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Sakson R, Beedgen L, Bernhard P, Alp KM, Lübbehusen N, Röth R, Niesler B, Luzarowski M, Shevchuk O, Mayer MP, Thiel C, Ruppert T. Targeted Proteomics Reveals Quantitative Differences in Low-Abundance Glycosyltransferases of Patients with Congenital Disorders of Glycosylation. Int J Mol Sci 2024; 25:1191. [PMID: 38256263 PMCID: PMC10816918 DOI: 10.3390/ijms25021191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
Protein glycosylation is an essential post-translational modification in all domains of life. Its impairment in humans can result in severe diseases named congenital disorders of glycosylation (CDGs). Most of the glycosyltransferases (GTs) responsible for proper glycosylation are polytopic membrane proteins that represent challenging targets in proteomics. We established a multiple reaction monitoring (MRM) assay to comprehensively quantify GTs involved in the processes of N-glycosylation and O- and C-mannosylation in the endoplasmic reticulum. High robustness was achieved by using an enriched membrane protein fraction of isotopically labeled HEK 293T cells as an internal protein standard. The analysis of primary skin fibroblasts from eight CDG type I patients with impaired ALG1, ALG2, and ALG11 genes, respectively, revealed a substantial reduction in the corresponding protein levels. The abundance of the other GTs, however, remained unchanged at the transcript and protein levels, indicating that there is no fail-safe mechanism for the early steps of glycosylation in the endoplasmic reticulum. The established MRM assay was shared with the scientific community via the commonly used open source Skyline software environment, including Skyline Batch for automated data analysis. We demonstrate that another research group could easily reproduce all analysis steps, even while using different LC-MS hardware.
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Affiliation(s)
- Roman Sakson
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
- Heidelberg Biosciences International Graduate School (HBIGS), Heidelberg University, 69120 Heidelberg, Germany
| | - Lars Beedgen
- Center for Child and Adolescent Medicine, Department Pediatrics I, Heidelberg University, 69120 Heidelberg, Germany
| | - Patrick Bernhard
- Institute for Surgical Pathology, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - K. Merve Alp
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Nicole Lübbehusen
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Ralph Röth
- nCounter Core Facility, Institute of Human Genetics, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Beate Niesler
- nCounter Core Facility, Institute of Human Genetics, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Interdisciplinary Center for Neurosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Marcin Luzarowski
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Olga Shevchuk
- Department of Immunodynamics, Institute of Experimental Immunology and Imaging, University Hospital Essen, 45147 Essen, Germany
| | - Matthias P. Mayer
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Christian Thiel
- Center for Child and Adolescent Medicine, Department Pediatrics I, Heidelberg University, 69120 Heidelberg, Germany
| | - Thomas Ruppert
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
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2
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Li Q, Dou L, Zhang Y, Luo L, Yang H, Wen K, Yu X, Shen J, Wang Z. A comprehensive review on the detection of Staphylococcus aureus enterotoxins in food samples. Compr Rev Food Sci Food Saf 2024; 23:e13264. [PMID: 38284582 DOI: 10.1111/1541-4337.13264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/12/2023] [Accepted: 10/15/2023] [Indexed: 01/30/2024]
Abstract
Staphylococcal enterotoxins (SEs), the major virulence factors of Staphylococcus aureus, cause a wide range of food poisoning and seriously threaten human health by infiltrating the food supply chain at different phases of manufacture, processes, distribution, and market. The significant prevalence of Staphylococcus aureus calls for efficient, fast, and sensitive methods for the early detection of SEs. Here, we provide a comprehensive review of the hazards of SEs in contaminated food, the characteristic and worldwide regulations of SEs, and various detection methods for SEs with extensive comparison and discussion of benefits and drawbacks, mainly including biological detection, genetic detection, and mass spectrometry detection and biosensors. We highlight the biosensors for the screening purpose of SEs, which are classified according to different recognition elements such as antibodies, aptamers, molecularly imprinted polymers, T-cell receptors, and transducers such as optical, electrochemical, and piezoelectric biosensors. We analyzed challenges of biosensors for the monitoring of SEs and conclude the trends for the development of novel biosensors should pay attention to improve samples pretreatment efficiency, employ innovative nanomaterials, and develop portable instruments. This review provides new information and insightful commentary, important to the development and innovation of further detection methods for SEs in food samples.
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Affiliation(s)
- Qing Li
- National Key Laboratory of Veterinary Public Health safety, College of Veterinary Medicine China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, and Beijing Laboratory for Food Quality and Safety, Beijing, China
| | - Leina Dou
- National Key Laboratory of Veterinary Public Health safety, College of Veterinary Medicine China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, and Beijing Laboratory for Food Quality and Safety, Beijing, China
| | - Yingjie Zhang
- National Key Laboratory of Veterinary Public Health safety, College of Veterinary Medicine China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, and Beijing Laboratory for Food Quality and Safety, Beijing, China
| | - Liang Luo
- National Key Laboratory of Veterinary Public Health safety, College of Veterinary Medicine China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, and Beijing Laboratory for Food Quality and Safety, Beijing, China
| | - Huijuan Yang
- National Key Laboratory of Veterinary Public Health safety, College of Veterinary Medicine China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, and Beijing Laboratory for Food Quality and Safety, Beijing, China
| | - Kai Wen
- National Key Laboratory of Veterinary Public Health safety, College of Veterinary Medicine China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, and Beijing Laboratory for Food Quality and Safety, Beijing, China
| | - Xuezhi Yu
- National Key Laboratory of Veterinary Public Health safety, College of Veterinary Medicine China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, and Beijing Laboratory for Food Quality and Safety, Beijing, China
| | - Jianzhong Shen
- National Key Laboratory of Veterinary Public Health safety, College of Veterinary Medicine China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, and Beijing Laboratory for Food Quality and Safety, Beijing, China
| | - Zhanhui Wang
- National Key Laboratory of Veterinary Public Health safety, College of Veterinary Medicine China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, and Beijing Laboratory for Food Quality and Safety, Beijing, China
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3
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Ras protein abundance correlates with Ras isoform mutation patterns in cancer. Oncogene 2023; 42:1224-1232. [PMID: 36864243 PMCID: PMC10079525 DOI: 10.1038/s41388-023-02638-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 03/04/2023]
Abstract
Activating mutations of Ras genes are often observed in cancer. The protein products of the three Ras genes are almost identical. However, for reasons that remain unclear, KRAS is far more frequently mutated than the other Ras isoforms in cancer and RASopathies. We have quantified HRAS, NRAS, KRAS4A and KRAS4B protein abundance across a large panel of cell lines and healthy tissues. We observe consistent patterns of KRAS > NRAS»HRAS protein expression in cells that correlate with the rank order of Ras mutation frequencies in cancer. Our data provide support for the model of a sweet-spot of Ras dosage mediating isoform-specific contributions to cancer and development. We suggest that in most cases, being the most abundant Ras isoform correlates with occupying the sweet-spot and that HRAS and NRAS expression is usually insufficient to promote oncogenesis when mutated. However, our results challenge the notion that rare codons mechanistically underpin the predominance of KRAS mutant cancers. Finally, direct measurement of mutant versus wildtype KRAS protein abundance revealed a frequent imbalance that may suggest additional non-gene duplication mechanisms for optimizing oncogenic Ras dosage.
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4
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Rusilowicz M, Newman DW, Creamer DR, Johnson J, Adair K, Harman VM, Grant CM, Beynon RJ, Hubbard SJ. AlacatDesigner─Computational Design of Peptide Concatamers for Protein Quantitation. J Proteome Res 2023; 22:594-604. [PMID: 36688735 PMCID: PMC9903321 DOI: 10.1021/acs.jproteome.2c00608] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Protein quantitation via mass spectrometry relies on peptide proxies for the parent protein from which abundances are estimated. Owing to the variability in signal from individual peptides, accurate absolute quantitation usually relies on the addition of an external standard. Typically, this involves stable isotope-labeled peptides, delivered singly or as a concatenated recombinant protein. Consequently, the selection of the most appropriate surrogate peptides and the attendant design in recombinant proteins termed QconCATs are challenges for proteome science. QconCATs can now be built in a "a-la-carte" assembly method using synthetic biology: ALACATs. To assist their design, we present "AlacatDesigner", a tool that supports the peptide selection for recombinant protein standards based on the user's target protein. The user-customizable tool considers existing databases, occurrence in the literature, potential post-translational modifications, predicted miscleavage, predicted divergence of the peptide and protein quantifications, and ionization potential within the mass spectrometer. We show that peptide selections are enriched for good proteotypic and quantotypic candidates compared to empirical data. The software is freely available to use either via a web interface AlacatDesigner, downloaded as a Desktop application or imported as a Python package for the command line interface or in scripts.
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Affiliation(s)
- Martin Rusilowicz
- Division
of Evolution, Infection and Genomics, School of Biological Sciences,
Faculty of Biology, Medicine and Health, Manchester Academic Health
Science Centre, University of Manchester, Manchester M13 9PT, United Kingdom
| | - David W. Newman
- Division
of Evolution, Infection and Genomics, School of Biological Sciences,
Faculty of Biology, Medicine and Health, Manchester Academic Health
Science Centre, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Declan R. Creamer
- Division
of Molecular and Cellular Function, School of Biological Sciences,
Faculty of Biology, Medicine and Health, Manchester Academic Health
Science Centre, University of Manchester, Manchester M13 9PT, United Kingdom
| | - James Johnson
- GeneMill,
Institute of Systems Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United
Kingdom
| | - Kareena Adair
- Centre
for Proteome Research, Institute of Systems and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United
Kingdom
| | - Victoria M. Harman
- Centre
for Proteome Research, Institute of Systems and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United
Kingdom
| | - Chris M. Grant
- Division
of Molecular and Cellular Function, School of Biological Sciences,
Faculty of Biology, Medicine and Health, Manchester Academic Health
Science Centre, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Robert J. Beynon
- Centre
for Proteome Research, Institute of Systems and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United
Kingdom
| | - Simon J. Hubbard
- Division
of Evolution, Infection and Genomics, School of Biological Sciences,
Faculty of Biology, Medicine and Health, Manchester Academic Health
Science Centre, University of Manchester, Manchester M13 9PT, United Kingdom,
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5
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Pandiselvam R, Kaavya R, Martinez Monteagudo SI, Divya V, Jain S, Khanashyam AC, Kothakota A, Prasath VA, Ramesh SV, Sruthi NU, Kumar M, Manikantan MR, Kumar CA, Khaneghah AM, Cozzolino D. Contemporary Developments and Emerging Trends in the Application of Spectroscopy Techniques: A Particular Reference to Coconut ( Cocos nucifera L.). Molecules 2022; 27:molecules27103250. [PMID: 35630725 PMCID: PMC9147692 DOI: 10.3390/molecules27103250] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/07/2022] [Accepted: 05/16/2022] [Indexed: 12/26/2022] Open
Abstract
The number of food frauds in coconut-based products is increasing due to higher consumer demands for these products. Rising health consciousness, public awareness and increased concerns about food safety and quality have made authorities and various other certifying agencies focus more on the authentication of coconut products. As the conventional techniques for determining the quality attributes of coconut are destructive and time-consuming, non-destructive testing methods which are accurate, rapid, and easy to perform with no detrimental sampling methods are currently gaining importance. Spectroscopic methods such as nuclear magnetic resonance (NMR), infrared (IR)spectroscopy, mid-infrared (MIR)spectroscopy, near-infrared (NIR) spectroscopy, ultraviolet-visible (UV-VIS) spectroscopy, fluorescence spectroscopy, Fourier-transform infrared spectroscopy (FTIR), and Raman spectroscopy (RS) are gaining in importance for determining the oxidative stability of coconut oil, the adulteration of oils, and the detection of harmful additives, pathogens, and toxins in coconut products and are also employed in deducing the interactions in food constituents, and microbial contaminations. The objective of this review is to provide a comprehensive analysis on the various spectroscopic techniques along with different chemometric approaches for the successful authentication and quality determination of coconut products. The manuscript was prepared by analyzing and compiling the articles that were collected from various databases such as PubMed, Google Scholar, Scopus and ScienceDirect. The spectroscopic techniques in combination with chemometrics were shown to be successful in the authentication of coconut products. RS and NMR spectroscopy techniques proved their utility and accuracy in assessing the changes in coconut oil’s chemical and viscosity profile. FTIR spectroscopy was successfully utilized to analyze the oxidation levels and determine the authenticity of coconut oils. An FT-NIR-based analysis of various coconut samples confirmed the acceptable levels of accuracy in prediction. These non-destructive methods of spectroscopy offer a broad spectrum of applications in food processing industries to detect adulterants. Moreover, the combined chemometrics and spectroscopy detection method is a versatile and accurate measurement for adulterant identification.
