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Pratelli G, Tamburini B, Carlisi D, De Blasio A, D’Anneo A, Emanuele S, Notaro A, Affranchi F, Giuliano M, Seidita A, Lauricella M, Di Liberto D. Foodomics-Based Approaches Shed Light on the Potential Protective Effects of Polyphenols in Inflammatory Bowel Disease. Int J Mol Sci 2023; 24:14619. [PMID: 37834065 PMCID: PMC10572570 DOI: 10.3390/ijms241914619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/19/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic and progressive inflammatory disorder affecting the gastrointestinal tract (GT) caused by a wide range of genetic, microbial, and environmental factors. IBD is characterized by chronic inflammation and decreased gut microbial diversity, dysbiosis, with a lower number of beneficial bacteria and a concomitant increase in pathogenic species. It is well known that dysbiosis is closely related to the induction of inflammation and oxidative stress, the latter caused by an imbalance between reactive oxygen species (ROS) production and cellular antioxidant capacity, leading to cellular ROS accumulation. ROS are responsible for intestinal epithelium oxidative damage and the increased intestinal permeability found in IBD patients, and their reduction could represent a potential therapeutic strategy to limit IBD progression and alleviate its symptoms. Recent evidence has highlighted that dietary polyphenols, the natural antioxidants, can maintain redox equilibrium in the GT, preventing gut dysbiosis, intestinal epithelium damage, and radical inflammatory responses. Here, we suggest that the relatively new foodomics approaches, together with new technologies for promoting the antioxidative properties of dietary polyphenols, including novel delivery systems, chemical modifications, and combination strategies, may provide critical insights to determine the clinical value of polyphenols for IBD therapy and a comprehensive perspective for implementing natural antioxidants as potential IBD candidate treatment.
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Affiliation(s)
- Giovanni Pratelli
- Department of Physics and Chemistry (DiFC) Emilio Segrè, University of Palermo, 90128 Palermo, Italy;
| | - Bartolo Tamburini
- Section of Biochemistry, Department of Biomedicine, Neurosciences and Advanced Diagnostics (BIND), University of Palermo, 90127 Palermo, Italy; (B.T.); (D.C.); (S.E.)
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties (ProMISE), University of Palermo, 90127 Palermo, Italy;
| | - Daniela Carlisi
- Section of Biochemistry, Department of Biomedicine, Neurosciences and Advanced Diagnostics (BIND), University of Palermo, 90127 Palermo, Italy; (B.T.); (D.C.); (S.E.)
| | - Anna De Blasio
- Laboratory of Biochemistry, Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90127 Palermo, Italy; (A.D.B.); (A.D.); (A.N.); (F.A.); (M.G.)
| | - Antonella D’Anneo
- Laboratory of Biochemistry, Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90127 Palermo, Italy; (A.D.B.); (A.D.); (A.N.); (F.A.); (M.G.)
| | - Sonia Emanuele
- Section of Biochemistry, Department of Biomedicine, Neurosciences and Advanced Diagnostics (BIND), University of Palermo, 90127 Palermo, Italy; (B.T.); (D.C.); (S.E.)
| | - Antonietta Notaro
- Laboratory of Biochemistry, Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90127 Palermo, Italy; (A.D.B.); (A.D.); (A.N.); (F.A.); (M.G.)
| | - Federica Affranchi
- Laboratory of Biochemistry, Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90127 Palermo, Italy; (A.D.B.); (A.D.); (A.N.); (F.A.); (M.G.)
| | - Michela Giuliano
- Laboratory of Biochemistry, Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90127 Palermo, Italy; (A.D.B.); (A.D.); (A.N.); (F.A.); (M.G.)
| | - Aurelio Seidita
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties (ProMISE), University of Palermo, 90127 Palermo, Italy;
| | - Marianna Lauricella
- Section of Biochemistry, Department of Biomedicine, Neurosciences and Advanced Diagnostics (BIND), University of Palermo, 90127 Palermo, Italy; (B.T.); (D.C.); (S.E.)
| | - Diana Di Liberto
- Section of Biochemistry, Department of Biomedicine, Neurosciences and Advanced Diagnostics (BIND), University of Palermo, 90127 Palermo, Italy; (B.T.); (D.C.); (S.E.)
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Patil LM, Parkinson DH, Zuniga NR, Lin HJL, Naylor BC, Price JC. Combining offline high performance liquid chromatography fractionation of peptides and intact proteins to enhance proteome coverage in bottom-up proteomics. J Chromatogr A 2023; 1701:464044. [PMID: 37196519 PMCID: PMC10226724 DOI: 10.1016/j.chroma.2023.464044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 04/10/2023] [Accepted: 05/02/2023] [Indexed: 05/19/2023]
Abstract
Offline peptide separation (PS) using high-performance liquid chromatography (HPLC) is currently used to enhance liquid chromatography-tandem mass spectrometry (LC-MS/MS) detection of proteins. In search of more effective methods for enhancing MS proteome coverage, we developed a robust method for intact protein separation (IPS), an alternative first-dimension separation technique, and explored additional benefits that it offers. Comparing IPS to the traditional PS method, we found that both enhance detection of unique protein IDs to a similar magnitude, though in diverse ways. IPS was especially effective in serum, which has a small number of extremely high abundance proteins. PS was more effective in tissues with fewer dominating high-abundance proteins and was more effective in enhancing detection of post-translational modifications (PTMs). Combining the IPS and PS methods together (IPS+PS) was especially beneficial, enhancing proteome detection more than either method could independently. The comparison of IPS+PS versus six PS fractionation pools increased total number of proteins IDs by nearly double, while also significantly increasing number of unique peptides detected per protein, percent peptide sequence coverage of each protein, and detection of PTMs. This IPS+PS combined method requires fewer LC-MS/MS runs than current PS methods would need to obtain similar improvements in proteome detection, and it is robust, time- and cost-effective, and generally applicable to various tissue and sample types.
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Affiliation(s)
- Leena M Patil
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA
| | - David H Parkinson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA
| | - Nathan R Zuniga
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA
| | - Hsien-Jung L Lin
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA
| | - Bradley C Naylor
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA
| | - John C Price
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA.
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3
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Zhang H, Situ C, Guo X. Recent progress of proteomic analysis on spermatogenesis. Biol Reprod 2022; 107:109-117. [DOI: 10.1093/biolre/ioac065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
Testis, the only organ responsible for generating sperm, is by far the organ with the largest variety of proteins and tissue-specific proteins in humans. In testis, spermatogenesis is a multi-step complex process well-accepted that protein and mRNA are decoupled in certain stages of spermatogenesis. With the fast development of mass spectrometry-based proteomics, it is possible to systemically study protein abundances and modifications in testis and sperm to help us understand the molecular mechanisms of spermatogenesis. This review provides an overview of the recent progress of proteomics analysis on spermatogenesis, including protein expression and multiple PTMs, such as phosphorylation, glycosylation, ubiquitylation, and acetylation.
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Affiliation(s)
- Haotian Zhang
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China
| | - Chenghao Situ
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China
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Shen K, Yuan Y, Zhang C, Yao J. Construction of a HPLC-SERS hyphenated system for continuous separation and detection based on paper substrates. Analyst 2022; 147:4073-4081. [DOI: 10.1039/d2an00993e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The HPLC-SERS hyphenated system exhibited the complementary capability of on-line separation and continuous structural identification. It was extended to the application in identifying the illegally added hypoglycemic drugs in the practical dietary supplements.
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Affiliation(s)
- Kerui Shen
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Yaxian Yuan
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Chenjie Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Jianlin Yao
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
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Dual-function monolithic enzyme reactor based on dopamine/graphene oxide coating for simultaneous protein enzymatic hydrolysis and glycopeptide enrichment. J Chromatogr A 2022; 1666:462848. [DOI: 10.1016/j.chroma.2022.462848] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/10/2022] [Accepted: 01/20/2022] [Indexed: 11/18/2022]
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Zhang W, Qi S, Xue X, Al Naggar Y, Wu L, Wang K. Understanding the Gastrointestinal Protective Effects of Polyphenols using Foodomics-Based Approaches. Front Immunol 2021; 12:671150. [PMID: 34276660 PMCID: PMC8283765 DOI: 10.3389/fimmu.2021.671150] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/07/2021] [Indexed: 12/12/2022] Open
Abstract
Plant polyphenols are rich sources of natural anti-oxidants and prebiotics. After ingestion, most polyphenols are absorbed in the intestine and interact with the gut microbiota and modulated metabolites produced by bacterial fermentation, such as short-chain fatty acids (SCFAs). Dietary polyphenols immunomodulatory role by regulating intestinal microorganisms, inhibiting the etiology and pathogenesis of various diseases including colon cancer, colorectal cancer, inflammatory bowel disease (IBD) and colitis. Foodomics is a novel high-throughput analysis approach widely applied in food and nutrition studies, incorporating genomics, transcriptomics, proteomics, metabolomics, and integrating multi-omics technologies. In this review, we present an overview of foodomics technologies for identifying active polyphenol components from natural foods, as well as a summary of the gastrointestinal protective effects of polyphenols based on foodomics approaches. Furthermore, we critically assess the limitations in applying foodomics technologies to investigate the protective effect of polyphenols on the gastrointestinal (GI) system. Finally, we outline future directions of foodomics techniques to investigate GI protective effects of polyphenols. Foodomics based on the combination of several analytical platforms and data processing for genomics, transcriptomics, proteomics and metabolomics studies, provides abundant data and a more comprehensive understanding of the interactions between polyphenols and the GI tract at the molecular level. This contribution provides a basis for further exploring the protective mechanisms of polyphenols on the GI system.
