in assay technology and sample preparation methods, sample collection and storage methods such as dried blood spots, dried urine spots, and volumetric absorptive microsampling are increasingly accepted because of their increased stability and cost-effectiveness. Significance MS significantly improves the efficiency of detecting doping agents of animal origin. With the continuous development of MS technology, its application in the fields of doping detection and the analysis of doping agents of animal origin is expected to become more extensive.
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Affiliation(s)
- Qiang Zhang
- Graduate School, Capital University of Physical Education and Sports, Beijing, China
| | - Hongying Du
- Tangshan Normal University, Tangshan, Hebei Province, China
| | - Yingjian Zhang
- Faculty of Sports, Langfang Normal University, Langfang, Hebei Province, China
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Zhu H, Wu X, Huo J, Hou J, Long H, Zhang Z, Wang B, Tian M, Chen K, Guo D, Lei M, Wu W. A five-dimensional data collection strategy for multicomponent discovery and characterization in Traditional Chinese Medicine: Gastrodia Rhizoma as a case study. J Chromatogr A 2021; 1653:462405. [PMID: 34332318 DOI: 10.1016/j.chroma.2021.462405] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 01/01/2023]
Abstract
Establishing the identity of bioactive compounds to control the quality of Traditional Chinese Medicines is made more challenging by the complexity of the metabolite matrix, the existence of isomers, and the range of compound concentration and polarity observed between individual samples of the same plant in a multicomponent preparation. In addition, LC-MS analysis has limited capability for the separation and analysis of potentially important trace compounds and isomers, which hinders the comprehensive metabolite characterization of functional foods and Traditional Natural Medicine. To facilitate and improve the chemical composition characterization and enhance metabolite discernment, a comprehensive strategy was developed which integrates ion mobility mass spectrometry (IMS) with offline two-dimensional liquid chromatography based on hydrophilic interaction chromatography (HILIC) and conventional reversed phase (RP) C18 chromatography. Through application of the HILIC × RP offline 2D-LC approach, trace compounds were enriched and separated promoting a more efficient and detailed analysis of the matrix complexity. Comprehensive non-targeted multidimensional data (Rt1D, Rt2D, MS, CCS and MS/MS) and data-independent-acquisition (DIA) mass data of the metabolites in complex food and drug samples were obtained in the IMS-DIA-MS/MS mode on a Waters-SYNAPT G2-Si mass spectrometer with an ESI source. Through the application of high-efficiency neutral loss (NLs) and diagnostic product ions (DPIs) filter strategies, information from DIA mass data permitted the rapid detection and identification of compounds. The identification coverage of metabolites with low-quality MS/MS data was also improved. In the absence of analytical standards, Collision Cross Section (CCS) prediction and matching strategies based on theoretical chemical structures provided a method to distingish isomers. To demonstrate the efficacy of the technique this comprehensive strategy was applied to the compound characterization of Gastrodia Rhizoma (GR). Characterization of 272 compounds was achieved, including 146 unreported compounds. The results affirm that this comprehensive five-dimensional data collection strategy has the capacity to support the in-depth study of the high level of chemical diversity in Traditional Chinese Medicines.
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Affiliation(s)
- Haodong Zhu
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, PR China; Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xingdong Wu
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Jiangyan Huo
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Jinjun Hou
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Huali Long
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Zijia Zhang
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Bing Wang
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, PR China; Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
| | - Menghua Tian
- Zhaotong Tianma Research Institute, Zhaotong, Yunnan 657000, PR China
| | - Kaixian Chen
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - De'an Guo
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Min Lei
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
| | - Wanying Wu
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
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Development of comprehensive two-dimensional low-flow liquid-chromatography setup coupled to high-resolution mass spectrometry for shotgun proteomics. Anal Chim Acta 2021; 1156:338349. [PMID: 33781465 DOI: 10.1016/j.aca.2021.338349] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 02/09/2021] [Accepted: 02/19/2021] [Indexed: 01/01/2023]
Abstract
Bottom-up proteomics provides often small amounts of highly complex samples that cannot be analysed by direct mass spectrometry (MS). To gain a better insight in the sample composition, liquid chromatography (LC) and (comprehensive) two-dimensional liquid chromatography (2D-LC or LC × LC) can be coupled to the MS. Low-flow separations are attractive for HRMS analysis, but they tend to be lengthy. In this work, a low-flow, online, actively modulated LC × LC system, based on hydrophilic-interaction liquid chromatography (HILIC) in the first dimension and reversed-phase liquid chromatography (RPLC) in the second dimension, was developed to separate complex mixtures of peptides. Miniaturization permitted the analysis of small sample amounts (1-5 μg) and direct coupling with micro-ESI MS (1 μL min-1). All components were focused and automatically transferred from HILIC to RPLC using stationary-phase-assisted active modulation (C18 traps) to deal with solvent-incompatibility or dilution issues. Optimization of the setup was performed for the HILIC columns and the RPLC columns to provide a more efficient separation and higher identification rates than obtained using one-dimensional (1D) LC. A 60% increase in peak capacity was obtained with the 2D setup compared to a 1D-RPLC separation and a 17-34% increase in the number of proteins identified was achieved for the samples analysed (2D-yeast-8280 peptides and 2D-kidney tissue-8843 peptides), without increasing the analysis time (2 h).
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8
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Molenaar SRA, Dahlseid TA, Leme GM, Stoll DR, Schoenmakers PJ, Pirok BWJ. Peak-tracking algorithm for use in comprehensive two-dimensional liquid chromatography - Application to monoclonal-antibody peptides. J Chromatogr A 2021; 1639:461922. [PMID: 33540183 DOI: 10.1016/j.chroma.2021.461922] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 01/14/2021] [Accepted: 01/16/2021] [Indexed: 10/22/2022]
Abstract
A peak-tracking algorithm was developed for use in comprehensive two-dimensional liquid chromatography coupled to mass spectrometry. Chromatographic peaks were tracked across two different chromatograms, utilizing the available spectral information, the statistical moments of the peaks and the relative retention times in both dimensions. The algorithm consists of three branches. In the pre-processing branch, system peaks are removed based on mass spectra compared to low intensity regions and search windows are applied, relative to the retention times in each dimension, to reduce the required computational power by elimination unlikely pairs. In the comparison branch, similarity between the spectral information and statistical moments of peaks within the search windows is calculated. Lastly, in the evaluation branch extracted-ion-current chromatograms are utilized to assess the validity of the pairing results. The algorithm was applied to peptide retention data recorded under varying chromatographic conditions for use in retention modelling as part of method optimization tools. Moreover, the algorithm was applied to complex peptide mixtures obtained from enzymatic digestion of monoclonal antibodies. The algorithm yielded no false positives. However, due to limitations in the peak-detection algorithm, cross-pairing within the same peaks occurred and six trace compounds remained falsely unpaired.