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Affiliation(s)
- Ravi Pandiselvam
- Physiology, Biochemistry and Post-Harvest Technology Division, ICAR-Central Plantation Crops Research Institute, Kasaragod 671124, Kerala, India;
- Correspondence: or (R.P.); (R.K.); (M.R.M.); (A.M.K.); (D.C.)
| | - Rathnakumar Kaavya
- Dairy and Food Science Department, South Dakota State University, Brookings, SD 57007, USA;
- Correspondence: or (R.P.); (R.K.); (M.R.M.); (A.M.K.); (D.C.)
| | - Sergio I. Martinez Monteagudo
- Dairy and Food Science Department, South Dakota State University, Brookings, SD 57007, USA;
- Department of Family and Consumer Sciences, New Mexico State University, Las Cruces, NM 88003, USA
- Chemical & Materials Engineering Department, New Mexico State University, Las Cruces, NM 88003, USA
| | - V. Divya
- School of BioSciences and Technology, VIT University, Vellore 632014, Tamil Nadu, India;
| | - Surangna Jain
- Department of Biotechnology, Mahidol University, Bangkok 12120, Thailand;
| | | | - Anjineyulu Kothakota
- Agro-Processing & Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (NIIST), Trivandrum 695019, Kerala, India;
| | - V. Arun Prasath
- Department of Food Process Engineering, NIT, Rourkela 769008, Odisha, India;
| | - S. V. Ramesh
- Physiology, Biochemistry and Post-Harvest Technology Division, ICAR-Central Plantation Crops Research Institute, Kasaragod 671124, Kerala, India;
| | - N. U. Sruthi
- Agricultural and Food Engineering Department, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India;
| | - Manoj Kumar
- Chemical and Biochemical Processing Division, ICAR-Central Institute for Research on Cotton Technology, Mumbai 400019, Maharashtra, India;
| | - M. R. Manikantan
- Physiology, Biochemistry and Post-Harvest Technology Division, ICAR-Central Plantation Crops Research Institute, Kasaragod 671124, Kerala, India;
- Correspondence: or (R.P.); (R.K.); (M.R.M.); (A.M.K.); (D.C.)
| | - Chinnaraja Ashok Kumar
- Department of Food Safety and Quality Assurance, College of Food and Dairy Technology, Chennai 600051, Tamil Nadu, India;
| | - Amin Mousavi Khaneghah
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas (UNICAMP), Campinas 13083-875, SP, Brazil
- Department of Fruit and Vegetable Product Technology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology, 02-532 Warsaw, Poland
- Correspondence: or (R.P.); (R.K.); (M.R.M.); (A.M.K.); (D.C.)
| | - Daniel Cozzolino
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Brisbane 4072, Australia
- Correspondence: or (R.P.); (R.K.); (M.R.M.); (A.M.K.); (D.C.)
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6
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Johnson J, Harman VM, Franco C, Emmott E, Rockliffe N, Sun Y, Liu LN, Takemori A, Takemori N, Beynon RJ. Construction of à la carte QconCAT protein standards for multiplexed quantification of user-specified target proteins. BMC Biol 2021; 19:195. [PMID: 34496840 PMCID: PMC8425055 DOI: 10.1186/s12915-021-01135-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 08/28/2021] [Indexed: 11/17/2022] Open
Abstract
Background QconCATs are quantitative concatamers for proteomic applications that yield stoichiometric quantities of sets of stable isotope-labelled internal standards. However, changing a QconCAT design, for example, to replace poorly performing peptide standards has been a protracted process. Results We report a new approach to the assembly and construction of QconCATs, based on synthetic biology precepts of biobricks, making use of loop assembly to construct larger entities from individual biobricks. The basic building block (a Qbrick) is a segment of DNA that encodes two or more quantification peptides for a single protein, readily held in a repository as a library resource. These Qbricks are then assembled in a one tube ligation reaction that enforces the order of assembly, to yield short QconCATs that are useable for small quantification products. However, the DNA context of the short construct also allows a second cycle of loop assembly such that five different short QconCATs can be assembled into a longer QconCAT in a second, single tube ligation. From a library of Qbricks, a bespoke QconCAT can be assembled quickly and efficiently in a form suitable for expression and labelling in vivo or in vitro. Conclusions We refer to this approach as the ALACAT strategy as it permits à la carte design of quantification standards. ALACAT methodology is a major gain in flexibility of QconCAT implementation as it supports rapid editing and improvement of QconCATs and permits, for example, substitution of one peptide by another. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01135-9.
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Affiliation(s)
- James Johnson
- GeneMill, Institute of Systems Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Victoria M Harman
- Centre for Proteome Research, Institute of Systems and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L697ZB, UK
| | - Catarina Franco
- Centre for Proteome Research, Institute of Systems and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L697ZB, UK
| | - Edward Emmott
- Centre for Proteome Research, Institute of Systems and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L697ZB, UK
| | - Nichola Rockliffe
- GeneMill, Institute of Systems Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Yaqi Sun
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L697ZB, UK
| | - Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L697ZB, UK
| | - Ayako Takemori
- Division of Analytical Bio-Medicine, Advanced Research Support Center, Ehime University, Shitsukawa, Toon, Ehime, Japan
| | - Nobuaki Takemori
- Division of Analytical Bio-Medicine, Advanced Research Support Center, Ehime University, Shitsukawa, Toon, Ehime, Japan
| | - Robert J Beynon
- Centre for Proteome Research, Institute of Systems and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L697ZB, UK.
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7
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Lefebvre D, Blanco-Valle K, Feraudet-Tarisse C, Merda D, Simon S, Fenaille F, Hennekinne JA, Nia Y, Becher F. Quantitative Determination of Staphylococcus aureus Enterotoxins Types A to I and Variants in Dairy Food Products by Multiplex Immuno-LC-MS/MS. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:2603-2610. [PMID: 33596646 DOI: 10.1021/acs.jafc.0c07545] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Staphylococcal enterotoxins (SEs) are responsible for frequent food poisoning outbreaks worldwide. Specific identification of SEs is crucial for confirmation of food poisoning, tracking of the incriminated foods or food ingredients, and removal from the food chain. Here, we report on a new food testing protocol addressing the challenge of low abundance of SEs in contaminated food and high sequence heterogeneity. Multiplex ability of targeted high-resolution mass spectrometry was succesfully applied to the simultaneous and quantitative determination of the eight most frequent SEs including sequence variants. In this aim, between three and eight proteotypic peptides of each SE were selected by carefully considering amino acid variations within each type, and sequence homology between types. Quantification of trace levels of SEs directly in food samples was reached by immunoaffinity enrichment and optimized analytical conditions. The assay was validated in dairy food products with a lower limit of quantification down to 0.1 ng/g (in milk), and quantification of SEs was successfully demonstrated in real-life samples collected during staphylococcal food poisoning outbreaks. Importantly, the ability of the method to detect diverse sequence variants was also illustrated. By enabling for the first time the simultaneous quantification of the eight most frequent SEs, the new mass spectrometry-based assay would facilitate the laboratory confirmation of positive samples in situation of food poisoning outbreaks.
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Affiliation(s)
- Donatien Lefebvre
- Département Médicaments et Technologies pour la Santé (DMTS), SPI, Université Paris-Saclay, CEA, INRAE, 91191 Gif-sur-Yvette, France
- Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Université Paris-Est, 94700 Maisons-Alfort, France
| | - Kevin Blanco-Valle
- Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Université Paris-Est, 94700 Maisons-Alfort, France
| | - Cécile Feraudet-Tarisse
- Département Médicaments et Technologies pour la Santé (DMTS), SPI, Université Paris-Saclay, CEA, INRAE, 91191 Gif-sur-Yvette, France
| | - Déborah Merda
- Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Université Paris-Est, 94700 Maisons-Alfort, France
| | - Stéphanie Simon
- Département Médicaments et Technologies pour la Santé (DMTS), SPI, Université Paris-Saclay, CEA, INRAE, 91191 Gif-sur-Yvette, France
| | - François Fenaille
- Département Médicaments et Technologies pour la Santé (DMTS), SPI, Université Paris-Saclay, CEA, INRAE, 91191 Gif-sur-Yvette, France
| | - Jacques-Antoine Hennekinne
- Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Université Paris-Est, 94700 Maisons-Alfort, France
| | - Yacine Nia
- Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Université Paris-Est, 94700 Maisons-Alfort, France
| | - François Becher
- Département Médicaments et Technologies pour la Santé (DMTS), SPI, Université Paris-Saclay, CEA, INRAE, 91191 Gif-sur-Yvette, France
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8
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Zhang Q, Cai Z, Lin H, Han L, Yan J, Wang J, Ke P, Zhuang J, Huang X. Expression, purification and identification of isotope-labeled recombinant cystatin C protein in Escheichia coli intended for absolute quantification using isotope dilution mass spectrometry. Protein Expr Purif 2020; 178:105785. [PMID: 33152458 DOI: 10.1016/j.pep.2020.105785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 09/04/2020] [Accepted: 10/29/2020] [Indexed: 10/23/2022]
Abstract
Isotope-labeled proteins are expected to be used as internal standard proteins in the field of protein quantification by isotope dilution mass spectrometry (ID/MS). To achieve the absolute quantification of Cystatin C (Cys C) based on ID/MS, we aims to obtain 15N isotope-labeled recombinant Cys C (15N-Cys C) protein. Firstly, the Cys C gene was optimized based on the preferred codons of Escherichia coli, and inserted into the pET-28a(+) expression plasmid. Then, the plasmid was transformed into TOP10 and BL21 strains, and 15N-Cys C was expressed in M9 medium using 15N as the only nitrogen source. 15N-Cys C was detected by SDS-PAGE, protein immunoblotting and matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS). The characteristic peptides obtained from 15N-Cys C were analyzed by a Q Exactive Plus MS system. Results showed that 53.06% of the codons were optimized. The codon adaptation index of the Cys C genes increased from 0.31 to 0.95, and the GC content was adjusted from 64.85% to 54.88%. The purity of 15N-Cys C was higher than 95%. MALDI-TOF MS analysis showed that the m/z of 15N-Cys C had changed from 13 449 to 14 850. The characteristic peptides showed that 619.79 m/z (M+2H)2+ was the parent ion of 15N-Cys C and that the secondary ions of 15N-labeled peptides from y+5 to y+9 were 616.27 m/z, 716.33 m/z, 788.39 m/z, 936.43 m/z, and 1052.46 m/z, respectively. In conclusion, we successfully expressed, purified and identified of 15N-Cys C protein in Escheichia coli intended for absolute quantification using ID/MS.
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Affiliation(s)
- Qiaoxuan Zhang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China; Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, 510120, China
| | - Zhiliang Cai
- Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, 510120, China
| | - Haibiao Lin
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Liqiao Han
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jun Yan
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jianbing Wang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Peifeng Ke
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Junhua Zhuang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.
| | - Xianzhang Huang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.