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Affiliation(s)
- Wenwen Zhang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Suzhen Qi
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaofeng Xue
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yahya Al Naggar
- Zoology Department, Faculty of Science, Tanta University, Tanta, Egypt
- General Zoology, Institute for Biology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Liming Wu
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kai Wang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
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7
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Construction of a microfluidic platform integrating online protein fractionation, denaturation, digestion, and peptide enrichment. Talanta 2021; 224:121810. [PMID: 33379035 DOI: 10.1016/j.talanta.2020.121810] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/19/2020] [Accepted: 10/23/2020] [Indexed: 11/22/2022]
Abstract
Microfluidic system with multi-functional integration of high-throughput protein/peptide separation ability has great potential for improving the identification capacity of biological samples in proteomics. In this paper, a sample treatment platform was constructed by integrating reversed phase chromatography, immobilized enzyme reactor (IMER) and imprinted monolith through a microfluidic chip to achieve the online proteins fractionation, denaturation, digestion and peptides enrichment. We firstly synthesized a poly-allyl phenoxyacetate (AP) monolith and a lysine-glycine-glycine (KGG) imprinted monolith separately, and investigated in detail their performance in fractionating proteins and extracting KGG from the protein digests of MCF-7 cell. The removal percentage of 94.6% for MCF-7 cell protein and the recovery of 90.8% for KGG were obtained. The number of proteins and peptides identified on this microfluidic platform was 2,004 and 8,797, respectively, which was 2.8-fold and 3.0-fold higher than that of untreatment sample. The time consumed by this platform for a sample treatment was about 9.6 h, less than that of conventional method (approximate 13.3 h). In addition, this platform can enrich some peptide fragments containing KGG based on imprinted monolith, which can be served for the identification of ubiquitin-modified proteomics. The successful construction of this integrated microfluidic platform provides a considerable and efficient technical tool for simultaneous identification of proteomics and post-translational modification proteomics information.
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Liang F, Ding J, Liu S. Collective Solvation and Transport at Tetrahydrofuran-Silica Interfaces for Separation of Aromatic Compounds: Insight from Molecular Dynamics Simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:2091-2103. [PMID: 33533241 DOI: 10.1021/acs.langmuir.0c03077] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We have performed umbrella sampling molecular dynamics simulations to study the separation mechanism of aromatic compounds at the tetrahydrofuran (THF)-methanol-silica interface by liquid chromatography. Solute molecules with different polarities (naphthol and naphthalene) are selected as representative aromatic compounds. For the polar solute (naphthol), the free energy profile shows a deep minimum near the THF-silica interface, suggesting strong interactions with the polar surface. When methanol is added to the interface, there is a sharp increase in naphthol's free energy minimum, and the corresponding diffusion dynamics also undergoes a dramatic change. These findings explain the fast separation mechanism in recent experiments of separating fused ring compounds in asphaltenes with liquid chromatography. Further solvation structure and orientation analysis suggest that apolar and polar solutes may find their own comfort zones several angstroms away from the interface, and their phenyl ring's orientations would undergo a parallel-to-perpendicular transition as the solute molecule moves away from the surface. Extending our simulation studies to systems with different solute concentrations reveals that there is a decrease in the adsorption free energy accompanied by enhanced surface diffusion as the solute concentration increases, which is related to the crowding in the interfacial layers. Our simulation analysis gives a detailed microscopic description of solute solvation and transport at the THF-silica chromatography interface and will be helpful for improving separation protocols in future applications.
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Majuta SN, DeBastiani A, Li P, Valentine SJ. Combining Field-Enabled Capillary Vibrating Sharp-Edge Spray Ionization with Microflow Liquid Chromatography and Mass Spectrometry to Enhance 'Omics Analyses. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:473-485. [PMID: 33417454 PMCID: PMC8132193 DOI: 10.1021/jasms.0c00376] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Field-enabled capillary vibrating sharp-edge spray ionization (cVSSI) has been combined with high-flow liquid chromatography (LC) and mass spectrometry (MS) to establish current ionization capabilities for metabolomics and proteomics investigations. Comparisons are made between experiments employing cVSSI and a heated electrospray ionization probe representing the state-of-the-art in microflow LC-MS methods for 'omics studies. For metabolomics standards, cVSSI is shown to provide an ionization enhancement by factors of 4 ± 2 for both negative and positive ion mode analyses. For chymotryptic peptides, cVSSI is shown to provide an ionization enhancement by factors of 5 ± 2 and 2 ± 1 for negative and positive ion mode analyses, respectively. Slightly broader high-performance liquid chromatography peaks are observed in the cVSSI datasets, and several studies suggest that this results from a slightly decreased post-split flow rate. This may result from partial obstruction of the pulled-tip emitter over time. Such a challenge can be remedied with the use of LC pumps that operate in the 10 to 100 μL·min-1 flow regime. At this early stage, the proof-of-principle studies already show ion signal advantages over state-of-the-art electrospray ionization (ESI) for a wide variety of analytes in both positive and negative ion mode. Overall, this represents a ∼20-50-fold improvement over the first demonstration of LC-MS analyses by voltage-free cVSSI. Separate comparisons of the ion abundances of compounds eluting under identical solvent conditions reveal ionization efficiency differences between cVSSI and ESI and may suggest varied contributions to ionization from different physicochemical properties of the compounds. Future investigations of parameters that could further increase ionization gains in negative and positive ion mode analyses with the use of cVSSI are briefly presented.
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Affiliation(s)
- Sandra N. Majuta
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown WV 26501
| | - Anthony DeBastiani
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown WV 26501
| | - Peng Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown WV 26501
| | - Stephen J. Valentine
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown WV 26501
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Wang YP, Liang F, Liu S. Molecular dynamics simulations of amino acid adsorption and transport at the acetonitrile–water–silica interface: the role of side chains. RSC Adv 2021; 11:21666-21677. [PMID: 35478806 PMCID: PMC9034086 DOI: 10.1039/d1ra03982b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 06/14/2021] [Indexed: 11/24/2022] Open
Abstract
The solvation and transport of amino acid residues at liquid–solid interfaces have great importance for understanding the mechanism of separation of biomolecules in liquid chromatography. This study uses umbrella sampling molecular dynamics simulations to study the adsorption and transport of three amino acid molecules with different side chains (phenylalanine (Phe), leucine (Leu) and glutamine (Gln)) at the silica–water–acetonitrile interface in liquid chromatography. Free energy analysis shows that the Gln molecule has stronger binding affinity than the other two molecules, indicating the side chain polarity may play a primary role in adsorption at the liquid–solid interface. The Phe molecule with a phenyl side chain exhibits stronger adsorption free energy than Leu with a non-polar side chain, which can be ascribed to the better solvated configuration of Phe. Further analysis of molecular orientations found that the amino acid molecules with apolar side chains (Phe and Leu) have ‘standing up’ configurations at their stable adsorption state, where the polar functional groups are close to the interface and the side chain is far from the interface, whereas the amino acid molecule with a polar side chain (Gln) chooses the ‘lying’ configuration, and undergoes a sharp orientation transition when the molecule moves away from the silica surface. Extending our simulation studies to systems with different solute concentrations reveals that there is a decrease in the adsorption free energy as well as surface diffusion as the solute concentration increases, which is related to the crowding in the interfacial layers. This simulation study gives a detailed microscopic description of amino acid molecule solvation and transport at the acetonitrile–water–silica interface in liquid chromatography and will be helpful for understanding the retention mechanism for amino acid separation. The solvation and transport of amino acid residues at liquid–solid interfaces have great importance for understanding the mechanism of separation of biomolecules in liquid chromatography.![]()
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Affiliation(s)
- Yong-Peng Wang
- School of Materials Science and Engineering
- Sun Yat-sen University
- Guangzhou 510275
- P. R. China
| | - Fei Liang
- School of Materials Science and Engineering
- Sun Yat-sen University
- Guangzhou 510275
- P. R. China
| | - Shule Liu
- School of Materials Science and Engineering
- Sun Yat-sen University
- Guangzhou 510275
- P. R. China
- Key Laboratory for Polymeric Composite & Functional Materials of Ministry of Education
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11
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Tang XM, Guo JL, Chen L, Ho PCL. Application for proteomics analysis technology in studying animal-derived traditional Chinese medicine: A review. J Pharm Biomed Anal 2020; 191:113609. [PMID: 32966940 DOI: 10.1016/j.jpba.2020.113609] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/28/2020] [Accepted: 08/29/2020] [Indexed: 10/23/2022]
Abstract
Different therapeutically active ingredients, from plants, animals, and mineral sources, are prescribed as traditional Chinese medicines (TCM). TCMs, from animal sources, are rich in proteins and peptides. Different advanced proteomics technologies, such as two-dimensional gel electrophoresis (2-DE), multi-dimensional liquid chromatography (MDLC), matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF-MS), and isobaric tags for relative and absolute quantitation (iTRAQ), have been applied to analyze TCMs, from animal sources. This paper reviews the common proteomic techniques for analyzing animal - derived TCMs. Various scientific studies have reported the application of proteomics for locating drug targets, identifying active components, and elucidating the mechanisms of action of animal - derived TCMs. However, these researches are still at the preliminary stage. This review has also discussed the existing challenges and future directions in this field of research.