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Affiliation(s)
- Stef R A Molenaar
- van 't Hoff Institute for Molecular Sciences, Analytical Chemistry Group, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands; Centre for Analytical Sciences Amsterdam (CASA), the Netherlands.
| | - Tina A Dahlseid
- Department of Chemistry, Gustavus Adolphus College, Saint Peter, MN 56082, United States
| | - Gabriel M Leme
- Department of Chemistry, Gustavus Adolphus College, Saint Peter, MN 56082, United States
| | - Dwight R Stoll
- Department of Chemistry, Gustavus Adolphus College, Saint Peter, MN 56082, United States
| | - Peter J Schoenmakers
- van 't Hoff Institute for Molecular Sciences, Analytical Chemistry Group, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands; Centre for Analytical Sciences Amsterdam (CASA), the Netherlands
| | - Bob W J Pirok
- van 't Hoff Institute for Molecular Sciences, Analytical Chemistry Group, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands; Centre for Analytical Sciences Amsterdam (CASA), the Netherlands
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9
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Dos Santos-Silva CA, Zupin L, Oliveira-Lima M, Vilela LMB, Bezerra-Neto JP, Ferreira-Neto JR, Ferreira JDC, de Oliveira-Silva RL, Pires CDJ, Aburjaile FF, de Oliveira MF, Kido EA, Crovella S, Benko-Iseppon AM. Plant Antimicrobial Peptides: State of the Art, In Silico Prediction and Perspectives in the Omics Era. Bioinform Biol Insights 2020; 14:1177932220952739. [PMID: 32952397 PMCID: PMC7476358 DOI: 10.1177/1177932220952739] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 07/30/2020] [Indexed: 12/14/2022] Open
Abstract
Even before the perception or interaction with pathogens, plants rely on constitutively guardian molecules, often specific to tissue or stage, with further expression after contact with the pathogen. These guardians include small molecules as antimicrobial peptides (AMPs), generally cysteine-rich, functioning to prevent pathogen establishment. Some of these AMPs are shared among eukaryotes (eg, defensins and cyclotides), others are plant specific (eg, snakins), while some are specific to certain plant families (such as heveins). When compared with other organisms, plants tend to present a higher amount of AMP isoforms due to gene duplications or polyploidy, an occurrence possibly also associated with the sessile habit of plants, which prevents them from evading biotic and environmental stresses. Therefore, plants arise as a rich resource for new AMPs. As these molecules are difficult to retrieve from databases using simple sequence alignments, a description of their characteristics and in silico (bioinformatics) approaches used to retrieve them is provided, considering resources and databases available. The possibilities and applications based on tools versus database approaches are considerable and have been so far underestimated.
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Affiliation(s)
| | - Luisa Zupin
- Genetic Immunology laboratory, Institute for Maternal and Child Health-IRCCS, Burlo Garofolo, Trieste, Italy
| | - Marx Oliveira-Lima
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, Brazil
| | | | | | | | - José Diogo Cavalcanti Ferreira
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, Brazil.,Departamento de Genética, Instituto Federal de Pernambuco, Pesqueira, Brazil
| | | | | | | | | | - Ederson Akio Kido
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, Brazil
| | - Sergio Crovella
- Genetic Immunology laboratory, Institute for Maternal and Child Health-IRCCS, Burlo Garofolo, Trieste, Italy.,Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
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Issa Isaac N, Philippe D, Nicholas A, Raoult D, Eric C. Metaproteomics of the human gut microbiota: Challenges and contributions to other OMICS. CLINICAL MASS SPECTROMETRY 2019; 14 Pt A:18-30. [DOI: 10.1016/j.clinms.2019.06.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/02/2019] [Accepted: 06/03/2019] [Indexed: 12/22/2022]
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11
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Sun F, Zhuo R, Ma W, Yang D, Su T, Ye L, Xu D, Wang W. From clinic to mechanism: Proteomics-based assessment of angiogenesis in adrenal pheochromocytoma. J Cell Physiol 2019; 234:22057-22070. [PMID: 31106414 DOI: 10.1002/jcp.28769] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 04/13/2019] [Accepted: 04/17/2019] [Indexed: 01/05/2023]
Abstract
Adrenal pheochromocytoma (PCC) is a very rare tumor that stems from chromaffin cells, which can develop into malignant tumor. During the operation, abundant blood vessels were often observed in PCC than other adrenal tumors, which increases the difficulty and risk of the surgery. Therefore, it is important to investigate the mechanism of PCC angiogenesis. Twelve surgical specimens of PCC from Ruijin Hospital, Shanghai Jiaotong University were grouped into high and low microvessel density (MVD) group. They were also divided into rich blood supply and nonenriched blood supply group, according to computed tomography (CT) manifestation. Comparative proteomic analysis based on liquid chromatography-tandem mass spectrometry (LC-MS/MS) and bioinformatics analysis revealed that 206 proteins differentially regulated in the high MVD group compared with low MVD group (p < 0.05). Besides, 61 proteins were discovered to be significantly changed when the 12 samples were grouped according to CT manifestation. By intersecting the differentially changed protein from MVD and CT grouping, 25 proteins were filtered out, with pathological function. COX4I2 was verified to be increased gradually with angiogenesis with increasing severity, and PLAT was shown to be decreased with angiogenesis in PCC, by quantitative reverse-transcription polymerase chain reaction and immunohistochemistry. The quantitative proteomics result indicated that the tumor angiogenesis in PCC is associated with hypoxia. COX4I2 and PLAT were highly correlated with blood supply in PCC which contribute to angiogenesis in PCC, which could be used as biomarkers to better indicate tumor angiogenesis, or targets to regress tumor angiogenesis as treatment.
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Affiliation(s)
- Fukang Sun
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Ran Zhuo
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Wenming Ma
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Da Yang
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Tingwei Su
- Shanghai Key Laboratory for Endocrine Tumors, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of Chinese Health Ministry, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China.,Laboratory for Endocrine and Metabolic Diseases of Institute of Health Science, Shanghai Jiao Tong University School of Medicine and Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Lei Ye
- Shanghai Key Laboratory for Endocrine Tumors, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of Chinese Health Ministry, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China.,Laboratory for Endocrine and Metabolic Diseases of Institute of Health Science, Shanghai Jiao Tong University School of Medicine and Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Danfeng Xu
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Weiqing Wang
- Shanghai Key Laboratory for Endocrine Tumors, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of Chinese Health Ministry, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China.,Laboratory for Endocrine and Metabolic Diseases of Institute of Health Science, Shanghai Jiao Tong University School of Medicine and Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
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12
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Zhang D, Lan D, Pang X, Cui B, Bai L, Liu H, Yan H. Separation of proteins from complex bio-matrix samples using a double-functionalized polymer monolithic column. Analyst 2017; 143:280-288. [PMID: 29184931 DOI: 10.1039/c7an01491k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A double-functionalized polymer monolithic column was fabricated within the confines of a stainless-steel column (50 mm × 4.6 mm i.d.) via a facile method using iron porphyrin, ionic liquid (1-allyl-3-methylimidazolium chloride) and 1,10-decanediol dimethacrylate as tri-monomers; ethylene dimethacrylate as a crosslinker; polyethylene glycol 400 and N,N-dimethylformamide as co-porogens; benzoyl peroxide and N,N-dimethyl aniline as the redox initiation system. Results obtained from scanning electron microscopy, nitrogen adsorption-desorption, and mercury intrusion porosimetry confirmed the uniform pore structure and the pore size distribution of macro-pores. The home-made monolith was further characterized by elemental analysis to investigate the elemental composition of Fe supplied by iron porphyrin, confirming the synthetic process. The resulting optimized monolithic column was used as the stationary phase in high performance liquid chromatography for separating proteins, such as mixture of standard proteins, egg white, and human plasma, exhibiting good selectivity and high performance. It is worth noting that the home-made double-functionalized polymer monolithic column shows excellent selectivity for fractionation separation of human plasma proteins, and it is a promising separation tool for complex bio-samples in proteomic research.
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Affiliation(s)
- Doudou Zhang
- College of Pharmaceutical Sciences, Hebei University, Baoding, 071002, China.