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9
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Rajkovic A, Jovanovic J, Monteiro S, Decleer M, Andjelkovic M, Foubert A, Beloglazova N, Tsilla V, Sas B, Madder A, De Saeger S, Uyttendaele M. Detection of toxins involved in foodborne diseases caused by Gram‐positive bacteria. Compr Rev Food Sci Food Saf 2020; 19:1605-1657. [DOI: 10.1111/1541-4337.12571] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 04/10/2020] [Accepted: 04/14/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Andreja Rajkovic
- Laboratory of Food Microbiology and Food Preservation, Department of Food Technology, Safety and Health, Faculty of Bioscience EngineeringGhent University Ghent Belgium
| | - Jelena Jovanovic
- Laboratory of Food Microbiology and Food Preservation, Department of Food Technology, Safety and Health, Faculty of Bioscience EngineeringGhent University Ghent Belgium
| | - Silvia Monteiro
- Laboratorio Analises, Instituto Superior TecnicoUniversidade de Lisboa Lisbon Portugal
| | - Marlies Decleer
- Laboratory of Food Microbiology and Food Preservation, Department of Food Technology, Safety and Health, Faculty of Bioscience EngineeringGhent University Ghent Belgium
- Laboratory of Food Analysis, Department of Bioanalysis, Faculty of Pharmaceutical SciencesGhent University Ghent Belgium
| | - Mirjana Andjelkovic
- Operational Directorate Food, Medicines and Consumer SafetyService for Chemical Residues and Contaminants Brussels Belgium
| | - Astrid Foubert
- Laboratory of Food Analysis, Department of Bioanalysis, Faculty of Pharmaceutical SciencesGhent University Ghent Belgium
| | - Natalia Beloglazova
- Laboratory of Food Analysis, Department of Bioanalysis, Faculty of Pharmaceutical SciencesGhent University Ghent Belgium
- Nanotechnology Education and Research CenterSouth Ural State University Chelyabinsk Russia
| | - Varvara Tsilla
- Laboratory of Food Microbiology and Food Preservation, Department of Food Technology, Safety and Health, Faculty of Bioscience EngineeringGhent University Ghent Belgium
| | - Benedikt Sas
- Laboratory of Food Microbiology and Food Preservation, Department of Food Technology, Safety and Health, Faculty of Bioscience EngineeringGhent University Ghent Belgium
| | - Annemieke Madder
- Laboratorium for Organic and Biomimetic Chemistry, Department of Organic and Macromolecular ChemistryGhent University Ghent Belgium
| | - Sarah De Saeger
- Laboratory of Food Analysis, Department of Bioanalysis, Faculty of Pharmaceutical SciencesGhent University Ghent Belgium
| | - Mieke Uyttendaele
- Laboratory of Food Microbiology and Food Preservation, Department of Food Technology, Safety and Health, Faculty of Bioscience EngineeringGhent University Ghent Belgium
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10
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Koike H, Kanda M, Hayashi H, Matsushima Y, Yoshikawa S, Ohba Y, Hayashi M, Nagano C, Sekimura K, Otsuka K, Kamiie J, Sasamoto T, Hashimoto T. Development of an alternative approach for detecting botulinum neurotoxin type A in honey: Analysis of non-toxic peptides with a reference labelled protein via liquid chromatography-tandem mass spectrometry. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2020; 37:1359-1373. [PMID: 32515305 DOI: 10.1080/19440049.2020.1766121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In this study, we developed a reference labelled protein containing the partial amino acid sequence of botulinum neurotoxin type A (BoNTA). We also applied it as an internal standard to detect specific and non-toxic peptides originated from BoNTA in honey with the use of liquid chromatography-tandem mass spectrometry (LC-MS/MS). Original proteins in the honey sample were collected through a two-step process that included solubilisation and trichloroacetic acid (TCA) precipitation. Solubilisation by adding water enabled processing of proteins in honey. TCA precipitation collected proteins without specific binding. The combination of protein alkylation and an appropriate enzyme-to-protein ratio ensured feasibility of tryptic digestion. A desalting process eliminated a large amount of salts and other tryptic peptides in the honey sample. The use of the reference labelled protein enabled compensation for tryptic digestion efficiency and electrospray ionisation efficiency based on LC-MS/MS measurement. After the peptide selection and protein BlastP analysis, five unique peptides were chosen. The non-toxic peptides originating from BoNTA were reliably detected using LC-MS/MS based on a multiple-reaction monitoring mode. Detection of several peptides ensured screening of BoNTA in honey samples. Based on the responses, the proteotypic peptide LYGIAINPNR was selected as the quantitative peptide. Due to maintaining the relative ion ratios, the selective transition completely identified the non-toxic peptides. The intensity of the transitions established a detection limit of BoNTA estimated to be 9.4 ng mL-1. Although extraction efficiency was not evaluated using the BoNTA standard, the results suggested this method may be used for quantification of BoNTA in honey. The method was applied to 19 honey samples purchased in Tokyo; none of them was found to contain the target toxin. Overall, the method is expected to accelerate BoNTA monitoring for food safety.
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Affiliation(s)
- Hiroshi Koike
- Department of Food Safety, Tokyo Metropolitan Institute of Public Health , Tokyo, Japan
| | - Maki Kanda
- Department of Food Safety, Tokyo Metropolitan Institute of Public Health , Tokyo, Japan
| | - Hairoshi Hayashi
- Department of Food Safety, Tokyo Metropolitan Institute of Public Health , Tokyo, Japan
| | - Yoko Matsushima
- Department of Food Safety, Tokyo Metropolitan Institute of Public Health , Tokyo, Japan
| | - Souichi Yoshikawa
- Department of Food Safety, Tokyo Metropolitan Institute of Public Health , Tokyo, Japan
| | - Yumi Ohba
- Department of Food Safety, Tokyo Metropolitan Institute of Public Health , Tokyo, Japan
| | - Momoka Hayashi
- Department of Food Safety, Tokyo Metropolitan Institute of Public Health , Tokyo, Japan
| | - Chieko Nagano
- Department of Food Safety, Tokyo Metropolitan Institute of Public Health , Tokyo, Japan
| | - Kotaro Sekimura
- Department of Food Safety, Tokyo Metropolitan Institute of Public Health , Tokyo, Japan
| | - Kenji Otsuka
- Department of Food Safety, Tokyo Metropolitan Institute of Public Health , Tokyo, Japan
| | - Junichi Kamiie
- Laboratory of Veterinary Pathology, School of Veterinary Medicine, Azabu University , Sagamihara, Japan
| | - Takeo Sasamoto
- Department of Food Safety, Tokyo Metropolitan Institute of Public Health , Tokyo, Japan
| | - Tsuneo Hashimoto
- Department of Food Safety, Tokyo Metropolitan Institute of Public Health , Tokyo, Japan
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11
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Quantitative mass spectrometry-based proteomics in the era of model-informed drug development: Applications in translational pharmacology and recommendations for best practice. Pharmacol Ther 2019; 203:107397. [DOI: 10.1016/j.pharmthera.2019.107397] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 07/29/2019] [Indexed: 02/08/2023]
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12
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Selection of native bacterial starter culture in the production of fermented meat sausages: Application potential, safety aspects, and emerging technologies. Food Res Int 2019; 122:371-382. [DOI: 10.1016/j.foodres.2019.04.018] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 04/06/2019] [Accepted: 04/08/2019] [Indexed: 01/04/2023]
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13
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Koike H, Kanda M, Hayashi H, Matsushima Y, Ohba Y, Nakagawa Y, Nagano C, Sekimura K, Hirai A, Shindo T, Otsuka K, Kamiie J, Sasamoto T, Hashimoto T. Quantification of staphylococcal enterotoxin type A in cow milk by using a stable isotope-labelled peptide via liquid chromatography-tandem mass spectrometry. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2019; 36:1098-1108. [PMID: 31094669 DOI: 10.1080/19440049.2019.1615641] [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] [Indexed: 02/07/2023]
Abstract
In this study, the staphylococcal enterotoxin type A (SEA) contaminant was quantified in cow milk by liquid chromatography-tandem mass spectrometry (LC-MS/MS) with the use of a stable isotope-labelled peptide of SEA as an internal standard. SEA was cleaned up in a two-step process that included pH control and trichloroacetic acid (TCA) precipitation. The pH control phase eliminated other proteins. TCA precipitation cleaned up SEA without special equipment. An appropriate enzyme-to-protein ratio maximised tryptic digestion. A desalting process guaranteed the stable retention of SEA-digested peptides. The coverage of amino-acid sequences (>10%) clearly identified the toxin's presence. SEA was accurately quantified using LC-MS/MS based on a multiple-reaction monitoring mode. The developed method was validated based on spiked recovery tests at 50 and 100 µg kg-1 conducted with two samples collected on a daily basis for five days based on Japanese validation guidelines. The new method exhibited good accuracy which ranged from 80% to 82%. The relative standard deviations of repeatability were 13-14% and the relative standard deviations of within-laboratory reproducibility were 13-18%. These standard deviations satisfied the criteria of the Japanese validation guidelines. The quantification limit was estimated to be 10 µg kg-1.
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Affiliation(s)
- Hiroshi Koike
- a Department of Food Safety , Tokyo Metropolitan Institute of Public Health , Tokyo , Japan
| | - Maki Kanda
- a Department of Food Safety , Tokyo Metropolitan Institute of Public Health , Tokyo , Japan
| | - Hiroshi Hayashi
- a Department of Food Safety , Tokyo Metropolitan Institute of Public Health , Tokyo , Japan
| | - Yoko Matsushima
- a Department of Food Safety , Tokyo Metropolitan Institute of Public Health , Tokyo , Japan
| | - Yumi Ohba
- a Department of Food Safety , Tokyo Metropolitan Institute of Public Health , Tokyo , Japan
| | - Yukiko Nakagawa
- a Department of Food Safety , Tokyo Metropolitan Institute of Public Health , Tokyo , Japan
| | - Chieko Nagano
- a Department of Food Safety , Tokyo Metropolitan Institute of Public Health , Tokyo , Japan
| | - Kotaro Sekimura
- a Department of Food Safety , Tokyo Metropolitan Institute of Public Health , Tokyo , Japan
| | - Akihiko Hirai
- b Department of Microbiology , Tokyo Metropolitan Institute of Public Health , Tokyo , Japan
| | - Tetsuya Shindo
- a Department of Food Safety , Tokyo Metropolitan Institute of Public Health , Tokyo , Japan
| | - Kenji Otsuka
- a Department of Food Safety , Tokyo Metropolitan Institute of Public Health , Tokyo , Japan
| | - Junichi Kamiie
- c Laboratory of Veterinary Pathology, School of Veterinary Medicine , Azabu University , Sagamihara , Japan
| | - Takeo Sasamoto
- a Department of Food Safety , Tokyo Metropolitan Institute of Public Health , Tokyo , Japan
| | - Tsuneo Hashimoto
- a Department of Food Safety , Tokyo Metropolitan Institute of Public Health , Tokyo , Japan
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14
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Peffers MJ, Smagul A, Anderson JR. Proteomic analysis of synovial fluid: current and potential uses to improve clinical outcomes. Expert Rev Proteomics 2019; 16:287-302. [PMID: 30793992 DOI: 10.1080/14789450.2019.1578214] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
INTRODUCTION Synovial fluid (SF) is in close proximity to tissues which are primarily altered during articular disease and has significant potential to better understand the underlying disease pathogeneses of articular pathologies and biomarker discovery. Although development of mass spectrometry-based methods has allowed faster and higher sensitivity techniques, interrogation of the SF proteome has been hindered by its large protein concentration dynamic range, impeding quantification of lower abundant proteins. Areas covered: Recent advances have developed methodologies to reduce the large protein concentration dynamic range of SF and subsequently allow deeper exploration of the SF proteome. This review concentrates on methods to overcome biofluid complexity, mass spectrometry proteomics methodologies, extracellular vesicles proteomics and the application of advances within the field in clinical disease, including osteoarthritis, rheumatoid arthritis, spondyloarthritis and juvenile arthritis. A narrative review was conducted with articles searched using PubMed, 1991-2018. Expert opinion: The SF proteomics field faces various challenges, including the requirement for rigorous and standardised methods of sample collection/storage, the sensitivity and specificity of proteomic assays, techniques to combat the large protein concentration dynamic range and comprehensive data analysis to reduce falsely identified markers. Additionally, there are challenges in developing multi 'omic' integration techniques, with computational integration enhancing analysis.