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Affiliation(s)
- Xue-Mei Tang
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Jin-Lin Guo
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Lu Chen
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
| | - Paul Chi-Lui Ho
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore 117543, Singapore.
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Wicht K, Baert M, Kajtazi A, Schipperges S, von Doehren N, Desmet G, de Villiers A, Lynen F. Pharmaceutical impurity analysis by comprehensive two-dimensional temperature responsive × reversed phase liquid chromatography. J Chromatogr A 2020; 1630:461561. [PMID: 32992220 DOI: 10.1016/j.chroma.2020.461561] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/10/2020] [Accepted: 09/17/2020] [Indexed: 12/11/2022]
Abstract
In this study, the possibilities of temperature responsive × reversed phase liquid chromatography (TRLC × RPLC) are assessed in terms of pharmaceutical impurity analysis. Due to the increased peak capacity per unit time they offer, two-dimensional LC approaches are gaining relevance for the analysis of complex drug formulations. Because the latter depicts a larger predisposition for the occurrence of an increased number of impurities, current 1D-HPLC approaches often prove insufficient. Since many LC × LC methods are limited by modulation, solvent compatibility, orthogonality, and sensitivity issues, the combination of TRLC × RPLC is explored in this work for pharmaceutical impurity analysis. As this combination of a purely aqueous separation with RPLC allows for systematic and optimization-free refocusing in the second dimension, it opens possibilities for generic LC × LC requiring minimal to no method development, in this way overcoming a major perceived contemporary hurdle of LC × LC. The approach is demonstrated with a representative mixture of 17 solutes comprising 11 corticosteroids and 6 progestogens. Orthogonality and peak capacities were assessed on three RP core-shell column selectivities (Poroshell EC-C18, phenyl-hexyl and PFP). Although the TRLC × EC-C18 combination offered somewhat better orthogonality, the combination with the PFP column proved the best for the separation at hand. Depending on the composition of the mixture, the use of full, shifted, or segmented gradients allowed facile optimization of the separation. The developed platform allowed detection of the impurities at the 0.05% level compared to a selected main compound, while also opening up possibilities for analysis of formulations comprising two active ingredients.
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Affiliation(s)
- Kristina Wicht
- Separation Science Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, B-9000 Ghent, Belgium
| | - Mathijs Baert
- Separation Science Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, B-9000 Ghent, Belgium
| | - Ardiana Kajtazi
- Separation Science Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, B-9000 Ghent, Belgium
| | - Sonja Schipperges
- Agilent Technologies, Hewlett Packard St 8, D-76337 Waldbronn, Germany
| | | | - Gert Desmet
- Department of Chemical Engineering, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
| | - André de Villiers
- Department of Chemistry and Polymer Science, University of Stellenbosch, Private Bag X1, ZA-7602 Matieland, South Africa
| | - Frederic Lynen
- Separation Science Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, B-9000 Ghent, Belgium.
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13
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Simulation of elution profiles in liquid chromatography – IV: Experimental characterization and modeling of solute injection profiles from a modulation valve used in two-dimensional liquid chromatography. J Chromatogr A 2020; 1626:461373. [DOI: 10.1016/j.chroma.2020.461373] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 11/21/2022]
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Proteomic Profiling of Emiliania huxleyi Using a Three-Dimensional Separation Method Combined with Tandem Mass Spectrometry. Molecules 2020; 25:molecules25133028. [PMID: 32630776 PMCID: PMC7411631 DOI: 10.3390/molecules25133028] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/30/2020] [Accepted: 06/30/2020] [Indexed: 12/31/2022] Open
Abstract
Emiliania huxleyi is one of the most abundant marine planktons, and it has a crucial feature in the carbon cycle. However, proteomic analyses of Emiliania huxleyi have not been done extensively. In this study, a three-dimensional liquid chromatography (3D-LC) system consisting of strong cation exchange, high- and low-pH reversed-phase liquid chromatography was established for in-depth proteomic profiling of Emiliania huxleyi. From tryptic proteome digest, 70 fractions were generated and analyzed using liquid chromatography-tandem mass spectrometry. In total, more than 84,000 unique peptides and 10,000 proteins groups were identified with a false discovery rate of ≤0.01. The physicochemical properties of the identified peptides were evaluated. Using ClueGO, approximately 700 gene ontology terms and 15 pathways were defined from the identified protein groups with p-value ≤0.05, covering a wide range of biological processes, cellular components, and molecular functions. Many biological processes associated with CO2 fixation, photosynthesis, biosynthesis, and metabolic process were identified. Various molecular functions relating to protein binding and enzyme activities were also found. The 3D-LC strategy is a powerful approach for comparative proteomic studies on Emiliania huxleyi to reveal changes in its protein level and related mechanism.
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Integrated microfluidic chip for on-line proteome analysis with combination of denaturing and rapid digestion of protein. Anal Chim Acta 2020; 1102:1-10. [DOI: 10.1016/j.aca.2020.01.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/10/2020] [Accepted: 01/12/2020] [Indexed: 01/21/2023]
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16
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Review of Three-Dimensional Liquid Chromatography Platforms for Bottom-Up Proteomics. Int J Mol Sci 2020; 21:ijms21041524. [PMID: 32102244 PMCID: PMC7073195 DOI: 10.3390/ijms21041524] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/19/2020] [Accepted: 02/21/2020] [Indexed: 12/30/2022] Open
Abstract
Proteomics is a large-scale study of proteins, aiming at the description and characterization of all expressed proteins in biological systems. The expressed proteins are typically highly complex and large in abundance range. To fulfill high accuracy and sensitivity of proteome analysis, the hybrid platforms of multidimensional (MD) separations and mass spectrometry have provided the most powerful solution. Multidimensional separations provide enhanced peak capacity and reduce sample complexity, which enables mass spectrometry to analyze more proteins with high sensitivity. Although two-dimensional (2D) separations have been widely used since the early period of proteomics, three-dimensional (3D) separation was barely used by low reproducibility of separation, increased analysis time in mass spectrometry. With developments of novel microscale techniques such as nano-UPLC and improvements of mass spectrometry, the 3D separation becomes a reliable and practical selection. This review summarizes existing offline and online 3D-LC platforms developed for proteomics and their applications. In detail, setups and implementation of those systems as well as their advances are outlined. The performance of those platforms is also discussed and compared with the state-of-the-art 2D-LC. In addition, we provide some perspectives on the future developments and applications of 3D-LC in proteomics.
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17
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Nys G, Cobraiville G, Fillet M. Multidimensional performance assessment of micro pillar array column chromatography combined to ion mobility-mass spectrometry for proteome research. Anal Chim Acta 2019; 1086:1-13. [DOI: 10.1016/j.aca.2019.08.068] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 08/23/2019] [Accepted: 08/27/2019] [Indexed: 01/23/2023]
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18
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Ma S, Li Y, Ma C, Wang Y, Ou J, Ye M. Challenges and Advances in the Fabrication of Monolithic Bioseparation Materials and their Applications in Proteomics Research. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1902023. [PMID: 31502719 DOI: 10.1002/adma.201902023] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 06/29/2019] [Indexed: 06/10/2023]
Abstract
High-performance liquid chromatography integrated with tandem mass spectrometry (HPLC-MS/MS) has become a powerful technique for proteomics research. Its performance heavily depends on the separation efficiency of HPLC, which in turn depends on the chromatographic material. As the "heart" of the HPLC system, the chromatographic material is required to achieve excellent column efficiency and fast analysis. Monolithic materials, fabricated as continuous supports with interconnected skeletal structure and flow-through pores, are regarded as an alternative to particle-packed columns. Such materials are featured with easy preparation, fast mass transfer, high porosity, low back pressure, and miniaturization, and are next-generation separation materials for high-throughput proteins and peptides analysis. Herein, the recent progress regarding the fabrication of various monolithic materials is reviewed. Special emphasis is placed on studies of the fabrication of monolithic capillary columns and their applications in separation of biomolecules by capillary liquid chromatography (cLC). The applications of monolithic materials in the digestion, enrichment, and separation of phosphopeptides and glycopeptides from biological samples are also considered. Finally, advances in comprehensive 2D HPLC separations using monolithic columns are also shown.