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13
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Zhuo Y, Wu JL, Yan X, Guo MQ, Liu N, Zhou H, Liu L, Li N. Strategy for Hepatotoxicity Prediction Induced by Drug Reactive Metabolites Using Human Liver Microsome and Online 2D-Nano-LC-MS Analysis. Anal Chem 2017; 89:13167-13175. [DOI: 10.1021/acs.analchem.7b02684] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yue Zhuo
- State
Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao
| | - Jian-Lin Wu
- State
Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao
| | - Xiaojing Yan
- State
Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao
- Changzhou Affiliated Hospital of Nanjing University of Chinese Medicine, 25 Heping North Road, Changzhou 213003, China
| | - Ming-Quan Guo
- Key
Laboratory of Plant Germplasm Enhancement and Specialty Agriculture,
Wuhan Botanical Garden, Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Ning Liu
- Central
Laboratory, Second Hospital of Jilin University, Changchun, China
| | - Hua Zhou
- State
Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao
| | - Liang Liu
- State
Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao
| | - Na Li
- State
Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao
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14
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Fractionation separation of human plasma proteins using HPLC with a homemade iron porphyrin based monolithic column. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1068-1069:358-364. [DOI: 10.1016/j.jchromb.2017.11.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/01/2017] [Accepted: 11/02/2017] [Indexed: 11/18/2022]
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15
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Pienimaeki‐Roemer A, Konovalova T, Musri MM, Sigruener A, Boettcher A, Meister G, Schmitz G. Transcriptomic profiling of platelet senescence and platelet extracellular vesicles. Transfusion 2016; 57:144-156. [DOI: 10.1111/trf.13896] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 07/09/2016] [Accepted: 07/17/2016] [Indexed: 12/12/2022]
Affiliation(s)
| | - Tatiana Konovalova
- Institute for Clinical Chemistry and Laboratory Medicine, University Clinic of Regensburg
| | - Melina M. Musri
- Institute for Biochemistry I, Faculty of Biology and Preclinical Medicine, University of RegensburgRegensburg Germany
| | - Alexander Sigruener
- Institute for Clinical Chemistry and Laboratory Medicine, University Clinic of Regensburg
| | - Alfred Boettcher
- Institute for Clinical Chemistry and Laboratory Medicine, University Clinic of Regensburg
| | - Gunter Meister
- Institute for Biochemistry I, Faculty of Biology and Preclinical Medicine, University of RegensburgRegensburg Germany
| | - Gerd Schmitz
- Institute for Clinical Chemistry and Laboratory Medicine, University Clinic of Regensburg
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16
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Sidhu R, Jiang H, Farhat NY, Carrillo-Carrasco N, Woolery M, Ottinger E, Porter FD, Schaffer JE, Ory DS, Jiang X. A validated LC-MS/MS assay for quantification of 24(S)-hydroxycholesterol in plasma and cerebrospinal fluid. J Lipid Res 2015; 56:1222-33. [PMID: 25866316 PMCID: PMC4442878 DOI: 10.1194/jlr.d058487] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Indexed: 11/20/2022] Open
Abstract
24(S)-hydroxycholesterol [24(S)-HC] is a cholesterol metabolite that is formed almost exclusively in the brain. The concentrations of 24(S)-HC in cerebrospinal fluid (CSF) and/or plasma might be a sensitive marker of altered cholesterol metabolism in the CNS. A highly sensitive 2D-LC-MS/MS assay was developed for the quantification of 24(S)-HC in human plasma and CSF. In the development of an assay for 24(S)-HC in CSF, significant nonspecific binding of 24(S)-HC was observed and resolved with the addition of 2.5% 2-hydroxypropyl-β-cyclodextrin (HP-β-CD) into CSF samples. The sample preparation consists of liquid-liquid extraction with methyl-tert-butyl ether and derivatization with nicotinic acid. Good linearity was observed in a range from 1 to 200 ng/ml and from 0.025 to 5 ng/ml, for plasma and CSF, respectively. Acceptable precision and accuracy were obtained for concentrations over the calibration curve ranges. Stability of 24(S)-HC was reported under a variety of storage conditions. This method has been successfully applied to support a National Institutes of Health-sponsored clinical trial of HP-β-CD in Niemann-Pick type C1 patients, in which 24(S)-HC is used as a pharmacodynamic biomarker.
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Affiliation(s)
- Rohini Sidhu
- Diabetic Cardiovascular Disease Center, Washington University School of Medicine, St. Louis, MO 63110
| | - Hui Jiang
- Diabetic Cardiovascular Disease Center, Washington University School of Medicine, St. Louis, MO 63110
| | - Nicole Y Farhat
- Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Nuria Carrillo-Carrasco
- Therapeutics for Rare and Neglected Diseases National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
| | - Myra Woolery
- Nursing Department, National Institutes of Health, Bethesda, MD 20892
| | - Elizabeth Ottinger
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
| | - Forbes D Porter
- Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Jean E Schaffer
- Diabetic Cardiovascular Disease Center, Washington University School of Medicine, St. Louis, MO 63110
| | - Daniel S Ory
- Diabetic Cardiovascular Disease Center, Washington University School of Medicine, St. Louis, MO 63110
| | - Xuntian Jiang
- Diabetic Cardiovascular Disease Center, Washington University School of Medicine, St. Louis, MO 63110
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17
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Use of generic LC–MS/MS assays to characterize atypical PK profile of a biotherapeutic monoclonal antibody. Bioanalysis 2014; 6:3225-35. [DOI: 10.4155/bio.14.167] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Background: The fully human monoclonal antibody mAb123, which binds to and neutralizes chemokine motif ligand-21 (CCL21) displays a faster clearance in cynomolgus monkey compared with typical IgG kinetics. A direct and an immunoaffinity LC–MS/MS assays were developed to compare with the previously established ligand-binding assays (LBAs). Results: A strong correlation of LC–MS/MS pharmacokinetic data with LBA data confirmed the rapid drug disposition of mAb123 is an intrinsic property of the molecule, rather than interference of anti-mAb123 antibodies in the LBA. Conclusion: The data illustrate that in cases of unexpected results from LBA, application of orthogonal bioanalytical techniques such as LC–MS/MS can help in in interpretation of pharmacokinetic as determined by LBAs.
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18
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Iqbal J, Li W, Hasan M, Liu K, Awan U, Saeed Y, Zhang Y, Muhammad Khan A, Shah A, Qing H, Deng Y. Differential expression of specific cellular defense proteins in rat hypothalamus under simulated microgravity induced conditions: comparative proteomics. Proteomics 2014; 14:1424-33. [PMID: 24648329 DOI: 10.1002/pmic.201400019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 02/16/2014] [Accepted: 03/10/2014] [Indexed: 12/14/2022]
Abstract
Microgravity severely halts the structural and functional cerebral capacity of astronauts especially affecting their brains due to the stress produced by cephalic fluid shift. We employed a rat tail suspension model to substantiate simulated microgravity (SM) in brain. In this study, comparative mass spectrometry was applied in order to demonstrate the differential expression of 17 specific cellular defense proteins. Gamma-enolase, peptidyl-prolyl cis-trans isomerase A, glial fibrillary acidic protein, heat shock protein HSP 90-alpha, 10 kDa heat shock protein, mitochondrial, heat shock cognate 71 kDa protein, superoxide dismutase 1 and dihydropyrimidinase-related protein 2 were found to be upregulated by HPLC/ESI-TOF. Furthermore, five differentially expressed proteins including 60 kDa heat shock protein, mitochondrial, heat shock protein HSP 90-beta, peroxiredoxin-2, stress-induced-phosphoprotein, and UCHL-1 were found to be upregulated by HPLC/ESI-Q-TOF MS. In addition, downregulated proteins include cytochrome C, superoxide dismutase 2, somatic, and excitatory amino acid transporter 1 and protein DJ-1. Validity of MS results was successfully performed by Western blot analysis of DJ-1 protein. This study will not only help to understand the neurochemical responses produced under microgravity but also will give future direction to cure the proteomic losses and their after effects in astronauts.