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Affiliation(s)
- Mandy Jayne Peffers
- a Comparative Musculoskeletal Biology, Institute of Ageing and Chronic Disease , University of Liverpool , Liverpool , UK
| | - Aibek Smagul
- a Comparative Musculoskeletal Biology, Institute of Ageing and Chronic Disease , University of Liverpool , Liverpool , UK
| | - James Ross Anderson
- a Comparative Musculoskeletal Biology, Institute of Ageing and Chronic Disease , University of Liverpool , Liverpool , UK
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15
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Wang C, Zhang Q, Liu X, Li G, Kong H, Khan MI, Xiao H, Wang Y, Liu W, Cao C. Double inner standard plot model of an electrophoresis titration chip for a portable and green assay of protein content in milk. LAB ON A CHIP 2019; 19:484-492. [PMID: 30601538 DOI: 10.1039/c8lc01015c] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
High portability and environmental safety ("green") are two of the most important objectives pursued by microfluidic methods. However, there remain many challenges for the design of portable and visual microfluidic methods (e.g., chip electrophoresis) due to use of a cumbersome pump, power supply and detector. Herein, a facile double inner standard plot (DISP) model of electrophoresis titration (ET) was proposed for portable and visual assay of proteins in test milk samples without use of a pump, power supply or detector based on a moving reaction boundary (MRB) chip. The DISP-ET model predicted that: (i) by setting the upper limit (UL) and lower limit (LL) of double inner standard milk protein contents, points U and L were, respectively, achieved in the relationship D = -aC + b (D: MRB motion distance; C: protein content); and (ii) the two points divided both the C-axis and D-axis into "poor", "eligible" and "superior" rulers scaled for quantitative assay of test samples. To demonstrate the model of DISP-ET, an original portable device (120 mm × 78 mm × 30 mm, 341 g) was designed, which had a chip (25 mm × 25 mm × 4 mm) of three channels (15 mm × 200 μm × 80 μm), platinum electrodes, a lithium cell and touch screen. A series of experiments were undertaken based on the developed portable device. The relevant experiments demonstrated systemically the validity of the DISP-ET model, theory and method. In particular, the experiments clearly showed the advantages of the DISP-ET chip: portability, visuality, green use, rapidity, and flexibility for real-life use. Finally, the device was applied for a portable and visual assay of fresh milk from a cow on a dairy farm. The DISP-ET model opens a window for designing portable and visual quantitative methods of food-safety control and clinical diagnoses.
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Affiliation(s)
- Cunhuai Wang
- Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
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16
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Smith BJ, Martins-de-Souza D, Fioramonte M. A Guide to Mass Spectrometry-Based Quantitative Proteomics. Methods Mol Biol 2019; 1916:3-39. [PMID: 30535679 DOI: 10.1007/978-1-4939-8994-2_1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Proteomics has become an attractive science in the postgenomic era, given its capacity to identify up to thousands of molecules in a single, complex sample and quantify them in an absolute and/or relative manner. The use of these techniques enables understanding of cellular and molecular mechanisms of diseases and other biological conditions, as well as identification and screening of protein biomarkers. Here we provide a straightforward, up-to-date compilation and comparison of the main quantitation techniques used in comparative proteomics such as in vitro and in vivo stable isotope labeling and label-free techniques. Additionally, this chapter includes common methods for data acquisition in proteomics and some appropriate methods for data processing. This compilation can serve as a reference for scientists who are new to, or already familiar with, quantitative proteomics.
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Affiliation(s)
- Bradley J Smith
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- Center for Neurobiology, University of Campinas (UNICAMP), Campinas, Brazil
- Instituto Nacional de Biomarcadores em Neuropsiquiatria (INBION), Conselho Nacional de Desenvolvimento Cientifico e Tecnologico, Sao Paulo, Brazil
| | - Mariana Fioramonte
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil.
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17
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Alternative to Animal Use for Detecting Biologically Active Staphylococcal Enterotoxin Type A. Toxins (Basel) 2018; 10:toxins10120540. [PMID: 30558281 PMCID: PMC6316127 DOI: 10.3390/toxins10120540] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 12/10/2018] [Accepted: 12/13/2018] [Indexed: 11/17/2022] Open
Abstract
Staphylococcal enterotoxins (SEs) are a food safety concern. Existing methods for biologically active SE detection rely on the emetic response in live kittens or monkeys. This method suffers from low sensitivity, poor reproducibility, and causes ethical concerns regarding the use of experimental animals. The Lautenberg Chemical Safety Act encourages the development and adoption of alternatives to testing on animals for chemical toxicity methodologies. In this study, we utilized the superantigenic effect of SE type A (SEA) and used an ex vivo bioassay as an alternative to live animal testing. We found that interleukin-2 (IL-2) secreted by splenocyte can be utilized for quantifiable detection of SEA in food products. To avoid food matrix interference and attenuation of signal, we separated SEA from spiked food products by employing immunomagnetic beads that were coated with an anti-SEA antibody. This ex vivo method has achieved the detection of 1 ng mL−1 of SEA, which is 107 times more sensitive than the existing live animal testing methods. However, this ex vivo bioassay requires sacrificing of mice. To overcome this limitation, we established a cell based in vitro assay using CCRF-CEM, a human CD4+ T-cell line, for the quantitative detection of SEA. Incubation of SEA with CCRF-CEM human T-cells and Raji cells led to quantifiable and dose dependent secretion of IL-2. This novel cell-based assay is highly specific to biologically active SEA, compared with the related SE toxin subtypes B, D, and E or heat inactivated SEA, which produce no secretion of IL-2. This is the first demonstration of an alternative assay that completely eliminates the use of animals for quantitative detection of active SEA.
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18
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Walper SA, Lasarte Aragonés G, Sapsford KE, Brown CW, Rowland CE, Breger JC, Medintz IL. Detecting Biothreat Agents: From Current Diagnostics to Developing Sensor Technologies. ACS Sens 2018; 3:1894-2024. [PMID: 30080029 DOI: 10.1021/acssensors.8b00420] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Although a fundamental understanding of the pathogenicity of most biothreat agents has been elucidated and available treatments have increased substantially over the past decades, they still represent a significant public health threat in this age of (bio)terrorism, indiscriminate warfare, pollution, climate change, unchecked population growth, and globalization. The key step to almost all prevention, protection, prophylaxis, post-exposure treatment, and mitigation of any bioagent is early detection. Here, we review available methods for detecting bioagents including pathogenic bacteria and viruses along with their toxins. An introduction placing this subject in the historical context of previous naturally occurring outbreaks and efforts to weaponize selected agents is first provided along with definitions and relevant considerations. An overview of the detection technologies that find use in this endeavor along with how they provide data or transduce signal within a sensing configuration follows. Current "gold" standards for biothreat detection/diagnostics along with a listing of relevant FDA approved in vitro diagnostic devices is then discussed to provide an overview of the current state of the art. Given the 2014 outbreak of Ebola virus in Western Africa and the recent 2016 spread of Zika virus in the Americas, discussion of what constitutes a public health emergency and how new in vitro diagnostic devices are authorized for emergency use in the U.S. are also included. The majority of the Review is then subdivided around the sensing of bacterial, viral, and toxin biothreats with each including an overview of the major agents in that class, a detailed cross-section of different sensing methods in development based on assay format or analytical technique, and some discussion of related microfluidic lab-on-a-chip/point-of-care devices. Finally, an outlook is given on how this field will develop from the perspective of the biosensing technology itself and the new emerging threats they may face.
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Affiliation(s)
- Scott A. Walper
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Guillermo Lasarte Aragonés
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University Fairfax, Virginia 22030, United States
| | - Kim E. Sapsford
- OMPT/CDRH/OIR/DMD Bacterial Respiratory and Medical Countermeasures Branch, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Carl W. Brown
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University Fairfax, Virginia 22030, United States
| | - Clare E. Rowland
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- National Research Council, Washington, D.C. 20036, United States
| | - Joyce C. Breger
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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19
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Duracova M, Klimentova J, Fucikova A, Dresler J. Proteomic Methods of Detection and Quantification of Protein Toxins. Toxins (Basel) 2018; 10:toxins10030099. [PMID: 29495560 PMCID: PMC5869387 DOI: 10.3390/toxins10030099] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 02/21/2018] [Accepted: 02/23/2018] [Indexed: 12/11/2022] Open
Abstract
Biological toxins are a heterogeneous group of compounds that share commonalities with biological and chemical agents. Among them, protein toxins represent a considerable, diverse set. They cover a broad range of molecular weights from less than 1000 Da to more than 150 kDa. This review aims to compare conventional detection methods of protein toxins such as in vitro bioassays with proteomic methods, including immunoassays and mass spectrometry-based techniques and their combination. Special emphasis is given to toxins falling into a group of selected agents, according to the Centers for Disease Control and Prevention, such as Staphylococcal enterotoxins, Bacillus anthracis toxins, Clostridium botulinum toxins, Clostridium perfringens epsilon toxin, ricin from Ricinus communis, Abrin from Abrus precatorius or control of trade in dual-use items in the European Union, including lesser known protein toxins such as Viscumin from Viscum album. The analysis of protein toxins and monitoring for biological threats, i.e., the deliberate spread of infectious microorganisms or toxins through water, food, or the air, requires rapid and reliable methods for the early identification of these agents.
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Affiliation(s)
- Miloslava Duracova
- Faculty of Military Health Sciences, University of Defense in Brno, Třebešská 1575, CZ-500 01 Hradec Králové, Czech Republic.
| | - Jana Klimentova
- Faculty of Military Health Sciences, University of Defense in Brno, Třebešská 1575, CZ-500 01 Hradec Králové, Czech Republic.
| | - Alena Fucikova
- Faculty of Military Health Sciences, University of Defense in Brno, Třebešská 1575, CZ-500 01 Hradec Králové, Czech Republic.
| | - Jiri Dresler
- Military Health Institute, Military Medical Agency, Tychonova 1, CZ-160 00 Prague 6, Czech Republic.
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20
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Narumi R, Masuda K, Tomonaga T, Adachi J, Ueda HR, Shimizu Y. Cell-free synthesis of stable isotope-labeled internal standards for targeted quantitative proteomics. Synth Syst Biotechnol 2018; 3:97-104. [PMID: 29900422 PMCID: PMC5995455 DOI: 10.1016/j.synbio.2018.02.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 02/16/2018] [Accepted: 02/18/2018] [Indexed: 01/04/2023] Open
Abstract
High-sensitivity mass spectrometry approaches using selected reaction monitoring (SRM) or multiple reaction monitoring (MRM) methods are powerful tools for targeted quantitative proteomics-based investigation of dynamics in specific biological systems. Both high-sensitivity detection of low-abundance proteins and their quantification using this technique employ stable isotope-labeled peptide internal standards. Currently, there are various ways for preparing standards, including chemical peptide synthesis, cellular protein expression, and cell-free protein or peptide synthesis. Cell-free protein synthesis (CFPS) or in vitro translation (IVT) systems in particular provide high-throughput and low-cost preparation methods, and various cell types and reconstituted forms are now commercially available. Herein, we review the use of such systems for precise and reliable protein quantification.
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Affiliation(s)
- Ryohei Narumi
- Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8, Satio-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Keiko Masuda
- Laboratory for Single Cell Mass Spectrometry, RIKEN Quantitative Biology Center (QBiC), 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan
| | - Takeshi Tomonaga
- Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8, Satio-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Jun Adachi
- Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8, Satio-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Hiroki R. Ueda
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center (QBiC), 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan
| | - Yoshihiro Shimizu
- Laboratory for Single Cell Mass Spectrometry, RIKEN Quantitative Biology Center (QBiC), 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan
- Laboratory for Cell-Free Protein Synthesis, RIKEN Quantitative Biology Center (QBiC), 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan
- Corresponding author. Laboratory for Cell-Free Protein Synthesis, RIKEN Quantitative Biology Center (QBiC), 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan.
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21
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Takemori N, Takemori A, Tanaka Y, Endo Y, Hurst JL, Gómez-Baena G, Harman VM, Beynon RJ. MEERCAT: Multiplexed Efficient Cell Free Expression of Recombinant QconCATs For Large Scale Absolute Proteome Quantification. Mol Cell Proteomics 2017; 16:2169-2183. [PMID: 29055021 PMCID: PMC5724179 DOI: 10.1074/mcp.ra117.000284] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 10/15/2017] [Indexed: 01/25/2023] Open
Abstract
A major challenge in proteomics is the absolute accurate quantification of large numbers of proteins. QconCATs, artificial proteins that are concatenations of multiple standard peptides, are well established as an efficient means to generate standards for proteome quantification. Previously, QconCATs have been expressed in bacteria, but we now describe QconCAT expression in a robust, cell-free system. The new expression approach rescues QconCATs that previously were unable to be expressed in bacteria and can reduce the incidence of proteolytic damage to QconCATs. Moreover, it is possible to cosynthesize QconCATs in a highly-multiplexed translation reaction, coexpressing tens or hundreds of QconCATs simultaneously. By obviating bacterial culture and through the gain of high level multiplexing, it is now possible to generate tens of thousands of standard peptides in a matter of weeks, rendering absolute quantification of a complex proteome highly achievable in a reproducible, broadly deployable system.