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Affiliation(s)
- Shujuan Ma
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
| | - Ya Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
| | - Chen Ma
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
| | - Yan Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
| | - Junjie Ou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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19
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Huguet R, Mullen C, Srzentić K, Greer JB, Fellers RT, Zabrouskov V, Syka JEP, Kelleher NL, Fornelli L. Proton Transfer Charge Reduction Enables High-Throughput Top-Down Analysis of Large Proteoforms. Anal Chem 2019; 91:15732-15739. [PMID: 31714757 DOI: 10.1021/acs.analchem.9b03925] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Despite the recent technological advances in Fourier transform mass spectrometry (FTMS) instrumentation, top-down proteomics (TDP) is currently mostly applied to the characterization of proteoforms <30 kDa due to the poor performance of high-resolution FTMS for the analysis of larger proteoforms and the high complexity of intact proteomes in the 30-60 kDa mass range. Here, we propose a novel data acquisition method based on ion-ion proton transfer, herein termed proton transfer charge reduction (PTCR), to investigate large proteoforms of Pseudomonas aeruginosa in a high-throughput fashion. We designed a targeted data acquisition strategy, named tPTCR, which applies two consecutive gas phase fractionation steps for obtaining intact precursor masses: first, a narrow (1.5 m/z-wide) quadrupole filter m/z transmission window is used to select a subset of charge states from all ionized proteoform cations; second, this aliquot of protein cations is subjected to PTCR in order to reduce their average charge state: upon m/z analysis in an Orbitrap, proteoform mass spectra with minimal m/z peak overlap and easy-to-interpret charge state distributions are obtained, simplifying the proteoform mass calculation. Subsequently, the same quadrupole-selected narrow m/z region of analytes is subjected to collisional dissociation to obtain proteoform sequence information, which used in combination with intact mass information leads to proteoform identification through an off-line database search. The newly proposed method was benchmarked against the previously developed "medium/high" data-dependent acquisition strategy and doubled the number of UniProt entries and proteoforms >30 kDa identified on the liquid chromatography time scale.
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Affiliation(s)
- Romain Huguet
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Christopher Mullen
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Kristina Srzentić
- Thermo Fisher Scientific , 790 Memorial Drive, Suite 2D , Cambridge , Massachusetts 02139 , United States
| | - Joseph B Greer
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence , Northwestern University , 2170 Campus Drive , Evanston , Illinois 60208 , United States
| | - Ryan T Fellers
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence , Northwestern University , 2170 Campus Drive , Evanston , Illinois 60208 , United States
| | - Vlad Zabrouskov
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - John E P Syka
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence , Northwestern University , 2170 Campus Drive , Evanston , Illinois 60208 , United States
| | - Luca Fornelli
- Department of Biology , University of Oklahoma , 730 Van Vleet Oval , Norman , Oklahoma 73071 , United States
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20
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Dou M, Tsai CF, Piehowski PD, Wang Y, Fillmore TL, Zhao R, Moore RJ, Zhang P, Qian WJ, Smith RD, Liu T, Kelly RT, Shi T, Zhu Y. Automated Nanoflow Two-Dimensional Reversed-Phase Liquid Chromatography System Enables In-Depth Proteome and Phosphoproteome Profiling of Nanoscale Samples. Anal Chem 2019; 91:9707-9715. [PMID: 31241912 DOI: 10.1021/acs.analchem.9b01248] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Two-dimensional reversed-phase capillary liquid chromatography (2D RPLC) separations have enabled comprehensive proteome profiling of biological systems. However, milligram sample quantities of proteins are typically required due to significant losses during offline fractionation. Such a large sample requirement generally precludes the application samples in the nanogram to low-microgram range. To achieve in-depth proteomic analysis of such small-sized samples, we have developed the nanoFAC (nanoflow Fractionation and Automated Concatenation) 2D RPLC platform, in which the first dimension high-pH fractionation was performed on a 75-μm i.d. capillary column at a 300 nL/min flow rate with automated fraction concatenation, instead of on a typically used 2.1 mm column at a 200 μL/min flow rate with manual concatenation. Each fraction was then fully transferred to the second-dimension low-pH nanoLC separation using an autosampler equipped with a custom-machined syringe. We have found that using a polypropylene 96-well plate as collection device as well as the addition of n-Dodecyl β-d-maltoside (0.01%) in the collection buffer can significantly improve sample recovery. We have demonstrated the nanoFAC 2D RPLC platform can achieve confident identifications of ∼49,000-94,000 unique peptides, corresponding to ∼6,700-8,300 protein groups using only 100-1000 ng of HeLa tryptic digest (equivalent to ∼500-5,000 cells). Furthermore, by integrating with phosphopeptide enrichment, the nanoFAC 2D RPLC platform can identify ∼20,000 phosphopeptides from 100 μg of MCF-7 cell lysate.
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Affiliation(s)
- Maowei Dou
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Chia-Feng Tsai
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Paul D Piehowski
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Yang Wang
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Thomas L Fillmore
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Rui Zhao
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Ronald J Moore
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Pengfei Zhang
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Wei-Jun Qian
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Richard D Smith
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Tao Liu
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Ryan T Kelly
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States.,Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84604 , United States
| | - Tujin Shi
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
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21
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An improved peak clustering algorithm for comprehensive two-dimensional liquid chromatography data analysis. J Chromatogr A 2019; 1602:273-283. [PMID: 31182307 DOI: 10.1016/j.chroma.2019.05.046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 05/22/2019] [Accepted: 05/23/2019] [Indexed: 01/01/2023]
Abstract
In this work, an improved algorithm was developed for two-dimensional (2D) peak detection in complex two-dimensional liquid chromatography (LC×LC) data sets. In the first step, conventional one-dimensional peak detection was performed. In the second step, retention time, bidirectional overlap and unimodality criteria were applied to decide which of the individual peaks should be merged. To improve the peak detection with LC×LC analysis using shifting second dimension (2D) gradients, the variable thresholds, which permitted different thresholds for candidate peaks at different first dimension (1D) retention times, were employed for examination of the 2D retention time differences. Furthermore, the bidirectional overlap criterion performed at specified height was recommended to improve detection for tailing peaks. The developed algorithm was further tested on data sets from different LC×LC analyses of a complex peptide mixture, and then quantitatively evaluated by comparison between the results by the algorithm and mass analysis. Evidently improved performance with an accuracy rate over 60% was obtained by the algorithm, even for peak detection with LC×LC analysis under relatively low 1D sampling frequency or shifting 2D gradients. This would help to improve LC×LC quantitative analysis and performance assessment.
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22
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Lakshmanan R, Loo JA. Top-Down Protein Identification using a Time-of-Flight Mass Spectrometer and Data Independent Acquisition. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2019; 435:136-144. [PMID: 31105465 PMCID: PMC6519736 DOI: 10.1016/j.ijms.2018.10.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Top-down mass spectrometry and direct dissociation of gas phase intact proteins have been demonstrated to be a powerful platform for identifying proteins from complex mixtures and for elucidating post-translational modifications (PTMs). Fragmentation of proteins in the atmospheric pressure/vacuum interface of the electrospray ionization mass spectrometer is an effective dissociation technique that can be utilized for on-line HPLC top-down analysis. We demonstrate the capability to perform intact protein identifications in a single-stage time-of- flight (TOF) mass spectrometer in a data independent (DIA) acquisition fashion by rapidly switching the in-source dissociation (ISD) energy during protein elution from a liquid chromatography (LC) column. The intact protein and product ion masses obtained at low and high ISD energies, respectively, were measured using a TOF mass analyzer. By coupling on-line protein separations to dissociation in the atmospheric pressure/vacuum interface region of the mass spectrometer, we identified proteins in simple complexity mixtures, including subunits from the human 20S proteasome complex, and PTMs such as phosphorylation and N-terminal acetylation events. This proof-of-principle study demonstrates that a data-independent pseudo- MS/MS method could be a relatively in-expensive platform for top-down MS.
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Affiliation(s)
- Rajeswari Lakshmanan
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA 90095
| | - Joseph A. Loo
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA 90095
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Molecular Biology Institute, and UCLA/DOE Institute for Genomics and Proteomics, University of California-Los Angeles, Los Angeles, CA 90095
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23
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Gradual Gradient Two-Dimensional Preparative Liquid Chromatography System for Preparative Separation of Complex Natural Products. Chromatographia 2018. [DOI: 10.1007/s10337-018-3652-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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24
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Santos KS, Barbosa AM, Freitas V, Muniz AVCS, Mendonça MC, Calhelha RC, Ferreira ICFR, Franceschi E, Padilha FF, Oliveira MBPP, Dariva C. Antiproliferative Activity of Neem Leaf Extracts Obtained by a Sequential Pressurized Liquid Extraction. Pharmaceuticals (Basel) 2018; 11:ph11030076. [PMID: 30061479 PMCID: PMC6160913 DOI: 10.3390/ph11030076] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 07/25/2018] [Indexed: 12/17/2022] Open
Abstract
Azadirachta indica A. Juss (neem) extracts have been used in pharmaceutical applications as antitumor agents, due to their terpenes and phenolic compounds. To obtain extracts from neem leaves with potential antiproliferative effect, a sequential process of pressurized liquid extraction was carried out in a fixed bed extractor at 25 °C and 100 bar, using hexane (SH), ethyl acetate (SEA), and ethanol (SE) as solvents. Extractions using only ethanol (EE) was also conducted to compare the characteristics of the fractionated extracts. The results obtained by liquid chromatography-electrospray ionization mass spectrometry suggested a higher concentration of terpenes in the SEA extract in comparison to SH, SE, and EE extracts. Therefore, antiproliferative activity showed that SEA extracts were the most efficient inhibitor to human tumor cells MCF-7, NCI-H460, HeLa, and HepG2. Hepatocellular cells were more resistant to SH, SEA, SE, and EE compared to breast, lung, hepatocellular, and cervical malignant cells. Neem fractioned extracts obtained in the present study seem to be more selective for malignant cells compared to the non-tumor cells.