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Affiliation(s)
- Javed Iqbal
- School of Life Sciences, Beijing Institute of Technology, Beijing, P. R. China
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19
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Paoletti AC, Zybailov B, Washburn MP. Principles and applications of Multidimensional Protein Identification Technology. Expert Rev Proteomics 2014; 1:275-82. [PMID: 15966824 DOI: 10.1586/14789450.1.3.275] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Multidimensional chromatography coupled to tandem mass spectrometry is an emerging technique for the analysis of proteomes and is rapidly being implemented by many researchers for proteomic analysis. In this technology profile, a particular proteomic approach known as multidimensional protein identification technology (MudPIT) is discussed. In MudPIT, a biphasic microcapillary column is packed with high-performance liquid chromatography grade reversed phase and strong cation exchange packing materials, loaded with a complex peptide mixture and placed in line with quaternary high-performance liquid chromatography and a tandem mass spectrometer. MudPIT has the capability to analyze highly complex proteomic mixtures such as whole proteomes, organelles and protein complexes.
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Affiliation(s)
- Andrew C Paoletti
- Stowers Institute for Medical Research, 1000 E. 50th St., Kansas City, MO 64110, USA.
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20
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Liuni P, Wilson DJ. Understanding and optimizing electrospray ionization techniques for proteomic analysis. Expert Rev Proteomics 2014; 8:197-209. [DOI: 10.1586/epr.10.111] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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21
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Valsasina B, Kalisz HM, Isacchi A. Kinase selectivity profiling by inhibitor affinity chromatography. Expert Rev Proteomics 2014; 1:303-15. [PMID: 15966827 DOI: 10.1586/14789450.1.3.303] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
As new drugs rapidly advance into clinical trials, comprehensive identification of their intracellular targets becomes fundamental for the full understanding of the molecular basis of their efficacy and toxicity. This is particularly important when the targets belong to a large family and the inhibitors recognize a conserved site among different members of the class. A typical example is the kinase family, where efforts are aimed at the development of inhibitors of distinct kinases for therapeutic applications in oncology, inflammation and other disease areas. In this case, inhibitors targeting the ATP pocket may cross react with different kinases, as well as with other proteins that bind ATP. This review critically discusses the available approaches for kinase selectivity profiling. It also reviews some examples of inhibitor affinity chromatography applied to inhibitors of kinases and other protein families as a tool to identify and characterize their intracellular targets.
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22
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Wu L, Han DK. Overcoming the dynamic range problem in mass spectrometry-based shotgun proteomics. Expert Rev Proteomics 2014; 3:611-9. [PMID: 17181475 DOI: 10.1586/14789450.3.6.611] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Protein profiling using mass spectrometry technology has emerged as a powerful method for analyzing large-scale protein-expression patterns in cells and tissues. However, a number of challenges are present in proteomics research, one of the greatest being the high degree of protein complexity and huge dynamic range of proteins expressed in the complex biological mixtures, which exceeds six orders of magnitude in cells and ten orders of magnitude in body fluids. Since many important signaling proteins have low expression levels, methods to detect the low-abundance proteins in a complex sample are required. This review will focus on the fundamental fractionation and mass spectrometry techniques currently used for large-scale shotgun proteomics research.
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Affiliation(s)
- Linfeng Wu
- University of Connecticut, School of Medicine, Department of Cell Biology, Farmington, Connecticut, CT 06030, USA.
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23
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Lee H, Lee JH, Kim H, Kim SJ, Bae J, Kim HK, Lee SW. A fully automated dual-online multifunctional ultrahigh pressure liquid chromatography system for high-throughput proteomics analysis. J Chromatogr A 2014; 1329:83-9. [PMID: 24412000 DOI: 10.1016/j.chroma.2013.12.084] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 12/25/2013] [Accepted: 12/28/2013] [Indexed: 11/19/2022]
Abstract
A fully automated dual-online multifunctional ultrahigh pressure liquid chromatography (DO-MULTI-UPLC) system has been developed for high throughput proteome analyses of complex peptide mixtures. The system employs two online solid phase extraction (SPE) columns (150μm inner diameter×3cm), two capillary reverse phase (RP) columns (75μm×100cm) and a strong cation exchange (SCX) column (150μm×15cm) on a single system utilizing one binary pump and one isocratic pump. With the automated operation of six switching valves, the selection of LC experiments between single-dimensional RPLC and online two-dimensional SCX/RPLC were achieved automatically, without manual intervention, while two RPLC columns were used independently and alternatively. By essentially removing the dead time for column equilibration between experiments, in either 1D mode or 2D experimental mode, the current system was demonstrated to increase the experimental throughput by about two folds, while keeping the inter-column reproducibility of peptide elution time in less than 1% of gradient time. The advantageous features of the proposed system were demonstrated by its application to proteome samples of varying complexities.
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Affiliation(s)
- Hangyeore Lee
- Department of Chemistry, Research Institute for Natural Sciences, Korea University, Seoul 136-701, South Korea.
| | - Jung Hwa Lee
- Department of Chemistry, Research Institute for Natural Sciences, Korea University, Seoul 136-701, South Korea.
| | - Hokeun Kim
- Department of Chemistry, Research Institute for Natural Sciences, Korea University, Seoul 136-701, South Korea.
| | - Su-Jin Kim
- Department of Chemistry, Research Institute for Natural Sciences, Korea University, Seoul 136-701, South Korea.
| | - Jingi Bae
- Department of Chemistry, Research Institute for Natural Sciences, Korea University, Seoul 136-701, South Korea.
| | - Hark Kyun Kim
- National Cancer Center, Goyang 410-769, South Korea.
| | - Sang-Won Lee
- Department of Chemistry, Research Institute for Natural Sciences, Korea University, Seoul 136-701, South Korea.
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24
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Petriz BA, Franco OL. Application of Cutting-Edge Proteomics Technologies for Elucidating Host–Bacteria Interactions. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 95:1-24. [DOI: 10.1016/b978-0-12-800453-1.00001-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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25
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Chionh YH, Ho CH, Pruksakorn D, Ramesh Babu I, Ng CS, Hia F, McBee ME, Su D, Pang YLJ, Gu C, Dong H, Prestwich EG, Shi PY, Preiser PR, Alonso S, Dedon PC. A multidimensional platform for the purification of non-coding RNA species. Nucleic Acids Res 2013; 41:e168. [PMID: 23907385 PMCID: PMC3783195 DOI: 10.1093/nar/gkt668] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A renewed interest in non-coding RNA (ncRNA) has led to the discovery of novel RNA species and post-transcriptional ribonucleoside modifications, and an emerging appreciation for the role of ncRNA in RNA epigenetics. Although much can be learned by amplification-based analysis of ncRNA sequence and quantity, there is a significant need for direct analysis of RNA, which has led to numerous methods for purification of specific ncRNA molecules. However, no single method allows purification of the full range of cellular ncRNA species. To this end, we developed a multidimensional chromatographic platform to resolve, isolate and quantify all canonical ncRNAs in a single sample of cells or tissue, as well as novel ncRNA species. The applicability of the platform is demonstrated in analyses of ncRNA from bacteria, human cells and plasmodium-infected reticulocytes, as well as a viral RNA genome. Among the many potential applications of this platform are a system-level analysis of the dozens of modified ribonucleosides in ncRNA, characterization of novel long ncRNA species, enhanced detection of rare transcript variants and analysis of viral genomes.