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Affiliation(s)
- Nobuaki Takemori
- From the ‡Proteo-Science Center, Ehime University, Ehime, 791-0295, Japan; .,§Advanced Research Support Center, Ehime University, Ehime, 791-0295, Japan
| | - Ayako Takemori
- From the ‡Proteo-Science Center, Ehime University, Ehime, 791-0295, Japan.,¶The United Graduate School of Agricultural Sciences, Ehime University, Ehime, 790-8566, Japan
| | - Yuki Tanaka
- §Advanced Research Support Center, Ehime University, Ehime, 791-0295, Japan
| | - Yaeta Endo
- From the ‡Proteo-Science Center, Ehime University, Ehime, 791-0295, Japan
| | - Jane L Hurst
- **Mammalian Behaviour and Evolution Group, Institute of Integrative Biology, University of Liverpool, Leahurst Campus, Neston CH64 7TE
| | - Guadalupe Gómez-Baena
- ‖Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Victoria M Harman
- ‖Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Robert J Beynon
- ‖Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK;
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22
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Armengaud J. Striking against bioterrorism with advanced proteomics and reference methods. Proteomics 2017; 17. [PMID: 27928908 DOI: 10.1002/pmic.201600412] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Revised: 11/29/2016] [Accepted: 12/01/2016] [Indexed: 02/02/2023]
Abstract
The intentional use by terrorists of biological toxins as weapons has been of great concern for many years. Among the numerous toxins produced by plants, animals, algae, fungi, and bacteria, ricin is one of the most scrutinized by the media because it has already been used in biocrimes and acts of bioterrorism. Improving the analytical toolbox of national authorities to monitor these potential bioweapons all at once is of the utmost interest. MS/MS allows their absolute quantitation and exhibits advantageous sensitivity, discriminative power, multiplexing possibilities, and speed. In this issue of Proteomics, Gilquin et al. (Proteomics 2017, 17, 1600357) present a robust multiplex assay to quantify a set of eight toxins in the presence of a complex food matrix. This MS/MS reference method is based on scheduled SRM and high-quality standards consisting of isotopically labeled versions of these toxins. Their results demonstrate robust reliability based on rather loose scheduling of SRM transitions and good sensitivity for the eight toxins, lower than their oral median lethal doses. In the face of an increased threat from terrorism, relevant reference assays based on advanced proteomics and high-quality companion toxin standards are reliable and firm answers.
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Affiliation(s)
- Jean Armengaud
- CEA, DRF, IBiTec-S, SPI, Li2D, Laboratory "Innovative technologies for Detection and Diagnostics", Bagnols-sur-Cèze, France
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23
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Lehmann S, Picas A, Tiers L, Vialaret J, Hirtz C. Clinical perspectives of dried blood spot protein quantification using mass spectrometry methods. Crit Rev Clin Lab Sci 2017; 54:173-184. [DOI: 10.1080/10408363.2017.1297358] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Sylvain Lehmann
- Laboratory of Biochemistry and Clinical Proteomics, CHU Montpellier, Institute of Regenerative Medicine & Biotherapy, Montpellier, France
| | - Alexia Picas
- Laboratory of Biochemistry and Clinical Proteomics, CHU Montpellier, Institute of Regenerative Medicine & Biotherapy, Montpellier, France
| | - Laurent Tiers
- Laboratory of Biochemistry and Clinical Proteomics, CHU Montpellier, Institute of Regenerative Medicine & Biotherapy, Montpellier, France
| | - Jerome Vialaret
- Laboratory of Biochemistry and Clinical Proteomics, CHU Montpellier, Institute of Regenerative Medicine & Biotherapy, Montpellier, France
| | - Christophe Hirtz
- Laboratory of Biochemistry and Clinical Proteomics, CHU Montpellier, Institute of Regenerative Medicine & Biotherapy, Montpellier, France
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24
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A Comprehensive Guide for Performing Sample Preparation and Top-Down Protein Analysis. Proteomes 2017; 5:proteomes5020011. [PMID: 28387712 PMCID: PMC5489772 DOI: 10.3390/proteomes5020011] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 04/04/2017] [Accepted: 04/04/2017] [Indexed: 12/21/2022] Open
Abstract
Methodologies for the global analysis of proteins in a sample, or proteome analysis, have been available since 1975 when Patrick O′Farrell published the first paper describing two-dimensional gel electrophoresis (2D-PAGE). This technique allowed the resolution of single protein isoforms, or proteoforms, into single ‘spots’ in a polyacrylamide gel, allowing the quantitation of changes in a proteoform′s abundance to ascertain changes in an organism′s phenotype when conditions change. In pursuit of the comprehensive profiling of the proteome, significant advances in technology have made the identification and quantitation of intact proteoforms from complex mixtures of proteins more routine, allowing analysis of the proteome from the ‘Top-Down’. However, the number of proteoforms detected by Top-Down methodologies such as 2D-PAGE or mass spectrometry has not significantly increased since O’Farrell’s paper when compared to Bottom-Up, peptide-centric techniques. This article explores and explains the numerous methodologies and technologies available to analyse the proteome from the Top-Down with a strong emphasis on the necessity to analyse intact proteoforms as a better indicator of changes in biology and phenotype. We arrive at the conclusion that the complete and comprehensive profiling of an organism′s proteome is still, at present, beyond our reach but the continuing evolution of protein fractionation techniques and mass spectrometry brings comprehensive Top-Down proteome profiling closer.
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25
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Exploring the metabolic heterogeneity of coagulase-negative staphylococci to improve the quality and safety of fermented meats: a review. Int J Food Microbiol 2017; 247:24-37. [DOI: 10.1016/j.ijfoodmicro.2016.05.021] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 03/15/2016] [Accepted: 05/15/2016] [Indexed: 12/16/2022]
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26
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Staphylococcus enterotoxin profile of China isolates and the superantigenicity of some novel enterotoxins. Arch Microbiol 2017; 199:723-736. [PMID: 28235987 DOI: 10.1007/s00203-017-1345-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Revised: 12/28/2016] [Accepted: 01/20/2017] [Indexed: 10/20/2022]
Abstract
The genus of staphylococcus widely distributes in environments and contributes to a variety of animal and human diseases. The enterotoxins (SEs) secreted by this type of pathogen have been the leading cause of bacterial toxic shock syndrome and food poisoning, and thus present a substantial concern to public health. In this study, we analyzed the superantigen profile of 122 staphylococcus strains isolated from diverse sources. When screened for the presence and prevalence of 17 known se or se-like (sel) genes, except selj, all other genes were detected in these isolates. In particular, 95.9% of the isolates harbored at least one se/sel gene. Moreover, 47.5% of them bore at least 5. Remarkably, several non-pathogenic species of animal- and environment-origin were also found to carry multiple se/sels. The most frequent genes detected were tsst (62.3%), sei (54.1%), and seb (46.7%), followed by some sel genes (selo, selu, and selm), which also were present at relatively high frequency (20-30%). The generated data improved understanding of strain-specific differences in enterotoxin expression. The gene products of the latter (selo and selu) were subsequently analyzed for their antigenicity in a mouse model using purified E. coli-based recombinant proteins. The studies revealed a strong activity for SEO in induction of T-lymphocyte proliferation and production of various inflammatory cytokines either in vivo or in vitro. In contrast, SEU exhibited little superantigenic effects. The molecular basis for the difference in antigenicity was analyzed by 3D homology remodeling, which revealed a difference in binding and affinities for MHC-II molecules and TCR Vβ region.
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27
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Rasooly R, Do PM, Hernlem BJ. Rapid Cell-Based Assay for Detection and Quantification of Active Staphylococcal Enterotoxin Type D. J Food Sci 2017; 82:718-723. [PMID: 28135403 DOI: 10.1111/1750-3841.13634] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 11/28/2016] [Accepted: 12/29/2016] [Indexed: 11/29/2022]
Abstract
Food poisoning by Staphylococcus aureus is a result of ingestion of Staphylococcal enterotoxins (SEs) produced by this bacterium and is a major source of foodborne illness. Staphylococcal enterotoxin D (SED) is one of the predominant enterotoxins recovered in Staphylococcal food poisoning incidences, including a recent outbreak in Guam affecting 300 children. Current immunology methods for SED detection cannot distinguish between the biologically active form of the toxin, which poses a threat, from the inactive form, which poses no threat. In vivo bioassays that measure emetic activity in kitten and monkeys have been used, but these methods rely upon expensive procedures using live animals and raising ethical concerns. A rapid (5 h) quantitative bioluminescence assay, using a genetically engineered T-cell Jurkat cell line expressing luciferase under regulation of nuclear factor of activated T cells response elements, in combination with the lymphoblastoid B-cell line Raji for antigen presentation, was developed. In this assay, the detection limit of biologically active SED is 100 ng/mL, which is 10 times more sensitive than the splenocyte proliferation assay, and 105 times more sensitive than monkey or kitten bioassay. Pasteurization or repeated freeze-thaw cycles had no effect on SED activity, but reduction in SED activity was shown with heat treatment at 100°C for 5 min. It was also shown that milk exhibits a protective effect on SED. This bioluminescence assay may also be used to rapidly evaluate antibodies to SED for potential therapeutic application as a measurement of neutralizing biological effects of SED.
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Affiliation(s)
- Reuven Rasooly
- Western Regional Research Center, Foodborne Toxin Detection and Prevention Research Unit, Agricultural Research Service, USDA, Albany, CA, U.S.A
| | - Paula M Do
- Western Regional Research Center, Foodborne Toxin Detection and Prevention Research Unit, Agricultural Research Service, USDA, Albany, CA, U.S.A
| | - Bradley J Hernlem
- Western Regional Research Center, Foodborne Toxin Detection and Prevention Research Unit, Agricultural Research Service, USDA, Albany, CA, U.S.A
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28
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Lehmann WD. A timeline of stable isotopes and mass spectrometry in the life sciences. MASS SPECTROMETRY REVIEWS 2017; 36:58-85. [PMID: 26919394 DOI: 10.1002/mas.21497] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 01/21/2016] [Indexed: 06/05/2023]
Abstract
This review retraces the role of stable isotopes and mass spectrometry in the life sciences. The timeline is divided into four segments covering the years 1920-1950, 1950-1980, 1980-2000, and 2000 until today. For each period methodic progress and typical applications are discussed. Application of stable isotopes is driven by improvements of mass spectrometry, chromatography, and related fields in sensitivity, mass accuracy, structural specificity, complex sample handling ability, data output, and data evaluation. We currently experience the vision of omics-type analyses, that is, the comprehensive identification and quantification of a complete compound class within one or a few analytical runs. This development is driven by stable isotopes without competition by radioisotopes. In metabolic studies as classic field of isotopic tracer experiments, stable isotopes and radioisotopes were competing solutions, with stable isotopes as the long-term junior partner. Since the 1990s the number of metabolic studies with radioisotopes decreases, whereas stable isotope studies retain their slow but stable upward tendency. Unique fields of stable isotopes are metabolic tests in newborns, metabolic experiments in healthy controls, newborn screening for inborn errors, quantification of drugs and drug metabolites in doping control, natural isotope fractionation in geology, ecology, food authentication, or doping control, and more recently the field of quantitative omics-type analyses. There, cells or whole organisms are systematically labeled with stable isotopes to study proteomic differences or specific responses to stimuli or genetic manipulation. The duo of stable isotopes and mass spectrometry will probably continue to grow in the life sciences, since it delivers reference-quality quantitative data with molecular specificity, often combined with informative isotope effects. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:58-85, 2017.