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Affiliation(s)
- Klebson S Santos
- NUESC/ITP, Program in Industrial Biotechnology-Tiradentes University, Aracaju 49032-490, Brazil.
- REQUIMTE/LAQV, Department of Chemistry Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal.
| | - Andriele M Barbosa
- NUESC/ITP, Program in Industrial Biotechnology-Tiradentes University, Aracaju 49032-490, Brazil.
| | - Victor Freitas
- Chemistry Investigation Centre (CIQ), Department of Chemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal.
| | | | - Marcelo C Mendonça
- NUESC/ITP, Program in Industrial Biotechnology-Tiradentes University, Aracaju 49032-490, Brazil.
| | - Ricardo C Calhelha
- Mountain Research Center (CIMO), School of Agriculture, Polytechnic Institute of Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal.
| | - Isabel C F R Ferreira
- Mountain Research Center (CIMO), School of Agriculture, Polytechnic Institute of Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal.
| | - Elton Franceschi
- NUESC/ITP, Program in Industrial Biotechnology-Tiradentes University, Aracaju 49032-490, Brazil.
| | - Francine F Padilha
- NUESC/ITP, Program in Industrial Biotechnology-Tiradentes University, Aracaju 49032-490, Brazil.
| | - Maria Beatriz P P Oliveira
- REQUIMTE/LAQV, Department of Chemistry Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal.
| | - Cláudio Dariva
- NUESC/ITP, Program in Industrial Biotechnology-Tiradentes University, Aracaju 49032-490, Brazil.
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25
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Zhuo Y, Wu JL, Yan X, Guo MQ, Liu N, Zhou H, Liu L, Li N. Strategy for Hepatotoxicity Prediction Induced by Drug Reactive Metabolites Using Human Liver Microsome and Online 2D-Nano-LC-MS Analysis. Anal Chem 2017; 89:13167-13175. [DOI: 10.1021/acs.analchem.7b02684] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yue Zhuo
- State
Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao
| | - Jian-Lin Wu
- State
Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao
| | - Xiaojing Yan
- State
Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao
- Changzhou Affiliated Hospital of Nanjing University of Chinese Medicine, 25 Heping North Road, Changzhou 213003, China
| | - Ming-Quan Guo
- Key
Laboratory of Plant Germplasm Enhancement and Specialty Agriculture,
Wuhan Botanical Garden, Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Ning Liu
- Central
Laboratory, Second Hospital of Jilin University, Changchun, China
| | - Hua Zhou
- State
Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao
| | - Liang Liu
- State
Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao
| | - Na Li
- State
Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao
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26
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27
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Zhu MZ, Li N, Wang YT, Liu N, Guo MQ, Sun BQ, Zhou H, Liu L, Wu JL. Acid/Salt/pH Gradient Improved Resolution and Sensitivity in Proteomics Study Using 2D SCX-RP LC–MS. J Proteome Res 2017; 16:3470-3475. [DOI: 10.1021/acs.jproteome.7b00443] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Ming-Zhi Zhu
- State
Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Macao, China
- Key
Laboratory of Plant Germplasm Enhancement and Specialty Agriculture,
Wuhan Botanical Garden, Chinese Academy of Sciences, Sino-Africa Joint
Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Na Li
- State
Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Macao, China
| | - Yi-Tong Wang
- State
Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Macao, China
| | - Ning Liu
- Central
Laboratory, Second Hospital of Jilin University, Changchun, China
| | - Ming-Quan Guo
- Key
Laboratory of Plant Germplasm Enhancement and Specialty Agriculture,
Wuhan Botanical Garden, Chinese Academy of Sciences, Sino-Africa Joint
Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Bao-qing Sun
- State
Key Laboratory of Respiratory Disease, National Clinical Center for
Respiratory Diseases, Guangzhou Institute of Respiratory Diseases,
First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Hua Zhou
- State
Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Macao, China
| | - Liang Liu
- State
Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Macao, China
| | - Jian-Lin Wu
- State
Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Macao, China
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28
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Stoll DR, Shoykhet K, Petersson P, Buckenmaier S. Active Solvent Modulation: A Valve-Based Approach To Improve Separation Compatibility in Two-Dimensional Liquid Chromatography. Anal Chem 2017; 89:9260-9267. [DOI: 10.1021/acs.analchem.7b02046] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Dwight R. Stoll
- Department
of Chemistry, Gustavus Adolphus College, 800 West College Avenue, Saint Peter, Minnesota 56082, United States
| | - Konstantin Shoykhet
- R&D and Marketing GmbH & Co KG, Agilent Technologies, Hewlett-Packard-Str. 8, 76337 Waldbronn, Germany
| | - Patrik Petersson
- Global
Research, Novo Nordisk A/S, Novo Nordisk Park, DK-2760, Måløv, Denmark
| | - Stephan Buckenmaier
- R&D and Marketing GmbH & Co KG, Agilent Technologies, Hewlett-Packard-Str. 8, 76337 Waldbronn, Germany
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29
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Capitanio D, Moriggi M, Gelfi C. Mapping the human skeletal muscle proteome: progress and potential. Expert Rev Proteomics 2017; 14:825-839. [PMID: 28780899 DOI: 10.1080/14789450.2017.1364996] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
INTRODUCTION Human skeletal muscle represents 40% of our body mass and deciphering its proteome composition to further understand mechanisms regulating muscle function under physiological and pathological conditions has proved a challenge. The inter-individual variability, the presence of structurally and functionally different muscle types and the high protein dynamic range require carefully selected methodologies for the assessment of the muscle proteome. Furthermore, physiological studies are understandingly hampered by ethical issues related to biopsies on healthy subjects, making it difficult to recruit matched controls essential for comparative studies. Areas covered: This review critically analyses studies performed on muscle to date and identifies what still remains unknown or poorly investigated in physiological and pathological states, such as training, aging, metabolic disorders and muscular dystrophies. Expert commentary: Efforts should be made on biological fluid analyses targeting low abundant/low molecular weight fragments generated from muscle cell disruption to improve diagnosis and clinical monitoring. From a methodological point of view, particular attention should be paid to improve the characterization of intact proteins and unknown post translational modifications to better understand the molecular mechanisms of muscle disorders.
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Affiliation(s)
- Daniele Capitanio
- a Department of Biomedical Sciences for Health , University of Milan , Segrate , Milan , Italy
| | - Manuela Moriggi
- a Department of Biomedical Sciences for Health , University of Milan , Segrate , Milan , Italy
| | - Cecilia Gelfi
- a Department of Biomedical Sciences for Health , University of Milan , Segrate , Milan , Italy
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30
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Jin P, Wang K, Huang C, Nice EC. Mining the fecal proteome: from biomarkers to personalised medicine. Expert Rev Proteomics 2017; 14:445-459. [PMID: 28361558 DOI: 10.1080/14789450.2017.1314786] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Fecal proteomics has gained increased prominence in recent years. It can provide insights into the diagnosis and surveillance of many bowel diseases by both identifying potential biomarkers in stool samples and helping identify disease-related pathways. Fecal proteomics has already shown its potential for the discovery and validation of biomarkers for colorectal cancer screening, and the analysis of fecal microbiota by MALDI-MS for the diagnosis of a range of bowel diseases is gaining clinical acceptance. Areas covered: Based on a comprehensive analysis of the current literature, we introduce the range of sensitive and specific proteomics methods which comprise the current 'Proteomics Toolbox', explain how the integration of fecal proteomics with data processing/bioinformatics has been used for the identification of potential biomarkers for both CRC and other gut-related pathologies and analysis of the fecal microbiome, outline some of the current fecal assays in current clinical practice and introduce the concept of personalised medicine which these technologies will help inform. Expert commentary: Integration of fecal proteomics with other proteomics and genomics strategies as well as bioinformatics is paving the way towards personalised medicine, which will bring with it improved global healthcare.