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Affiliation(s)
- Yok Hian Chionh
- Singapore-MIT Alliance for Research and Technology, Infectious Disease Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore 138602, Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Department of Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA, Applied Biological Science Program, Chulabhorn Graduate Institute, Bangkok 10210, Thailand, Division of Molecular Genetics & Cell Biology, School of Biological Sciences, Nanyang Technological University, Singapore 637551, Immunology Programme, Life Science Institute, Centre for Life Science, Singapore 117456 and Novartis Institute for Tropical Disease, Singapore 138670
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26
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Beltrán NC, Horváthová L, Jedelský PL, Šedinová M, Rada P, Marcinčiková M, Hrdý I, Tachezy J. Iron-induced changes in the proteome of Trichomonas vaginalis hydrogenosomes. PLoS One 2013; 8:e65148. [PMID: 23741475 PMCID: PMC3669245 DOI: 10.1371/journal.pone.0065148] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 04/17/2013] [Indexed: 12/02/2022] Open
Abstract
Iron plays a crucial role in metabolism as a key component of catalytic and redox cofactors, such as heme or iron-sulfur clusters in enzymes and electron-transporting or regulatory proteins. Limitation of iron availability by the host is also one of the mechanisms involved in immunity. Pathogens must regulate their protein expression according to the iron concentration in their environment and optimize their metabolic pathways in cases of limitation through the availability of respective cofactors. Trichomonas vaginalis, a sexually transmitted pathogen of humans, requires high iron levels for optimal growth. It is an anaerobe that possesses hydrogenosomes, mitochondrion-related organelles that harbor pathways of energy metabolism and iron-sulfur cluster assembly. We analyzed the proteomes of hydrogenosomes obtained from cells cultivated under iron-rich and iron-deficient conditions employing two-dimensional peptide separation combining IEF and nano-HPLC with quantitative MALDI-MS/MS. We identified 179 proteins, of which 58 were differentially expressed. Iron deficiency led to the upregulation of proteins involved in iron-sulfur cluster assembly and the downregulation of enzymes involved in carbohydrate metabolism. Interestingly, iron affected the expression of only some of multiple protein paralogues, whereas the expression of others was iron independent. This finding indicates a stringent regulation of differentially expressed multiple gene copies in response to changes in the availability of exogenous iron.
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Affiliation(s)
- Neritza Campo Beltrán
- Department of Parasitology, Charles University in Prague, Faculty of Science, Prague, Czech Republic
| | - Lenka Horváthová
- Department of Parasitology, Charles University in Prague, Faculty of Science, Prague, Czech Republic
| | - Petr L. Jedelský
- Department of Parasitology, Charles University in Prague, Faculty of Science, Prague, Czech Republic
| | - Miroslava Šedinová
- Department of Parasitology, Charles University in Prague, Faculty of Science, Prague, Czech Republic
| | - Petr Rada
- Department of Parasitology, Charles University in Prague, Faculty of Science, Prague, Czech Republic
| | - Michaela Marcinčiková
- Department of Parasitology, Charles University in Prague, Faculty of Science, Prague, Czech Republic
| | - Ivan Hrdý
- Department of Parasitology, Charles University in Prague, Faculty of Science, Prague, Czech Republic
| | - Jan Tachezy
- Department of Parasitology, Charles University in Prague, Faculty of Science, Prague, Czech Republic
- * E-mail:
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27
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Optimized proteomic analysis of rat liver microsomes using dual enzyme digestion with 2D-LC–MS/MS. J Proteomics 2013; 82:166-78. [DOI: 10.1016/j.jprot.2013.02.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 01/24/2013] [Accepted: 02/08/2013] [Indexed: 12/23/2022]
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28
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Zhang Y, Wang H, Lai C, Wang L, Deng Y. Comparative proteomic analysis of human SH-SY5Y neuroblastoma cells under simulated microgravity. ASTROBIOLOGY 2013; 13:143-150. [PMID: 23421552 DOI: 10.1089/ast.2012.0822] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Microgravity is one of the most important features in spaceflight. Previous evidence has shown that neurophysiological impairment signs occurred under microgravity. The present study was undertaken to explore the change in protein abundance in human SH-SY5Y neuroblastoma cells that were grown in a microgravity environment. The comparative proteomic method based on the (18)O labeling technique was applied to investigate the up-regulated proteins and down-regulated proteins in SH-SY5Y under simulated microgravity. Twenty-two differentially abundant proteins were quantified in human SH-SY5Y neuroblastoma cells. The cell microfilament network was disrupted under simulated microgravity, which was determined by the immunocytochemistry. The concentration of reactive oxygen species, malondialdehyde, and free Ca2+ ion significantly increased, and the level of ATP significantly decreased under simulated microgravity. However, there was no obvious cell apoptosis observed under simulated microgravity. These results provide new molecular evidence for the change in protein abundance in SH-SY5Y cells under simulated microgravity, which might unfold biological mechanisms and the development of effective countermeasures to deal with microgravity-related neurological problems. We believe that the state-of-the-art proteomic assay may be a means by which aerospace scientists will begin to understand the underlying mechanisms of space life activities at the protein level.
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Affiliation(s)
- Yongqian Zhang
- School of Life Science, Beijing Institute of Technology, Beijing, China
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Amado FML, Ferreira RP, Vitorino R. One decade of salivary proteomics: current approaches and outstanding challenges. Clin Biochem 2012; 46:506-17. [PMID: 23103441 DOI: 10.1016/j.clinbiochem.2012.10.024] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 10/13/2012] [Accepted: 10/16/2012] [Indexed: 12/12/2022]
Abstract
Efforts have been made in the last decade towards the complete characterization of saliva proteome using gel-based and gel-free approaches. The combination of these strategies resulted in the increment of the dynamic range of saliva proteome, which yield in the identification of more than 3,000 different protein species. Comparative protein profiling using isotope labeling and label free approaches has been used for the identification of novel biomarkers for oral and related diseases. Although progresses have been made in saliva proteome characterization, the comparative profiling in different pathophysiological conditions is still at the beginning if compared to other bodily fluids. The potential biomarkers identified so far lack specificity once common differentially expressed proteins were detected in the saliva of patients with distinct diseases. In addition, recent research works focused on saliva peptidome profiling already allowed a better understanding of peptides' physiological role in oral cavity. This review provides an overview of the major achievements in saliva proteomics giving emphasis to methodological concerns related with saliva collection, treatment and analysis, as well as the main advantages and pitfalls underlying salivary proteomic strategies and potential clinical outcomes.
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Affiliation(s)
- Francisco M L Amado
- QOPNA, Mass Spectrometry Center, Department of Chemistry, University of Aveiro, Aveiro, Portugal.