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Affiliation(s)
- Wolf D Lehmann
- German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
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29
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Alam SI, Uppal A, Gupta P, Kamboj DV. Multiple-reaction monitoring for multiplex detection of three bacterial toxins using liquid chromatography-tandem mass spectrometry. Lett Appl Microbiol 2016; 64:217-224. [PMID: 28024103 DOI: 10.1111/lam.12706] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 12/09/2016] [Accepted: 12/10/2016] [Indexed: 11/28/2022]
Abstract
Clostridium perfringens epsilon toxin, staphylococcal enterotoxin B and shiga toxin are implicated in a number of diseases and food-borne intoxications and are considered potential agents for bioterrorism and warfare. Artificially generated aerosol is the likely mode of delivery of these for nefarious uses, potentially capable of causing mass destruction to human and animal health by inhalation of toxic bioaerosol. Multiplex and unambiguous detection of these agents is of paramount importance for emergency response in a biothreat scenario and for food safety. Multiple-reaction monitoring (MRM) assay for simultaneous monitoring of the three toxins is reported here using reverse-phase high-performance liquid chromatography-electrospray ionization-tandem mass spectrometry. Three different peptides with two fragment ions each were considered for quantification and confirmation. One of the three MRM transitions from each toxin, which exhibited the best sensitivity, was selected for multiplexing of the assay. Simulating a biothreat scenario wherein the bioaerosol is collected in 10 ml of buffer, the multiplex assay was tested with blind samples with one or more of the three toxins even in the presence of interfering Escherichia coli lysate proteins.
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Affiliation(s)
- S I Alam
- Biotechnology Division, Defence Research and Development Establishment, Gwalior, India
| | - A Uppal
- Sciex, A Division of DHR Holding India Pvt. Ltd., Gurgaon, India
| | - P Gupta
- Biotechnology Division, Defence Research and Development Establishment, Gwalior, India
| | - D V Kamboj
- Biotechnology Division, Defence Research and Development Establishment, Gwalior, India
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30
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Gilquin B, Jaquinod M, Louwagie M, Kieffer-Jaquinod S, Kraut A, Ferro M, Becher F, Brun V. A proteomics assay to detect eight CBRN-relevant toxins in food. Proteomics 2016; 17. [PMID: 28008711 DOI: 10.1002/pmic.201600357] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 10/07/2016] [Accepted: 10/27/2016] [Indexed: 02/06/2023]
Abstract
A proteomics assay was set up to analyze food substrates for eight toxins of the CBRN (chemical, biological, radiological and nuclear) threat, namely ricin, Clostridium perfringens epsilon toxin (ETX), Staphylococcus aureus enterotoxins (SEA, SEB and SED), shigatoxins from Shigella dysenteriae and entero-hemorragic Escherichia coli strains (STX1 and STX2) and Campylobacter jejuni cytolethal distending toxin (CDT). The assay developed was based on an antibody-free sample preparation followed by bottom-up LC-MS/MS analysis operated in targeted mode. Highly specific detection and absolute quantification were obtained using isotopically labeled proteins (PSAQ standards) spiked into the food matrix. The sensitivity of the assay for the eight toxins was lower than the oral LD50 which would likely be used in a criminal contamination of food supply. This assay should be useful in monitoring biological threats. In the public-health domain, it opens the way for multiplex investigation of food-borne toxins using targeted LC-MS/MS.
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Affiliation(s)
- Benoit Gilquin
- Université Grenoble-Alpes, Grenoble, France.,CEA, BIG, Biologie à Grande Echelle, Grenoble, France.,INSERM, U1038, Grenoble, France.,CEA, LETI, Clinatec, Grenoble, France
| | - Michel Jaquinod
- Université Grenoble-Alpes, Grenoble, France.,CEA, BIG, Biologie à Grande Echelle, Grenoble, France.,INSERM, U1038, Grenoble, France
| | - Mathilde Louwagie
- Université Grenoble-Alpes, Grenoble, France.,CEA, BIG, Biologie à Grande Echelle, Grenoble, France.,INSERM, U1038, Grenoble, France
| | - Sylvie Kieffer-Jaquinod
- Université Grenoble-Alpes, Grenoble, France.,CEA, BIG, Biologie à Grande Echelle, Grenoble, France.,INSERM, U1038, Grenoble, France
| | - Alexandra Kraut
- Université Grenoble-Alpes, Grenoble, France.,CEA, BIG, Biologie à Grande Echelle, Grenoble, France.,INSERM, U1038, Grenoble, France
| | - Myriam Ferro
- Université Grenoble-Alpes, Grenoble, France.,CEA, BIG, Biologie à Grande Echelle, Grenoble, France.,INSERM, U1038, Grenoble, France
| | - François Becher
- CEA, iBiTec-S, Laboratoire d'Etude du Métabolisme des Médicaments, Gif-sur-Yvette, France
| | - Virginie Brun
- Université Grenoble-Alpes, Grenoble, France.,CEA, BIG, Biologie à Grande Echelle, Grenoble, France.,INSERM, U1038, Grenoble, France
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31
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Nia Y, Rodriguez M, Zeleny R, Herbin S, Auvray F, Fiebig U, Avondet MA, Munoz A, Hennekinne JA. Organization and ELISA-Based Results of the First Proficiency Testing to Evaluate the Ability of European Union Laboratories to Detect Staphylococcal Enterotoxin Type B (SEB) in Buffer and Milk. Toxins (Basel) 2016; 8:E268. [PMID: 27649244 PMCID: PMC5037494 DOI: 10.3390/toxins8090268] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 08/31/2016] [Accepted: 08/31/2016] [Indexed: 11/26/2022] Open
Abstract
The aim of this work was to organize the first proficiency test (PT) dedicated to staphylococcal enterotoxin B (SEB) detection in milk and buffer solutions. This paper describes the organization of the PT trial according to EN ISO 17043 requirements. Characterization of the SEB stock solution was performed using SDS-PAGE and SE-specific ELISA, and amino acid analysis was used to assign its protein concentration. The solution was then used to prepare six PT materials (four milk and two buffer batches) at a ng/g toxin level, which included one blank and one SEA-containing milk as specificity control. Suitable material homogeneity and stability were assessed using screening and quantitative ELISAs. Among the methods used by the participants, ELISA-based methods demonstrated their efficiency for the detection of SEB in both simple and complex matrices. The results serve as a basis for further improving the detection capabilities in expert laboratories and can therefore be considered as a contribution to biopreparedness.
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Affiliation(s)
- Yacine Nia
- Laboratory for food safety, ANSES, Université Paris-Est, Maisons-Alfort F-94700, France.
| | - Mélanie Rodriguez
- Laboratory for food safety, ANSES, Université Paris-Est, Maisons-Alfort F-94700, France.
| | - Reinhard Zeleny
- Joint Research Centre, Directorate for Health, Consumers and Reference Materials, European Commission, Retieseweg 111, Geel 2440, Belgium.
| | - Sabine Herbin
- Laboratory for food safety, ANSES, Université Paris-Est, Maisons-Alfort F-94700, France.
| | - Frédéric Auvray
- Laboratory for food safety, ANSES, Université Paris-Est, Maisons-Alfort F-94700, France.
| | - Uwe Fiebig
- Centre for Biological Threats and Special Pathogens Biological Toxins, Robert Koch Institute, Berlin 13353, Germany.
| | - Marc-André Avondet
- LABOR SPIEZ, Eidgenössisches Departement für Verteidigung, Bevölkerungsschutz und Sport VBS Bundesamt für Bevölkerungsschutz BABS, Spiez 3700, Switzerland.
| | - Amalia Munoz
- Joint Research Centre, Directorate for Health, Consumers and Reference Materials, European Commission, Retieseweg 111, Geel 2440, Belgium.
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32
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Charretier Y, Schrenzel J. Mass spectrometry methods for predicting antibiotic resistance. Proteomics Clin Appl 2016; 10:964-981. [PMID: 27312049 DOI: 10.1002/prca.201600041] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/09/2016] [Accepted: 06/13/2016] [Indexed: 11/10/2022]
Abstract
Developing elaborate techniques for clinical applications can be a complicated process. Whole-cell MALDI-TOF MS revolutionized reliable microorganism identification in clinical microbiology laboratories and is now replacing phenotypic microbial identification. This technique is a generic, accurate, rapid, and cost-effective growth-based method. Antibiotic resistance keeps emerging in environmental and clinical microorganisms, leading to clinical therapeutic challenges, especially for Gram-negative bacteria. Antimicrobial susceptibility testing is used to reliably predict antimicrobial success in treating infection, but it is inherently limited by the need to isolate and grow cultures, delaying the application of appropriate therapies. Antibiotic resistance prediction by growth-independent methods is expected to reduce the turnaround time. Recently, the potential of next-generation sequencing and microarrays in predicting microbial resistance has been demonstrated, and this review evaluates the potential of MS in this field. First, technological advances are described, and the possibility of predicting antibiotic resistance by MS is then illustrated for three prototypical human pathogens: Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa. Clearly, MS methods can identify antimicrobial resistance mediated by horizontal gene transfers or by mutations that affect the quantity of a gene product, whereas antimicrobial resistance mediated by target mutations remains difficult to detect.
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Affiliation(s)
- Yannick Charretier
- Genomic Research Laboratory, Division of Infectious Diseases, Geneva University Hospitals.
| | - Jacques Schrenzel
- Genomic Research Laboratory, Division of Infectious Diseases, Geneva University Hospitals
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33
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Rasooly R, Do P, Hernlem B. Sensitive, Rapid, Quantitative and in Vitro Method for the Detection of Biologically Active Staphylococcal Enterotoxin Type E. Toxins (Basel) 2016; 8:toxins8050150. [PMID: 27187474 PMCID: PMC4885065 DOI: 10.3390/toxins8050150] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 05/06/2016] [Accepted: 05/09/2016] [Indexed: 11/24/2022] Open
Abstract
Staphylococcus aureus is a major bacterial cause of clinical infections and foodborne illnesses through its production of a group of enterotoxins (SEs) which cause gastroenteritis and also function as superantigens to massively activate T cells. In the present study, we tested Staphylococcal enterotoxin type E (SEE), which was detected in 17 of the 38 suspected staphylococcal food poisoning incidents in a British study and was the causative agent in outbreaks in France, UK and USA. The current method for detection of enterotoxin activity is an in vivo monkey or kitten bioassay; however, this expensive procedure has low sensitivity and poor reproducibility, requires many animals, is impractical to test on a large number of samples, and raises ethical concerns with regard to the use of experimental animals. The purpose of this study is to develop rapid sensitive and quantitative bioassays for detection of active SEE. We apply a genetically engineered T cell-line expressing the luciferase reporter gene under the regulation of nuclear factor of activated T-cells response element (NFAT-RE), combined with a Raji B-cell line that presents the SEE-MHC (major histocompatibility complex) class II to the engineered T cell line. Exposure of the above mixed culture to SEE induces differential expression of the luciferase gene and bioluminescence is read out in a dose dependent manner over a 6-log range. The limit of detection of biologically active SEE is 1 fg/mL which is 109 times more sensitive than the monkey and kitten bioassay.
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Affiliation(s)
- Reuven Rasooly
- Western Regional Research Center, Foodborne Toxin Detection & Prevention Research Unit, Agricultural Research Service, United States Department of Agriculture, Albany, CA 94710, USA.
| | - Paula Do
- Western Regional Research Center, Foodborne Toxin Detection & Prevention Research Unit, Agricultural Research Service, United States Department of Agriculture, Albany, CA 94710, USA.
| | - Bradley Hernlem
- Western Regional Research Center, Foodborne Toxin Detection & Prevention Research Unit, Agricultural Research Service, United States Department of Agriculture, Albany, CA 94710, USA.