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Affiliation(s)
- Ping Jin
- a Key Laboratory of Tropical Diseases and Translational Medicine of Ministry of Education & Department of Neurology , the Affiliated Hospital of Hainan Medical College , Haikou , China.,b State Key Laboratory of Biotherapy and Cancer Center , West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China
| | - Kui Wang
- b State Key Laboratory of Biotherapy and Cancer Center , West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China
| | - Canhua Huang
- a Key Laboratory of Tropical Diseases and Translational Medicine of Ministry of Education & Department of Neurology , the Affiliated Hospital of Hainan Medical College , Haikou , China.,b State Key Laboratory of Biotherapy and Cancer Center , West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China
| | - Edouard C Nice
- b State Key Laboratory of Biotherapy and Cancer Center , West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China.,c Department of Biochemistry and Molecular Biology , Monash University , Clayton , Australia
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31
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Coufalíková K, Benešová I, Vaculovič T, Kanický V, Preisler J. LC coupled to ESI, MALDI and ICP MS - A multiple hyphenation for metalloproteomic studies. Anal Chim Acta 2017; 968:58-65. [PMID: 28395775 DOI: 10.1016/j.aca.2017.03.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 02/27/2017] [Accepted: 03/02/2017] [Indexed: 12/17/2022]
Abstract
A new multiple detection arrangement for liquid chromatography (LC) that supplements conventional electrospray ionization (ESI) mass spectrometry (MS) detection with two complementary detection techniques, matrix-assisted laser desorption/ionization (MALDI) MS and substrate-assisted laser desorption inductively coupled plasma (SALD ICP) MS has been developed. The combination of the molecular and elemental detectors in a single separation run is accomplished by utilizing a commercial MALDI target made of conductive plastic. The proposed platform provides a number of benefits in today's metalloproteomic applications, which are demonstrated by analysis of a metallothionein mixture. To maintain metallothionein complexes, separation is carried out at a neutral pH. The effluent is split; a major portion is directed to ESI MS while the remaining 1.8% fraction is deposited onto a plastic MALDI target. Dried droplets are overlaid with MALDI matrix and analysed consecutively by MALDI MS and SALD ICP MS. In the ESI MS spectra, the MT isoform complexes with metals and their stoichiometry are determined; the apoforms are revealed in the MALDI MS spectra. Quantitative determination of metallothionein isoforms is performed via determination of metals in the complexes of the individual protein isoforms using SALD ICP MS.
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Affiliation(s)
- Kateřina Coufalíková
- Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Iva Benešová
- Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic; Central European Institute of Technology, CEITEC MU, Masaryk University, Brno, Czech Republic
| | - Tomáš Vaculovič
- Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic; Central European Institute of Technology, CEITEC MU, Masaryk University, Brno, Czech Republic
| | - Viktor Kanický
- Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic; Central European Institute of Technology, CEITEC MU, Masaryk University, Brno, Czech Republic
| | - Jan Preisler
- Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic; Central European Institute of Technology, CEITEC MU, Masaryk University, Brno, Czech Republic.
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32
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Padrão AI, Ferreira R, Amado F, Vitorino R, Duarte JA. Uncovering the exercise-related proteome signature in skeletal muscle. Proteomics 2016; 16:816-30. [PMID: 26632760 DOI: 10.1002/pmic.201500382] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Revised: 10/13/2015] [Accepted: 11/30/2015] [Indexed: 01/01/2023]
Abstract
Exercise training has been recommended as a nonpharmacological strategy for the prevention and attenuation of skeletal muscle atrophy in distinct pathophysiological conditions. Despite the well-established phenotypic alterations, the molecular mechanisms underlying exercise-induced skeletal muscle remodeling are poorly characterized. Proteomics based on mass spectrometry have been successfully applied for the characterization of skeletal muscle proteome, representing a pivotal approach for the wide characterization of the molecular networks that lead to skeletal muscle remodeling. Nevertheless, few studies were performed to characterize the exercise-induced proteome remodeling of skeletal muscle, with only six research papers focused on the cross-talk between exercise and pathophysiological conditions. In order to add new insights on the impact of distinct exercise programs on skeletal muscle proteome, molecular network analysis was performed with bioinformatics tools. This analysis highlighted an exercise-related proteome signature characterized by the up-regulation of the capacity for ATP generation, oxygen delivery, antioxidant capacity and regulation of mitochondrial protein synthesis. Chronic endurance training up-regulates the tricarboxylic acid cycle and oxidative phosphorylation system, whereas the release of calcium ion into cytosol and amino acid metabolism are the biological processes up-regulated by a single bout of exercise. Other issues as exercise intensity, load, mode and regimen as well as muscle type also influence the exercise-induced proteome signature. The comprehensive analysis of the molecular networks modulated by exercise training in health and disease, taking in consideration all these variables, might not only support the therapeutic effect of exercise but also highlight novel targets for the development of enhanced pharmacological strategies.
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Affiliation(s)
- Ana Isabel Padrão
- QOPNA, Department of Chemistry, University of Aveiro, Aveiro, Portugal.,CIAFEL, Faculty of Sports, University of Porto, Porto, Portugal
| | - Rita Ferreira
- QOPNA, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Francisco Amado
- QOPNA, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Rui Vitorino
- Department of Medical Sciences and Institute for Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal.,Department of Physiology and Cardiothoracic Surgery, Faculty of Medicine, University of Porto, Porto, Portugal
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33
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Affiliation(s)
- Dwight R. Stoll
- Department
of Chemistry, Gustavus Adolphus College, Saint Peter, Minnesota 56082, United States
| | - Peter W. Carr
- Department
of Chemistry, University of Minnesota, Minneapolis, Minnesota 55104, United States
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34
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Ferguson LR, Barnett MPG. Why Are Omics Technologies Important to Understanding the Role of Nutrition in Inflammatory Bowel Diseases? Int J Mol Sci 2016; 17:E1763. [PMID: 27775675 PMCID: PMC5085787 DOI: 10.3390/ijms17101763] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 09/29/2016] [Accepted: 10/10/2016] [Indexed: 12/18/2022] Open
Abstract
For many years, there has been confusion about the role that nutrition plays in inflammatory bowel diseases (IBD). It is apparent that good dietary advice for one individual may prove inappropriate for another. As with many diseases, genome-wide association studies across large collaborative groups have been important in revealing the role of genetics in IBD, with more than 200 genes associated with susceptibility to the disease. These associations provide clues to explain the differences in nutrient requirements among individuals. In addition to genes directly involved in the control of inflammation, a number of the associated genes play roles in modulating the gut microbiota. Cell line models enable the generation of hypotheses as to how various bioactive dietary components might be especially beneficial for certain genetic groups. Animal models are necessary to mimic aspects of the complex aetiology of IBD, and provide an important link between tissue culture studies and human trials. Once we are sufficiently confident of our hypotheses, we can then take modified diets to an IBD population that is stratified according to genotype. Studies in IBD patients fed a Mediterranean-style diet have been important in validating our hypotheses and as a proof-of-principle for the application of these sensitive omics technologies to aiding in the control of IBD symptoms.
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Affiliation(s)
- Lynnette R Ferguson
- Discipline of Nutrition and Dietetics and Auckland Cancer Research Society, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
| | - Matthew P G Barnett
- Food Nutrition & Health Team, Food & Bio-Based Products Group, AgResearch Limited, Palmerston North 4442, New Zealand.
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35
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Yan X, Wang LJ, Wu Z, Wu YL, Liu XX, Chang FR, Fang MJ, Qiu YK. New on-line separation workflow of microbial metabolites via hyphenation of analytical and preparative comprehensive two-dimensional liquid chromatography. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1033-1034:1-8. [PMID: 27517521 DOI: 10.1016/j.jchromb.2016.07.053] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 07/29/2016] [Accepted: 07/31/2016] [Indexed: 01/17/2023]
Abstract
Microbial metabolites represent an important source of bioactive natural products, but always exhibit diverse of chemical structures or complicated chemical composition with low active ingredients content. Traditional separation methods rely mainly on off-line combination of open-column chromatography and preparative high performance liquid chromatography (HPLC). However, the multi-step and prolonged separation procedure might lead to exposure to oxygen and structural transformation of metabolites. In the present work, a new two-dimensional separation workflow for fast isolation and analysis of microbial metabolites from Chaetomium globosum SNSHI-5, a cytotoxic fungus derived from extreme environment. The advantage of this analytical comprehensive two-dimensional liquid chromatography (2D-LC) lies on its ability to analyze the composition of the metabolites, and to optimize the separation conditions for the preparative 2D-LC. Furthermore, gram scale preparative 2D-LC separation of the crude fungus extract could be performed on a medium-pressure liquid chromatograph×preparative high-performance liquid chromatography system, under the optimized condition. Interestingly, 12 cytochalasan derivatives, including two new compounds named cytoglobosin Ab (3) and isochaetoglobosin Db (8), were successfully obtained with high purity in a short period of time. The structures of the isolated metabolites were comprehensively characterized by HR ESI-MS and NMR. To be highlighted, this is the first report on the combination of analytical and preparative 2D-LC for the separation of microbial metabolites. The new workflow exhibited apparent advantages in separation efficiency and sample treatment capacity compared with conventional methods.