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30
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Lee JH, Hyung SW, Mun DG, Jung HJ, Kim H, Lee H, Kim SJ, Park KS, Moore RJ, Smith RD, Lee SW. Fully automated multifunctional ultrahigh pressure liquid chromatography system for advanced proteome analyses. J Proteome Res 2012; 11:4373-81. [PMID: 22709424 DOI: 10.1021/pr3004166] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A multifunctional liquid chromatography system that performs 1-dimensional, 2-dimensional (strong cation exchange/reverse phase liquid chromatography or SCX/RPLC) separations and online phosphopeptide enrichment using a single binary nanoflow pump has been developed. With a simple operation of a function selection valve equipped with a SCX column and a TiO2 (titanium dioxide) column, a fully automated selection of three different experiment modes was achieved. Because the current system uses essentially the same solvent flow paths, the same trap column, and the same separation column for reverse-phase separation of 1D, 2D, and online phosphopeptides enrichment experiments, the elution time information obtained from these experiments is in excellent agreement, which facilitates correlating peptide information from different experiments. The final reverse-phase separation of the three experiments is completely decoupled from all of the function selection processes; thereby salts or acids from SCX or TiO2 column do not affect the efficiency of the reverse-phase separation.
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Affiliation(s)
- Jung Hwa Lee
- Department of Chemistry, Research Institute for Natural Sciences, Korea University, Seoul 136-701, South Korea
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31
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Martins-de-Souza D, Guest PC, Rahmoune H, Bahn S. Proteomic approaches to unravel the complexity of schizophrenia. Expert Rev Proteomics 2012; 9:97-108. [PMID: 22292827 DOI: 10.1586/epr.11.70] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Schizophrenia is a debilitating mental disorder that affects approximately 30 million people worldwide. The development and progression of this disease is now thought to be precipitated through a complex interaction between altered gene function and environmental factors. Proteomic analyses have been applied extensively over the past 10 years in studies of several tissues from schizophrenic patients, resulting in increased insight into the affected molecular pathways. In addition, these proteomic approaches have led to the identification of a set of molecular biomarker assays as the first blood-based test to aid in the diagnosis of schizophrenia. Here, we discuss the main outcome of these investigations and suggest a practical means of integrating and translating the findings between the brain and peripheral blood to increase our understanding of schizophrenia pathophysiology.
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Affiliation(s)
- Daniel Martins-de-Souza
- Department of Chemical Engineering & Biotechnology, Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QT, UK.
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32
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Bora A, Anderson C, Bachani M, Nath A, Cotter RJ. Robust two-dimensional separation of intact proteins for bottom-up tandem mass spectrometry of the human CSF proteome. J Proteome Res 2012; 11:3143-9. [PMID: 22537003 DOI: 10.1021/pr300057v] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cerebrospinal fluid (CSF) is produced in the brain by cells in the choroid plexus at a rate of 500 mL/day. It is the only body fluid in direct contact with the brain. Thus, any changes in the CSF composition will reflect pathological processes and make CSF a potential source of biomarkers for different disease states. Proteomics offers a comprehensive view of the proteins found in CSF. In this study, we use a recently developed nongel based method of sample preparation of CSF followed by liquid chromatography-high accuracy mass spectrometry (LC-MS) for MS and MS/MS analyses, allowing unambiguous identification of peptides/proteins. Gel-eluted liquid fraction entrapment electrophoresis (Gelfree) is used to separate a CSF complex protein mixture in 12 user-selectable liquid-phase molecular weight fractions. Using this high throughput workflow, we have been able to separate CSF intact proteins over a broad mass range (3.5-100 kDa) with high resolution (between 15 and 100 kDa) in 2 h and 40 min. We have completely eliminated albumin and were able to interrogate the low abundance CSF proteins in a highly reproducible manner from different CSF samples at the same time. Using LC-MS as a downstream analysis, we identified 368 proteins using MidiTrap G-10 desalting columns and 166 proteins (including 57 unique proteins) using Zeba spin columns with a 5% false discovery rate (FDR). Prostaglandin D2 synthase, Chromogranin A, Apolipoprotein E, Chromogranin B, Secretogranin III, Cystatin C, VGF nerve growth factor, and Cadherin 2 are a few of the proteins that were characterized. Gelfree-LC-MS is a robust method for the analysis of the human proteome that we will use to develop biomarkers for several neurodegenerative diseases and to quantitate these markers using multiple reaction monitoring.
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Affiliation(s)
- Adriana Bora
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine , Baltimore, Maryland, United States
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Stephanowitz H, Lange S, Lang D, Freund C, Krause E. Improved Two-Dimensional Reversed Phase-Reversed Phase LC-MS/MS Approach for Identification of Peptide-Protein Interactions. J Proteome Res 2011; 11:1175-83. [DOI: 10.1021/pr200900s] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Heike Stephanowitz
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Sabine Lange
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Diana Lang
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Christian Freund
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
- Freie Universität Berlin, 14195 Berlin, Germany
| | - Eberhard Krause
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
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34
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Sá-Correia I, Teixeira MC. 2D electrophoresis-based expression proteomics: a microbiologist's perspective. Expert Rev Proteomics 2011; 7:943-53. [PMID: 21142894 DOI: 10.1586/epr.10.76] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Quantitative proteomics based on 2D electrophoresis (2-DE) coupled with peptide mass fingerprinting is still one of the most widely used quantitative proteomics approaches in microbiology research. Our view on the exploitation of this global expression analysis technique and its contribution and potential to push forward the field of molecular microbial physiology towards a molecular systems microbiology perspective is discussed in this article. The advances registered in 2-DE-based quantitative proteomic analysis leading to increased protein resolution, sensitivity and accuracy, and the promising use of 2-DE to gain insights into post-translational modifications at a proteome-wide level (considering all the proteins/protein forms expressed by the genome) are focused on. Given the progress made in this field, it is foreseen that the 2-DE-based approach to quantitative proteomics will continue to be a fundamental tool for microbiologists working at a genome-wide scale. Guidelines are also provided for the exploitation of expression proteomics data, based on useful computational tools, and for the integration of these data with other genome-wide expression information. The advantages and limitations of a complete 2-DE-based expression proteomics analysis, envisaging the quantification of the global changes occurring in the proteome of a given cell depending on environmental or genetic manipulations, are discussed from the microbiologist's perspective. Particular focus is given to the emerging field of toxicoproteomics, a new systems toxicity approach that offers a powerful tool to directly monitor the earliest stages of the toxicological response by identifying critical proteins and pathways that are affected by, and respond to, a chemical stress. The experimental design and the bioinformatics analysis of data used in our laboratory to gain mechanistic insights through expression proteomics into the responses of the eukaryotic model Saccharomyces cerevisiae or of Pseudomonas strains to environmental toxicants are presented as case studies.
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Affiliation(s)
- Isabel Sá-Correia
- Institute for Biotechnology and Bioengineering, Biological Sciences Research Group, Centro de Engenharia Biológica e Química, Instituto Superior Técnico, Technical University of Lisbon, Av. Rovisco Pais, Lisbon, Portugal.
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May C, Brosseron F, Chartowski P, Schumbrutzki C, Schoenebeck B, Marcus K. Instruments and methods in proteomics. Methods Mol Biol 2011; 696:3-26. [PMID: 21063938 DOI: 10.1007/978-1-60761-987-1_1] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
In the past decade, major developments in instrumentation and methodology have been achieved in proteomics. For proteome investigations of complex biological samples derived from cell cultures, tissues, or whole organisms, several techniques are state of the art. Especially, many improvements have been undertaken to quantify differences in protein expression between samples from, e.g., treated vs. untreated cells and healthy vs. control patients. In this review, we give a brief insight into the main techniques, including gel-based protein separation techniques, and the growing field of mass spectrometry.