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34
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Kito K, Okada M, Ishibashi Y, Okada S, Ito T. A strategy for absolute proteome quantification with mass spectrometry by hierarchical use of peptide-concatenated standards. Proteomics 2016; 16:1457-73. [DOI: 10.1002/pmic.201500414] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 02/18/2016] [Accepted: 03/24/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Keiji Kito
- Department of Life Sciences, School of Agriculture; Meiji University; Kawasaki Japan
| | - Mitsuhiro Okada
- Department of Life Sciences, School of Agriculture; Meiji University; Kawasaki Japan
| | - Yuko Ishibashi
- Department of Life Sciences, School of Agriculture; Meiji University; Kawasaki Japan
| | - Satoshi Okada
- Department of Biochemistry; Kyushu University Graduate School of Medical Science; Fukuoka Japan
| | - Takashi Ito
- Department of Biochemistry; Kyushu University Graduate School of Medical Science; Fukuoka Japan
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35
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Andjelkovic M, Tsilia V, Rajkovic A, De Cremer K, Van Loco J. Application of LC-MS/MS MRM to Determine Staphylococcal Enterotoxins (SEB and SEA) in Milk. Toxins (Basel) 2016; 8:118. [PMID: 27104569 PMCID: PMC4848643 DOI: 10.3390/toxins8040118] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 03/25/2016] [Accepted: 04/06/2016] [Indexed: 12/29/2022] Open
Abstract
Staphylococcus aureus is one of the important aetiological agents of food intoxications in Europe and can cause gastro-enteritis through the production of various staphylococcal enterotoxins (SEs) in foods. Due to their stability and ease of production and dissemination, some SEs have also been studied as potential agents for bioterrorism. Therefore, specific and accurate analytical tools are required to detect and quantify SEs. Online solid-phase extraction liquid chromatography electrospray ionization tandem mass spectrometry (online SPE-LC-ESI-MS/MS) based on multiple reaction monitoring (MRM) was used to detect and quantify two types of SE (A and B) spiked in milk and buffer solution. SE extraction and concentration was performed according to the European Screening Method developed by the European Reference Laboratory for Coagulase Positive Staphylococci. Trypsin digests were screened for the presence of SEs using selected proteotypic heavy-labeled peptides as internal standards. SEA and SEB were successfully detected in milk samples using LC-MS/MS in MRM mode. The selected SE peptides were proteotypic for each toxin, allowing the discrimination of SEA and SEB in a single run. The detection limit of SEA and SEB was approximately 8 and 4 ng/g, respectively.
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Affiliation(s)
- Mirjana Andjelkovic
- Food, Medicine and Consumer Safety, Scientific Institute of Public Health (WIV-ISP), Juliette Wytsmanstraat 14, 1050 Brussels, Belgium.
| | - Varvara Tsilia
- Food, Medicine and Consumer Safety, Scientific Institute of Public Health (WIV-ISP), Juliette Wytsmanstraat 14, 1050 Brussels, Belgium.
| | - Andreja Rajkovic
- Laboratory of Food Microbiology and Food Preservation, Ghent University (UGent), Coupure Links 657, 9000 Ghent, Belgium.
| | - Koen De Cremer
- Food, Medicine and Consumer Safety, Scientific Institute of Public Health (WIV-ISP), Juliette Wytsmanstraat 14, 1050 Brussels, Belgium.
| | - Joris Van Loco
- Food, Medicine and Consumer Safety, Scientific Institute of Public Health (WIV-ISP), Juliette Wytsmanstraat 14, 1050 Brussels, Belgium.
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36
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Duriez E, Armengaud J, Fenaille F, Ezan E. Mass spectrometry for the detection of bioterrorism agents: from environmental to clinical applications. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:183-199. [PMID: 26956386 DOI: 10.1002/jms.3747] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 12/14/2015] [Accepted: 01/13/2016] [Indexed: 06/05/2023]
Abstract
In the current context of international conflicts and localized terrorist actions, there is unfortunately a permanent threat of attacks with unconventional warfare agents. Among these, biological agents such as toxins, microorganisms, and viruses deserve particular attention owing to their ease of production and dissemination. Mass spectrometry (MS)-based techniques for the detection and quantification of biological agents have a decisive role to play for countermeasures in a scenario of biological attacks. The application of MS to every field of both organic and macromolecular species has in recent years been revolutionized by the development of soft ionization techniques (MALDI and ESI), and by the continuous development of MS technologies (high resolution, accurate mass HR/AM instruments, novel analyzers, hybrid configurations). New possibilities have emerged for exquisite specific and sensitive detection of biological warfare agents. MS-based strategies for clinical application can now address a wide range of analytical questions mainly including issues related to the complexity of biological samples and their available volume. Multiplexed toxin detection, discovery of new markers through omics approaches, and identification of untargeted microbiological or of novel molecular targets are examples of applications. In this paper, we will present these technological advances along with the novel perspectives offered by omics approaches to clinical detection and follow-up.
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Affiliation(s)
| | - Jean Armengaud
- CEA, iBiTec-S, Service de Pharmacologie et d'Immunologie, 30207, Bagnols sur-Cèze, France
| | - François Fenaille
- CEA, iBiTec-S, Service de Pharmacologie et d'Immunoanalyse, Laboratoire d'Etude du Métabolisme des Médicaments, MetaboHUB-Paris, CEA Saclay, Building 136, 91191, Gif-sur-Yvette cedex, France
| | - Eric Ezan
- CEA, Programme Transversal Technologies pour la Santé, 91191, Gif sur Yvette, France
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Piras C, Roncada P, Rodrigues PM, Bonizzi L, Soggiu A. Proteomics in food: Quality, safety, microbes, and allergens. Proteomics 2016; 16:799-815. [PMID: 26603968 DOI: 10.1002/pmic.201500369] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 10/21/2015] [Accepted: 11/17/2015] [Indexed: 02/04/2023]
Abstract
Food safety and quality and their associated risks pose a major concern worldwide regarding not only the relative economical losses but also the potential danger to consumer's health. Customer's confidence in the integrity of the food supply could be hampered by inappropriate food safety measures. A lack of measures and reliable assays to evaluate and maintain a good control of food characteristics may affect the food industry economy and shatter consumer confidence. It is imperative to create and to establish fast and reliable analytical methods that allow a good and rapid analysis of food products during the whole food chain. Proteomics can represent a powerful tool to address this issue, due to its proven excellent quantitative and qualitative drawbacks in protein analysis. This review illustrates the applications of proteomics in the past few years in food science focusing on food of animal origin with some brief hints on other types. Aim of this review is to highlight the importance of this science as a valuable tool to assess food quality and safety. Emphasis is also posed in food processing, allergies, and possible contaminants like bacteria, fungi, and other pathogens.
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Affiliation(s)
- Cristian Piras
- Dipartimento di Scienze Veterinarie e Sanità Pubblica (DIVET), Università degli studi di Milano, Milano, Italy
| | - Paola Roncada
- Istituto Sperimentale Italiano L. Spallanzani, Milano, Italy
| | - Pedro M Rodrigues
- CCMAR, Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | - Luigi Bonizzi
- Dipartimento di Scienze Veterinarie e Sanità Pubblica (DIVET), Università degli studi di Milano, Milano, Italy
| | - Alessio Soggiu
- Dipartimento di Scienze Veterinarie e Sanità Pubblica (DIVET), Università degli studi di Milano, Milano, Italy
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Zhao Y, Brasier AR. Qualification and Verification of Protein Biomarker Candidates. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 919:493-514. [DOI: 10.1007/978-3-319-41448-5_23] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Mageean CJ, Griffiths JR, Smith DL, Clague MJ, Prior IA. Absolute Quantification of Endogenous Ras Isoform Abundance. PLoS One 2015; 10:e0142674. [PMID: 26560143 PMCID: PMC4641634 DOI: 10.1371/journal.pone.0142674] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/26/2015] [Indexed: 01/15/2023] Open
Abstract
Ras proteins are important signalling hubs situated near the top of networks controlling cell proliferation, differentiation and survival. Three almost identical isoforms, HRAS, KRAS and NRAS, are ubiquitously expressed yet have differing biological and oncogenic properties. In order to help understand the relative biological contributions of each isoform we have optimised a quantitative proteomics method for accurately measuring Ras isoform protein copy number per cell. The use of isotopic protein standards together with selected reaction monitoring for diagnostic peptides is sensitive, robust and suitable for application to sub-milligram quantities of lysates. We find that in a panel of isogenic SW48 colorectal cancer cells, endogenous Ras proteins are highly abundant with ≥260,000 total Ras protein copies per cell and the rank order of isoform abundance is KRAS>NRAS≥HRAS. A subset of oncogenic KRAS mutants exhibit increased total cellular Ras abundance and altered the ratio of mutant versus wild type KRAS protein. These data and methodology are significant because Ras protein copy number is required to parameterise models of signalling networks and informs interpretation of isoform-specific Ras functional data.
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Affiliation(s)
- Craig J. Mageean
- Division of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, L69 3BX, United Kingdom
| | - John R. Griffiths
- Cancer Research UK Manchester Institute, University of Manchester, Manchester, M20 4BX, United Kingdom
| | - Duncan L. Smith
- Cancer Research UK Manchester Institute, University of Manchester, Manchester, M20 4BX, United Kingdom
| | - Michael J. Clague
- Division of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, L69 3BX, United Kingdom
| | - Ian A. Prior
- Division of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, L69 3BX, United Kingdom
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Quantitative Analysis of Staphylococcal Enterotoxins A and B in Food Matrices Using Ultra High-Performance Liquid Chromatography Tandem Mass Spectrometry (UPLC-MS/MS). Toxins (Basel) 2015; 7:3637-56. [PMID: 26378579 PMCID: PMC4591654 DOI: 10.3390/toxins7093637] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 09/02/2015] [Accepted: 09/06/2015] [Indexed: 11/17/2022] Open
Abstract
A method that uses mass spectrometry (MS) for identification and quantification of protein toxins, staphylococcal enterotoxins A and B (SEA and SEB), in milk and shrimp is described. The analysis was performed using a tryptic peptide, from each of the toxins, as the target analyte together with the corresponding 13C-labeled synthetic internal standard peptide. The performance of the method was evaluated by analyzing spiked samples in the quantification range 2.5–30 ng/g (R2 = 0.92–0.99). The limit of quantification (LOQ) in milk and the limit of detection (LOD) in shrimp was 2.5 ng/g, for both SEA and SEB toxins. The in-house reproducibility (RSD) was 8%–30% and 5%–41% at different concentrations for milk and shrimp, respectively. The method was compared to the ELISA method, used at the EU-RL (France), for milk samples spiked with SEA at low levels, in the quantification range of 2.5 to 5 ng/g. The comparison showed good coherence for the two methods: 2.9 (MS)/1.8 (ELISA) and 3.6 (MS)/3.8 (ELISA) ng/g. The major advantage of the developed method is that it allows direct confirmation of the molecular identity and quantitative analysis of SEA and SEB at low nanogram levels using a label and antibody free approach. Therefore, this method is an important step in the development of alternatives to the immune-assay tests currently used for staphylococcal enterotoxin analysis.
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Rapid Bacterial Identification, Resistance, Virulence and Type Profiling using Selected Reaction Monitoring Mass Spectrometry. Sci Rep 2015; 5:13944. [PMID: 26350205 PMCID: PMC4563557 DOI: 10.1038/srep13944] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 08/05/2015] [Indexed: 11/08/2022] Open
Abstract
Mass spectrometry (MS) in Selected Reaction Monitoring (SRM) mode is proposed for in-depth characterisation of microorganisms in a multiplexed analysis. Within 60–80 minutes, the SRM method performs microbial identification (I), antibiotic-resistance detection (R), virulence assessment (V) and it provides epidemiological typing information (T). This SRM application is illustrated by the analysis of the human pathogen Staphylococcus aureus, demonstrating its promise for rapid characterisation of bacteria from positive blood cultures of sepsis patients.
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Ebhardt HA, Root A, Sander C, Aebersold R. Applications of targeted proteomics in systems biology and translational medicine. Proteomics 2015; 15:3193-208. [PMID: 26097198 PMCID: PMC4758406 DOI: 10.1002/pmic.201500004] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 04/27/2015] [Accepted: 06/09/2015] [Indexed: 01/28/2023]
Abstract
Biological systems are composed of numerous components of which proteins are of particularly high functional significance. Network models are useful abstractions for studying these components in context. Network representations display molecules as nodes and their interactions as edges. Because they are difficult to directly measure, functional edges are frequently inferred from suitably structured datasets consisting of the accurate and consistent quantification of network nodes under a multitude of perturbed conditions. For the precise quantification of a finite list of proteins across a wide range of samples, targeted proteomics exemplified by selected/multiple reaction monitoring (SRM, MRM) mass spectrometry has proven useful and has been applied to a variety of questions in systems biology and clinical studies. Here, we survey the literature of studies using SRM-MS in systems biology and clinical proteomics. Systems biology studies frequently examine fundamental questions in network biology, whereas clinical studies frequently focus on biomarker discovery and validation in a variety of diseases including cardiovascular disease and cancer. Targeted proteomics promises to advance our understanding of biological networks and the phenotypic significance of specific network states and to advance biomarkers into clinical use.