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Affiliation(s)
- Xia Yan
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, South Xiang-An Road, Xiamen, 361102, China
| | - Li-Juan Wang
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, South Xiang-An Road, Xiamen, 361102, China
| | - Zhen Wu
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, South Xiang-An Road, Xiamen, 361102, China
| | - Yun-Long Wu
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, South Xiang-An Road, Xiamen, 361102, China
| | - Xiu-Xiu Liu
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, South Xiang-An Road, Xiamen, 361102, China
| | - Fang-Rong Chang
- Graduate Institute of Natural Products, Kaohsiung Medical University, Kaohsiung 807, Taiwan, China
| | - Mei-Juan Fang
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, South Xiang-An Road, Xiamen, 361102, China.
| | - Ying-Kun Qiu
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, South Xiang-An Road, Xiamen, 361102, China.
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36
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Fast MS/MS acquisition without dynamic exclusion enables precise and accurate quantification of proteome by MS/MS fragment intensity. Sci Rep 2016; 6:26392. [PMID: 27198003 PMCID: PMC4873735 DOI: 10.1038/srep26392] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 04/28/2016] [Indexed: 12/25/2022] Open
Abstract
Most currently proteomic studies use data-dependent acquisition with dynamic exclusion to identify and quantify the peptides generated by the digestion of biological sample. Although dynamic exclusion permits more identifications and higher possibility to find low abundant proteins, stochastic and irreproducible precursor ion selection caused by dynamic exclusion limit the quantification capabilities, especially for MS/MS based quantification. This is because a peptide is usually triggered for fragmentation only once due to dynamic exclusion. Therefore the fragment ions used for quantification only reflect the peptide abundances at that given time point. Here, we propose a strategy of fast MS/MS acquisition without dynamic exclusion to enable precise and accurate quantification of proteome by MS/MS fragment intensity. The results showed comparable proteome identification efficiency compared to the traditional data-dependent acquisition with dynamic exclusion, better quantitative accuracy and reproducibility regardless of label-free based quantification or isobaric labeling based quantification. It provides us with new insights to fully explore the potential of modern mass spectrometers. This strategy was applied to the relative quantification of two human disease cell lines, showing great promises for quantitative proteomic applications.
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37
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Álvarez Porebski PW, Lynen F. Offline comprehensive liquid chromatography in combination with a Deoxyribonuclease I immobilized enzymatic reactor for selective screening of oligonucleotide mixtures. J Chromatogr A 2016; 1451:164-168. [PMID: 27208984 DOI: 10.1016/j.chroma.2016.05.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 05/01/2016] [Accepted: 05/04/2016] [Indexed: 10/21/2022]
Abstract
The development of a comprehensive ion-pair chromatography-immobilized enzyme reactor×ion-pair chromatography (IPC-IMER×IPC) methodology for the advanced characterization of DNA/RNA oligonucleotides (ONs) mixtures has been carried out. More in detail, a DNase I IMER has been coupled to IPC in the post column configuration, followed by the collection of the eluting fractions and reanalysis by IPC. The effect of the mobile phase over the IMER activity was qualitatively evaluated. The methodology proved to generate relevant ON degradation profiles that might be correlated with the ON stability towards nucleases. Moreover, this platform shows potential for its further implementation in selective analysis of ON mixtures and in mapping studies.
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Affiliation(s)
- Piotr Wiktor Álvarez Porebski
- Separation Science Group, Department of Organic and Macromolecular Chemistry, Universiteit Gent, Krijgslaan 281 S4-bis, 9000 Gent, Belgium.
| | - Frederic Lynen
- Separation Science Group, Department of Organic and Macromolecular Chemistry, Universiteit Gent, Krijgslaan 281 S4-bis, 9000 Gent, Belgium.
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38
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Franco MS, Padovan RN, Fumes BH, Lanças FM. An overview of multidimensional liquid phase separations in food analysis. Electrophoresis 2016; 37:1768-83. [PMID: 27030380 DOI: 10.1002/elps.201600028] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 03/14/2016] [Accepted: 03/15/2016] [Indexed: 01/06/2023]
Abstract
Food safety is a priority public health concern that demands analytical methods capable to detect low concentration level of contaminants (e.g. pesticides and antibiotics) in different food matrices. Due to the high complexity of these matrices, a sample preparation step is in most cases mandatory to achieve satisfactory results being usually tedious, lengthy, and prone to the introduction of errors. For this reason, many research groups have focused efforts on the development of online systems capable to do the cleanup, concentration, and separation steps at once through multidimensional separation techniques (MDS). Among several possible setups, the most popular are the multidimensional chromatographic techniques (MDC) that consist in combining more than one mobile and/or stationary phase to provide a satisfactory separation. In the present review, we selected a variety of multidimensional separation systems used for food contaminant analysis in order to discuss the instrumentation aspects, the concept of orthogonality, column approaches used in these systems, and new materials that can be used in these columns. Selected classes of contaminants present in food matrices are introduced and discussed as example of the potential applications of multidimensional liquid phase separation techniques in food safety.
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Affiliation(s)
- Maraíssa Silva Franco
- Institute of Chemistry of São Carlos, University of São Paulo, Sao Carlos, SP, Brasil
| | | | - Bruno Henrique Fumes
- Institute of Chemistry of São Carlos, University of São Paulo, Sao Carlos, SP, Brasil
| | - Fernando Mauro Lanças
- Institute of Chemistry of São Carlos, University of São Paulo, Sao Carlos, SP, Brasil
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39
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Zhang S, Yuan H, Zhao B, Zhou Y, Jiang H, Zhang L, Liang Z, Zhang Y. Integrated platform with a combination of online digestion and (18)O labeling for proteome quantification via an immobilized trypsin microreactor. Analyst 2016; 140:5227-34. [PMID: 26063120 DOI: 10.1039/c5an00887e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A novel automated integrated platform for quantitative proteome analysis was established with a combination of online digestion of proteins and in situ(18)O labeling by an immobilized enzyme reactor (IMER); digests were captured and desalted by a C18 trap column, and peptides were analyzed by nanoRPLC-ESI-MS/MS. Bovine serum albumin (BSA) was used to evaluate the performance of the developed platform. Compared with traditional offline methods, not only the digestion and labeling time was shortened from 36 h to just 1 h, but also the labeling efficiency was improved from 95% to 99%. Furthermore, the back-exchange from (18)O to (16)O could also be efficiently avoided by the use of IMER. The platform was further evaluated by the quantitative analysis of 100 ng (18)O and (16)O online labeled yeast sample with a mixing ratio of 1 : 1, and the results showed significantly improved sensitivity and reproducibility, as well as improved quantitative accuracy than offline method. With these advantages, the integrated platform was finally applied to the quantitative profiling of 100 ng proteins extracted from two mouse hepatocarcinoma ascites syngeneic cell lines with high and low lymph node metastases rates, and ten differentially expressed proteins were successfully found, most of which were related to tumorigenesis and tumor metastasis. All these results demonstrate that the developed integrated platform can provide a new way for high efficiency (18)O labeling and the quantitative analysis of trace amounts of sample with high accuracy and high reproducibility.
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Affiliation(s)
- Shen Zhang
- National Chromatographic Research and Analysis Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, 116023, China.
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40
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Burns M, Wiseman G, Knight A, Bramley P, Foster L, Rollinson S, Damant A, Primrose S. Measurement issues associated with quantitative molecular biology analysis of complex food matrices for the detection of food fraud. Analyst 2016; 141:45-61. [DOI: 10.1039/c5an01392e] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A review of measurement issues associated with quantitative molecular analysis of complex food matrices for the detection of food fraud.
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Affiliation(s)
| | - Gordon Wiseman
- Premier Analytical Services
- Premier Foods Group Ltd
- The Lord Rank Centre
- Bucks HP12 3QS
- UK
| | | | - Peter Bramley
- School of Biological Sciences
- Royal Holloway
- University of London
- Surrey TW20 0EX
- UK
| | - Lucy Foster
- Department for the Environment
- Food and Rural Affairs
- London SW1P 3JR
- UK
| | - Sophie Rollinson
- Department for the Environment
- Food and Rural Affairs
- London SW1P 3JR
- UK
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41
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Zhou L, Li Q, Wang J, Huang C, Nice EC. Oncoproteomics: Trials and tribulations. Proteomics Clin Appl 2015; 10:516-31. [PMID: 26518147 DOI: 10.1002/prca.201500081] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 09/19/2015] [Accepted: 10/27/2015] [Indexed: 02/05/2023]
Affiliation(s)
- Li Zhou
- State Key Laboratory of Biotherapy and Cancer Center; West China Hospital; Sichuan University, and Collaborative Innovation Center for Biotherapy; Chengdu P. R. China
- Department of Neurology; The Affiliated Hospital of Hainan Medical College; Haikou Hainan P. R. China
| | - Qifu Li
- Department of Neurology; The Affiliated Hospital of Hainan Medical College; Haikou Hainan P. R. China
| | - Jiandong Wang
- Department of Biomedical; Chengdu Medical College; Chengdu Sichuan Province P. R. China
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center; West China Hospital; Sichuan University, and Collaborative Innovation Center for Biotherapy; Chengdu P. R. China
| | - Edouard C. Nice
- State Key Laboratory of Biotherapy and Cancer Center; West China Hospital; Sichuan University, and Collaborative Innovation Center for Biotherapy; Chengdu P. R. China
- Department of Biochemistry and Molecular Biology; Monash University; Clayton Australia
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42
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Abstract
This article summarizes the most important developments in the use of 2D-LC for bioanalysis in the last 5 years. While several interesting and powerful applications have been developed recently, this work has been supported by continued, significant development of theoretical concepts, instrument development and practical aspects of method development. Some of the most exciting applications have been focused on the use of 2D-LC and characterize proteins both as biotherapeutic drug substances, and in formulations. These materials are inherently complex, difficult to resolve chromatographically and present problems that are essentially unknown (e.g., aggregation) in the small molecule world, thus 2D-LC can be leveraged very effectively to address these challenges.