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Affiliation(s)
- Caroline May
- Department of Functional Proteomics, Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany
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36
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Meehan KL, Rainczuk A, Salamonsen LA, Stephens AN. Proteomics and the search for biomarkers of female reproductive diseases. Reproduction 2010; 140:505-19. [PMID: 20628032 DOI: 10.1530/rep-10-0226] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Over the past decade, high-throughput proteomics technologies have evolved considerably and have become increasingly more commonly applied to the investigation of female reproductive diseases. Proteomic approaches facilitate the identification of new disease biomarkers by comparing the abundance of hundreds of proteins simultaneously to find those specific to a particular clinical condition. Some of the best studied areas of female reproductive biology applying proteomics include gynaecological cancers, endometriosis and endometrial infertility. This review will discuss the progress that has been made in these areas and will highlight some of the emerging technologies that promise to contribute to better understanding of the female reproductive disease.
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Affiliation(s)
- Katie L Meehan
- Prince Henry's Institute of Medical Research, Clayton, Victoria, Australia.
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37
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Tummala M, Lee SM, Chess E, Hu P. Characterization of pertussis toxoid by two-dimensional liquid chromatography–tandem mass spectrometry. Anal Biochem 2010; 401:295-302. [DOI: 10.1016/j.ab.2010.02.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2010] [Revised: 02/24/2010] [Accepted: 02/26/2010] [Indexed: 10/19/2022]
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38
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Yeung YG, Stanley ER. Rapid detergent removal from peptide samples with ethyl acetate for mass spectrometry analysis. ACTA ACUST UNITED AC 2010; Chapter 16:Unit 16.12. [PMID: 20155730 DOI: 10.1002/0471140864.ps1612s59] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Detergents are required for the extraction of hydrophobic proteins and for the maintenance of their solubility in solution. However, the presence of detergents in the peptide samples severely suppresses ionization in mass spectrometry (MS) analysis and decreases chromatographic resolution in LC-MS. Thus, detergents must be removed for sensitive detection of peptides by MS. This unit describes a rapid protocol in which ethyl acetate extraction is used to remove octylglucoside from protease digests without loss of peptides. This procedure can also be used to reduce interference by sodium dodecyl sulfate, Nonidet P-40, or Triton X-100 in peptide samples for MS analysis.
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Affiliation(s)
- Yee-Guide Yeung
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, New York, USA
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39
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Escoffier P, Paris L, Bodaghi B, Danis M, Mazier D, Marinach-Patrice C. Pooling aqueous humor samples: bias in 2D-LC-MS/MS strategy? J Proteome Res 2010; 9:789-97. [PMID: 19929026 DOI: 10.1021/pr9006602] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The proteomic analysis of body fluids presents a major challenge in studies of human diseases. Traditional techniques for protein separation require large volumes and large amounts of protein, which may be difficult to obtain for certain fluids, such as the aqueous humor (AH). Two-dimensional liquid chromatography (2D-LC-MS/MS), adapted for peptides separation from complex protein mixtures, provides an alternative approach in proteomic analysis with a potential utility in biomarker research. We investigated several different 2D-LC-MS/MS methods for use with the AH of patients with cataract, traditionally used as a control group in studies of ocular diseases. We compared analyses of individual samples with analyses of pools of proteins or peptides, and found that the investigation strategy used strongly influenced protein identification. We identified 71 proteins related to extracellular proteins highly abundant in serum (e.g., albumin or transferrin) and involved in various functions, such as transport and metabolism, together with intracellular (myeloblastin) or organelle-specific proteins (cytochrome c). An evaluation of the advantages and disadvantages of each method suggested that individual analyses and the use of peptide mixtures should be favored as complementary techniques in the search for biomarkers in ocular diseases.
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Affiliation(s)
- Patricia Escoffier
- Universite Pierre et Marie Curie-Paris6, UMR S 945, Paris F-75013, France
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40
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Wang L, Evaristo G, Zhou M, Pinkse M, Wang M, Xu Y, Jiang X, Chen T, Rao P, Verhaert P, Shaw C. Nigrocin-2 peptides from Chinese Odorrana frogs - integration of UPLC/MS/MS with molecular cloning in amphibian skin peptidome analysis. FEBS J 2010; 277:1519-31. [DOI: 10.1111/j.1742-4658.2010.07580.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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41
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42
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Mounicou S, Szpunar J, Lobinski R. Inductively-coupled plasma mass spectrometry in proteomics, metabolomics and metallomics studies. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2010; 16:243-253. [PMID: 20530834 DOI: 10.1255/ejms.1059] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The potential of inductively-coupled plasma mass spectrometry (ICP-MS) and its complementarity to soft- ionization MS techniques are discussed in the context of the analysis for biomolecules. ICP-MS offers detection limits in the attomolar range, regardless of the molecular environment of the target element. The sensitivity is hardly affected by the sample matrix, chromatographic mobile phase, or co-eluted compounds. The abundance sensitivity over six decades and the linear dynamic range over nine decades make simultaneous multi-isotopic analysis routinely possible. The manuscript discusses the state-of-the-art of ICP-MS for the detection of proteins in gel electrophoresis and of peptides in 2D high-performance liquid chromatography. The possibilities of quantification to the degree of some post-translational modifications are highlighted. Attention is also paid to the role of ICP-MS in protein quantification via metal-coded labeling and to the use of differentially-labeled antibodies for the multiplexed biomarker analysis. The key role of ICP-MS in the emerging area of metallomics is briefly discussed.
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Affiliation(s)
- Sandra Mounicou
- CNRS/UPPA UMR5254, Laboratoire de Chimie Analytique Bio-Inorganique et Environnement (LCABIE), Hélioparc, 2, av. Pr. Angot, Pau, France
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43
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Somasundaram K, Nijaguna MB, Kumar DM. Serum proteomics of glioma: methods and applications. Expert Rev Mol Diagn 2009; 9:695-707. [PMID: 19817554 DOI: 10.1586/erm.09.52] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The prognosis of patients with glioblastoma, the most malignant adult glial brain tumor, remains poor in spite of advances in treatment procedures, including surgical resection, irradiation and chemotherapy. Genetic heterogeneity of glioblastoma warrants extensive studies in order to gain a thorough understanding of the biology of this tumor. While there have been several studies of global transcript profiling of glioma with the identification of gene signatures for diagnosis and disease management, translation into clinics is yet to happen. Serum biomarkers have the potential to revolutionize the process of cancer diagnosis, grading, prognostication and treatment response monitoring. Besides having the advantage that serum can be obtained through a less invasive procedure, it contains molecules at an extraordinary dynamic range of ten orders of magnitude in terms of their concentrations. While the conventional methods, such as 2DE, have been in use for many years, the ability to identify the proteins through mass spectrometry techniques such as MALDI-TOF led to an explosion of interest in proteomics. Relatively new high-throughput proteomics methods such as SELDI-TOF and protein microarrays are expected to hasten the process of serum biomarker discovery. This review will highlight the recent advances in the proteomics platform in discovering serum biomarkers and the current status of glioma serum markers. We aim to provide the principles and potential of the latest proteomic approaches and their applications in the biomarker discovery process. Besides providing a comprehensive list of available serum biomarkers of glioma, we will also propose how these markers will revolutionize the clinical management of glioma patients.