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Affiliation(s)
- H Alexander Ebhardt
- Department of Biology, Institute of Molecular Systems Biology, Eidgenossische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Alex Root
- Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medical College, New York, NY, USA
| | - Chris Sander
- Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, Eidgenossische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
- Faculty of Science, University of Zurich, Zurich, Switzerland
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Dupré M, Gilquin B, Fenaille F, Feraudet-Tarisse C, Dano J, Ferro M, Simon S, Junot C, Brun V, Becher F. Multiplex Quantification of Protein Toxins in Human Biofluids and Food Matrices Using Immunoextraction and High-Resolution Targeted Mass Spectrometry. Anal Chem 2015; 87:8473-80. [DOI: 10.1021/acs.analchem.5b01900] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Mathieu Dupré
- CEA, DSV, iBiTec-S, Laboratoire d’études
du métabolisme des médicaments, 91191 Gif-sur-Yvette, France
| | - Benoit Gilquin
- Université
Grenoble Alpes, iRTSV-BGE, F-38000 Grenoble, France
- CEA, iRTSV-BGE, F-38000 Grenoble, France
- INSERM, BGE, F-38000 Grenoble, France
| | - François Fenaille
- CEA, DSV, iBiTec-S, Laboratoire d’études
du métabolisme des médicaments, 91191 Gif-sur-Yvette, France
| | - Cécile Feraudet-Tarisse
- CEA, DSV, iBiTec-S, Laboratoire d’études
et de recherches en immunoanalyse, 91191 Gif-sur-Yvette, France
| | - Julie Dano
- CEA, DSV, iBiTec-S, Laboratoire d’études
et de recherches en immunoanalyse, 91191 Gif-sur-Yvette, France
| | - Myriam Ferro
- Université
Grenoble Alpes, iRTSV-BGE, F-38000 Grenoble, France
- CEA, iRTSV-BGE, F-38000 Grenoble, France
- INSERM, BGE, F-38000 Grenoble, France
| | - Stéphanie Simon
- CEA, DSV, iBiTec-S, Laboratoire d’études
et de recherches en immunoanalyse, 91191 Gif-sur-Yvette, France
| | - Christophe Junot
- CEA, DSV, iBiTec-S, Laboratoire d’études
du métabolisme des médicaments, 91191 Gif-sur-Yvette, France
| | - Virginie Brun
- Université
Grenoble Alpes, iRTSV-BGE, F-38000 Grenoble, France
- CEA, iRTSV-BGE, F-38000 Grenoble, France
- INSERM, BGE, F-38000 Grenoble, France
| | - François Becher
- CEA, DSV, iBiTec-S, Laboratoire d’études
du métabolisme des médicaments, 91191 Gif-sur-Yvette, France
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44
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Al Feteisi H, Achour B, Rostami-Hodjegan A, Barber J. Translational value of liquid chromatography coupled with tandem mass spectrometry-based quantitative proteomics forin vitro–in vivoextrapolation of drug metabolism and transport and considerations in selecting appropriate techniques. Expert Opin Drug Metab Toxicol 2015; 11:1357-69. [DOI: 10.1517/17425255.2015.1055245] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Abstract
The high degree of protein sequence similarity in the MUPs (major urinary proteins) poses considerable challenges for their individual differentiation, analysis and quantification. In the present review, we discuss MS approaches for MUP quantification, at either the protein or the peptide level. In particular, we describe an approach to multiplexed quantification based on the design and synthesis of novel proteins (QconCATs) that are concatamers of quantification standards, providing a simple route to the generation of a set of stable-isotope-labelled peptide standards. The MUPs pose a particular challenge to QconCAT design, because of their sequence similarity and the limited number of peptides that can be used to construct the standards. Such difficulties can be overcome by careful attention to the analytical workflow.
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Al Feteisi H, Achour B, Barber J, Rostami-Hodjegan A. Choice of LC-MS methods for the absolute quantification of drug-metabolizing enzymes and transporters in human tissue: a comparative cost analysis. AAPS JOURNAL 2015; 17:438-46. [PMID: 25663651 DOI: 10.1208/s12248-014-9712-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 12/23/2014] [Indexed: 11/30/2022]
Abstract
The quantification of drug-metabolizing enzymes and transporters is important for in vitro-in vivo extrapolation (IVIVE) of xenobiotic clearance, which has become an integral part of drug development. There are different mass spectrometry-based techniques used for quantitative proteomics, and as more laboratories are opting for the use of these methods, selecting the most appropriate tool is becoming a concern. For the first time, we attempt to determine the significance of cost of different LC-MS methods of quantitative analysis of these proteins and to present a framework to objectively assess the choice of the techniques. Based on our analysis, quantification using labeled internal standards is more expensive per sample but provides higher quality data than label-free quantification. Quantification using absolute quantification synthetic peptides is the approach of choice for analyzing less than nine proteins, whereas when quantifying a defined set of proteins (10-50), such as enzymes, in a reasonably large number of samples (20-100), the quantification concatemer technique is more economical, followed by label-free quantification. When analyzing proteomes or sub-proteomes (≥500 proteins), label-free quantification is more cost-effective than the use of labeled internal standards. A cost-benefit approach is described to assess the choice of the most appropriate mass spectrometry-based approach for the quantification of proteins relevant to IVIVE.
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Affiliation(s)
- Hajar Al Feteisi
- Manchester Pharmacy School, University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, UK
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47
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Moczulska KE, Pichler P, Schutzbier M, Schleiffer A, Rumpel S, Mechtler K. Deep and precise quantification of the mouse synaptosomal proteome reveals substantial remodeling during postnatal maturation. J Proteome Res 2014; 13:4310-24. [PMID: 25157418 DOI: 10.1021/pr500456t] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
During postnatal murine maturation, behavioral patterns emerge and become shaped by experience-dependent adaptations. During the same period, the morphology of dendritic spines, the morphological correlates of excitatory synapses, is known to change, and there is evidence of concurrent alterations of the synaptosomal protein machinery. To obtain comprehensive and quantitative insights in the developmental regulation of the proteome of synapses, we prepared cortical synaptosomal fractions from a total of 16 individual juvenile and adult mouse brains (age 3 or 8 weeks, respectively). We then applied peptide-based iTRAQ labeling (four pools of 4 animals) and high-resolution two-dimensional peptide fractionation (99 SCX fractions and 3 h reversed-phase gradients) using a hybrid CID-HCD acquisition method on a Velos Orbitrap mass spectrometer to identify a comprehensive set of synaptic proteins and to quantify changes in protein expression. We obtained a data set tracking expression levels of 3500 proteins mapping to 3427 NCBI GeneIDs during development with complete quantification data available for 3422 GeneIDs, which, to the best of our knowledge, constitutes the deepest coverage of the synaptosome proteome to date. The inclusion of biological replicates in a single mass spectrometry analysis demonstrated both high reproducibility of our synaptosome preparation method as well as high precision of our quantitative data (correlation coefficient R = 0.87 for the biological replicates). To evaluate the validity of our data, the developmental regulation of eight proteins identified in our analysis was confirmed independently using western blotting. A gene ontology analysis confirmed the synaptosomal nature of a large fraction of identified proteins. Of note, the set of the most strongly regulated proteins revealed candidates involved in neurological processes in health and disease states. This highlights the fact that developmentally regulated proteins can play additional roles in neurological disease processes. All data have been deposited to the ProteomeXchange with identifier PXD000552.
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Affiliation(s)
- Kaja Ewa Moczulska
- Research Institute of Molecular Pathology , Dr. Bohr-Gasse 7, 1030 Vienna, Austria
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48
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Gianazza E, Tremoli E, Banfi C. The selected reaction monitoring/multiple reaction monitoring-based mass spectrometry approach for the accurate quantitation of proteins: clinical applications in the cardiovascular diseases. Expert Rev Proteomics 2014; 11:771-88. [PMID: 25400095 DOI: 10.1586/14789450.2014.947966] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Selected reaction monitoring, also known as multiple reaction monitoring, is a powerful targeted mass spectrometry approach for a confident quantitation of proteins/peptides in complex biological samples. In recent years, its optimization and application have become pivotal and of great interest in clinical research to derive useful outcomes for patient care. Thus, selected reaction monitoring/multiple reaction monitoring is now used as a highly sensitive and selective method for the evaluation of protein abundances and biomarker verification with potential applications in medical screening. This review describes technical aspects for the development of a robust multiplex assay and discussing its recent applications in cardiovascular proteomics: verification of promising disease candidates to select only the highest quality peptides/proteins for a preclinical validation, as well as quantitation of protein isoforms and post-translational modifications.
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Affiliation(s)
- Erica Gianazza
- Laboratory of Cell Biology and Biochemistry of Atherothrombosis, Unit of Proteomics, Centro Cardiologico Monzino IRCCS, Via Parea 4, 20138 Milan, Italy
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Chung LM, Colangelo CM, Zhao H. Data Pre-Processing for Label-Free Multiple Reaction Monitoring (MRM) Experiments. BIOLOGY 2014; 3:383-402. [PMID: 24905083 PMCID: PMC4085614 DOI: 10.3390/biology3020383] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 04/16/2014] [Accepted: 05/10/2014] [Indexed: 12/02/2022]
Abstract
Multiple Reaction Monitoring (MRM) conducted on a triple quadrupole mass spectrometer allows researchers to quantify the expression levels of a set of target proteins. Each protein is often characterized by several unique peptides that can be detected by monitoring predetermined fragment ions, called transitions, for each peptide. Concatenating large numbers of MRM transitions into a single assay enables simultaneous quantification of hundreds of peptides and proteins. In recognition of the important role that MRM can play in hypothesis-driven research and its increasing impact on clinical proteomics, targeted proteomics such as MRM was recently selected as the Nature Method of the Year. However, there are many challenges in MRM applications, especially data pre‑processing where many steps still rely on manual inspection of each observation in practice. In this paper, we discuss an analysis pipeline to automate MRM data pre‑processing. This pipeline includes data quality assessment across replicated samples, outlier detection, identification of inaccurate transitions, and data normalization. We demonstrate the utility of our pipeline through its applications to several real MRM data sets.
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Affiliation(s)
- Lisa M Chung
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06520, USA.
| | - Christopher M Colangelo
- Keck Foundation Biotechnology Resource Laboratory, Yale School of Medicine, New Haven, CT 06510, USA.
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06520, USA.
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50
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Rasooly R, Hernlem BJ. Quantitative analysis of staphylococcus enterotoxin A by differential expression of IFN-γ in splenocyte and CD4⁺ T-cells. SENSORS 2014; 14:8869-76. [PMID: 24854207 PMCID: PMC4063072 DOI: 10.3390/s140508869] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 05/15/2014] [Accepted: 05/15/2014] [Indexed: 11/21/2022]
Abstract
Staphylococcus aureus is an important bacterial pathogen that produces a range of Staphylococcal Enterotoxins (SEs) which cause gastroenteritis and superantigen activation of T cells, the mechanism of which is not well understood. The ability to rapidly detect and quantify SEs is very important in order to learn the causes of staphylococcal outbreaks and to stop similar outbreaks in the future. Enzyme-linked immunosorbent assays (ELISAs) have been developed for detection of several SEs. However, these immunological methods cannot distinguish between active and inactive toxin. It is known that interferon-gamma (IFN-γ) expressed in response to stimulation by SEs contributes significantly to the pathogenesis of S. aureus infection. Nonetheless, the cellular source of IFN-γ is still unclear and the contributions of the specific splenocyte types. In our effort to understand the immunologic response to Staphylococcal Enterotoxin A (SEA) exposure, we studied IFN-γ production in mouse splenocytes. We demonstrated that short term ex vivo exposure of splenocytes or primary naïve CD4+ T-cells to biologically active SEA induces differential expression of IFN-γ mRNA in a time and dose dependent manner and the expression levels reflect the levels of IFN-γ secreted protein. Positive isolated CD4+ T-cells accounted for only 10% of IFN-γ production. We also demonstrate that expression of IFN-γ can be used for rapid quantitative analysis of active SEA with a detection limit of 1 ng/mL.
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Affiliation(s)
- Reuven Rasooly
- Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA 94710, USA.
| | - Bradley J Hernlem
- Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA 94710, USA.
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