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Brunner Y, Schvartz D, Couté Y, Sanchez JC. Proteomics of regulated secretory organelles. MASS SPECTROMETRY REVIEWS 2009; 28:844-867. [PMID: 19301366 DOI: 10.1002/mas.20211] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Regulated secretory organelles are important subcellular structures of living cells that allow the release in the extracellular space of crucial compounds, such as hormones and neurotransmitters. Therefore, the regulation of biogenesis, trafficking, and exocytosis of regulated secretory organelles has been intensively studied during the last 30 years. However, due to the large number of different regulated secretory organelles, only a few of them have been specifically characterized. New insights into regulated secretory organelles open crucial perspectives for a better comprehension of the mechanisms that govern cell secretion. The combination of subcellular fractionation, protein separation, and mass spectrometry is also possible to study regulated secretory organelles at the proteome level. In this review, we present different strategies used to isolate regulated secretory organelles, separate their protein content, and identify the proteins by mass spectrometry. The biological significance of regulated secretory organelles-proteomic analysis is discussed as well.
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Affiliation(s)
- Yannick Brunner
- Biomedical Proteomics Research Group, University Medical Center, Geneva, Switzerland
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45
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Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics. Nat Protoc 2009; 4:484-94. [PMID: 19300442 DOI: 10.1038/nprot.2009.21] [Citation(s) in RCA: 1078] [Impact Index Per Article: 71.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Accurate quantification of protein expression in biological systems is an increasingly important part of proteomics research. Incorporation of differential stable isotopes in samples for relative protein quantification has been widely used. Stable isotope incorporation at the peptide level using dimethyl labeling is a reliable, cost-effective and undemanding procedure that can be easily automated and applied in high-throughput proteomics experiments. Although alternative multiplex quantitative proteomics approaches introduce isotope labels at the organism level ('stable isotope labeling by amino acids in cell culture' (SILAC)) or enable the simultaneous analysis of eight samples (isobaric tagging for relative and absolute quantification (iTRAQ)), stable isotope dimethyl labeling is advantageous in that it uses inexpensive reagents and is applicable to virtually any sample. We describe in-solution, online and on-column protocols for stable isotope dimethyl labeling of sample amounts ranging from sub-micrograms to milligrams. The labeling steps take approximately 60-90 min, whereas the full protocol including digestion and (two-dimensional) liquid chromatography-mass spectrometry takes approximately 1.5-3 days to complete.
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46
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Zhu M, Dai S, McClung S, Yan X, Chen S. Functional differentiation of Brassica napus guard cells and mesophyll cells revealed by comparative proteomics. Mol Cell Proteomics 2009; 8:752-66. [PMID: 19106087 PMCID: PMC2667361 DOI: 10.1074/mcp.m800343-mcp200] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2008] [Revised: 12/02/2008] [Indexed: 12/28/2022] Open
Abstract
Guard cells are highly specialized cells that form tiny pores called stomata on the leaf surface. The opening and closing of stomata control leaf gas exchange and water transpiration as well as allow plants to quickly respond and adjust to new environmental conditions. Mesophyll cells are specialized for photosynthesis. Despite the phenotypic and obvious functional differences between the two types of cells, the full protein components and their functions have not been explored but are addressed here through a global comparative proteomics analysis of purified guard cells and mesophyll cells. With the use of isobaric tags for relative and absolute quantification (iTRAQ) tagging and two-dimensional liquid chromatography mass spectrometry, we identified 1458 non-redundant proteins in both guard cells and mesophyll cells of Brassica napus leaves. Based on stringent statistical criteria, a total of 427 proteins were quantified, and 74 proteins were found to be enriched in guard cells. Proteins involved in energy (respiration), transport, transcription (nucleosome), cell structure, and signaling are preferentially expressed in guard cells. We observed several well characterized guard cell proteins. By contrast, proteins involved in photosynthesis, starch synthesis, disease/defense/stress, and other metabolisms are preferentially represented in mesophyll cells. Of the identified proteins, 110 have corresponding microarray data obtained from Arabidopsis guard cells and mesophyll cells. About 72% of these proteins follow the same trend of expression at the transcript and protein levels. For the rest of proteins, the correlation between proteomics data and the microarray data is poor. This highlights the importance of quantitative profiling at the protein level. Collectively this work represents the most extensive proteomic description of B. napus guard cells and has improved our knowledge of the functional specification of guard cells and mesophyll cells.
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Affiliation(s)
- Mengmeng Zhu
- Department of Botany, Genetics Institute, University of Florida, Gainesville, Florida 32610, USA
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47
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Intoh A, Kurisaki A, Yamanaka Y, Hirano H, Fukuda H, Sugino H, Asashima M. Proteomic analysis of membrane proteins expressed specifically in pluripotent murine embryonic stem cells. Proteomics 2009; 9:126-37. [DOI: 10.1002/pmic.200800496] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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48
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Metzger J, Luppa PB, Good DM, Mischak H. Adapting mass spectrometry-based platforms for clinical proteomics applications: The capillary electrophoresis coupled mass spectrometry paradigm. Crit Rev Clin Lab Sci 2009; 46:129-52. [PMID: 19404829 PMCID: PMC5769463 DOI: 10.1080/10408360902805261] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Single biomarker detection is common in clinical laboratories due to the currently available method spectrum. For various diseases, however, no specific single biomarker could be identified. A strategy to overcome this diagnostic void is to shift from single analyte detection to multiplexed biomarker profiling. Mass spectrometric methods were employed for biomarker discovery in body fluids. The enormous complexity of biofluidic proteome compartments implies upstream fractionation. For this reason, mass spectrometry (MS) was coupled to two-dimensional gel electrophoresis, liquid chromatography, surface-enhanced laser desorption/ionization, or capillary electrophoresis (CE). Differences in performance and operating characteristics make them differentially suited for routine laboratory applications. Progress in the field of clinical proteomics relies not only on the use of an adequate technological platform, but also on a fast and efficient proteomic workflow including standardized sample preparation, proteomic data processing, statistical validation of biomarker selection, and sample classification. Based on CE-MS analysis, we describe how proteomic technology can be implemented in a clinical laboratory environment. In the last part of this review, we give an overview of CE-MS-based clinical studies and present information on identity and biological significance of the identified peptide biomarkers providing evidence of disease-induced changes in proteolytic processing and posttranslational modification.
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Affiliation(s)
- Jochen Metzger
- Mosaiques Diagnostics and Terapeutics AG, Mellendorfer Str. 7-9, Hannover 30625, Germany.
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49
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Mounicou S, Szpunar J, Lobinski R. Metallomics: the concept and methodology. Chem Soc Rev 2009; 38:1119-38. [DOI: 10.1039/b713633c] [Citation(s) in RCA: 262] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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50
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Yeung YG, Nieves E, Angeletti RH, Stanley ER. Removal of detergents from protein digests for mass spectrometry analysis. Anal Biochem 2008; 382:135-7. [PMID: 18713617 DOI: 10.1016/j.ab.2008.07.034] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2008] [Revised: 07/28/2008] [Accepted: 07/29/2008] [Indexed: 12/01/2022]
Abstract
Detergents are commonly used for the extraction of hydrophobic proteins and must be removed for sensitive detection of peptides by mass spectrometry. We demonstrate that ethyl acetate is able to extract octylglycoside from a protease digest without loss of peptides or interference with the peptide mass spectral profile. Ethyl acetate extraction was also found to reduce interference by sodium dodecyl sulfate, Nonidet P-40, or Triton X-100 in the mass spectrometry analysis.
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Affiliation(s)
- Yee-Guide Yeung
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
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