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43
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Porous silica enhanced proteolysis during Off-Gel separation for efficient protein identification. Talanta 2015; 144:1182-8. [PMID: 26452945 DOI: 10.1016/j.talanta.2015.07.087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 07/30/2015] [Indexed: 11/22/2022]
Abstract
An advanced approach is developed in this work for simultaneous on-line separation and digestion of proteins by combining the Off-Gel isoelectric focusing (IEF) and enzymatic nanoreactor enhanced proteolysis. The nanoreactor was prepared by preloading trypsin in amino-functionalized macroporous silica, and then directly added into Off-Gel wells. With the nanoreactor loaded Off-Gel device, effective digestion of proteins happened during IEF electrophoresis to generate directly fractionated tryptic peptides, which not only accelerated the experimental flow but also avoided sample loss, leading to a more comprehensive protein identification from complex biological samples. A successful identification of 3592 proteins was achieved from Hela cell line by using the approach followed with LC-MS/MS analysis, while only 1877 proteins were identified from the same sample when using standard in-solution proteolysis followed with Off-Gel electrophoresis and then LC-MS/MS analysis. Therefore, we have demonstrated that the approach can greatly simplify high-throughput proteomics and significantly improve protein identification.
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44
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Interface-free two-dimensional heart-cutting capillary electrophoresis for the separation and stacking of anionic and neutral analytes. J Sep Sci 2015; 38:2532-7. [DOI: 10.1002/jssc.201500268] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 04/13/2015] [Accepted: 04/14/2015] [Indexed: 02/01/2023]
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45
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López-Villar E, Martos-Moreno GÁ, Chowen JA, Okada S, Kopchick JJ, Argente J. A proteomic approach to obesity and type 2 diabetes. J Cell Mol Med 2015; 19:1455-70. [PMID: 25960181 PMCID: PMC4511345 DOI: 10.1111/jcmm.12600] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 04/02/2015] [Indexed: 12/13/2022] Open
Abstract
The incidence of obesity and type diabetes 2 has increased dramatically resulting in an increased interest in its biomedical relevance. However, the mechanisms that trigger the development of diabetes type 2 in obese patients remain largely unknown. Scientific, clinical and pharmaceutical communities are dedicating vast resources to unravel this issue by applying different omics tools. During the last decade, the advances in proteomic approaches and the Human Proteome Organization have opened and are opening a new door that may be helpful in the identification of patients at risk and to improve current therapies. Here, we briefly review some of the advances in our understanding of type 2 diabetes that have occurred through the application of proteomics. We also review, in detail, the current improvements in proteomic methodologies and new strategies that could be employed to further advance our understanding of this pathology. By applying these new proteomic advances, novel therapeutic and/or diagnostic protein targets will be discovered in the obesity/Type 2 diabetes area.
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Affiliation(s)
- Elena López-Villar
- Departments of Endocrinology and Pediatrics, Hospital Infantil Universitario Niño Jesús, Universidad Autónoma de Madrid, Madrid, Spain.,Oncohematology and Pediatrics, Hospital Infantil Universitario Niño Jesús, Madrid, Spain
| | - Gabriel Á Martos-Moreno
- Departments of Endocrinology and Pediatrics, Hospital Infantil Universitario Niño Jesús, Universidad Autónoma de Madrid, Madrid, Spain.,Instituto de Investigación La Princesa, Madrid, Spain.,Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Julie A Chowen
- Departments of Endocrinology and Pediatrics, Hospital Infantil Universitario Niño Jesús, Universidad Autónoma de Madrid, Madrid, Spain.,Instituto de Investigación La Princesa, Madrid, Spain.,Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Shigeru Okada
- Edison Biotechnology Institute, Ohio University, Konneker Research Laboratories, Athens, OH, USA.,Department of Pediatrics, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, USA
| | - John J Kopchick
- Edison Biotechnology Institute, Ohio University, Konneker Research Laboratories, Athens, OH, USA.,Molecular and Cellular Biology Program, Ohio University, Athens, OH, USA.,Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, USA
| | - Jesús Argente
- Departments of Endocrinology and Pediatrics, Hospital Infantil Universitario Niño Jesús, Universidad Autónoma de Madrid, Madrid, Spain.,Instituto de Investigación La Princesa, Madrid, Spain.,Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
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46
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Determination of variation parameters as a crucial step in designing TMT-based clinical proteomics experiments. PLoS One 2015; 10:e0120115. [PMID: 25775046 PMCID: PMC4361338 DOI: 10.1371/journal.pone.0120115] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 02/04/2015] [Indexed: 02/06/2023] Open
Abstract
In quantitative shotgun proteomic analyses by liquid chromatography and mass spectrometry, a rigid study design is necessary in order to obtain statistically relevant results. Hypothesis testing, sample size calculation and power estimation are fundamental concepts that require consideration upon designing an experiment. For this reason, the reproducibility and variability of the proteomic platform needs to be assessed. In this study, we evaluate the technical (sample preparation), labeling (isobaric labels), and total (biological + technical + labeling + experimental) variability and reproducibility of a workflow that employs a shotgun LC-MS/MS approach in combination with TMT peptide labeling for the quantification of peripheral blood mononuclear cell (PBMC) proteome. We illustrate that the variability induced by TMT labeling is small when compared to the technical variation. The latter is also responsible for a substantial part of the total variation. Prior knowledge about the experimental variability allows for a correct design, a prerequisite for the detection of biologically significant disease-specific differential proteins in clinical proteomics experiments.
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47
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Golizeh M, Schneider C, Ohlund LB, Sleno L. Multidimensional LC–MS/MS analysis of liver proteins in rat, mouse and human microsomal and S9 fractions. EUPA OPEN PROTEOMICS 2015. [DOI: 10.1016/j.euprot.2015.01.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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48
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Guarnieri MT, Pienkos PT. Algal omics: unlocking bioproduct diversity in algae cell factories. PHOTOSYNTHESIS RESEARCH 2015; 123:255-63. [PMID: 24627032 DOI: 10.1007/s11120-014-9989-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 02/17/2014] [Indexed: 05/10/2023]
Abstract
Rapid advances in "omic" technologies are helping to unlock the full potential of microalgae as multi-use feedstocks, with utility in an array of industrial biotechnology, biofuel, and biomedical applications. In turn, algae are emerging as highly attractive candidates for development as microbial cell factories. In this review, we examine the wide array of potential algal bioproducts, with a focus upon the role of omic technologies in driving bioproduct discovery and optimization in microalgal systems.
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Affiliation(s)
- Michael T Guarnieri
- National Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, MS 3323, Golden, CO, 80401, USA,
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49
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Abdelhamid HN, Wu HF. Proteomics analysis of the mode of antibacterial action of nanoparticles and their interactions with proteins. Trends Analyt Chem 2015. [DOI: 10.1016/j.trac.2014.09.010] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Ferreira R, Moreira-Gonçalves D, Azevedo AL, Duarte JA, Amado F, Vitorino R. Unraveling the exercise-related proteome signature in heart. Basic Res Cardiol 2014; 110:454. [PMID: 25475830 DOI: 10.1007/s00395-014-0454-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 10/30/2014] [Accepted: 11/19/2014] [Indexed: 12/15/2022]
Abstract
Exercise training is a well-known non-pharmacological strategy for the prevention and treatment of cardiovascular diseases. Despite the established phenotypic knowledge, the molecular signature of exercise-induced cardiac remodeling remains poorly characterized. The great majority of studies dedicated to this topic use conventional reductionist methods, which only allow analyzing individual protein candidates. Nowadays, several methodologies based on mass spectrometry are available and have been successfully applied for the characterization of heart proteome, representing an attractive approach for the wide characterization of the complex molecular networks that underlie exercise-induced cardiac remodeling. Still, few studies have used these methodologies to understand the impact of exercise training on the remodeling of cardiac proteome. The present study analyzes the few available data obtained from mass spectrometry (MS)-based proteomic studies assessing the impact of distinct types of exercise training on the protein profile of heart (left ventricle and isolated mitochondria) and the potential cross-tolerance between exercise training and diseases as myocardial infarction and obesity. Network analysis was performed with bioinformatics to integrate data from distinct research papers, based on distinct exercise training protocols, animal models and methodological approaches applied in the characterization of heart proteome. The analysis revealed that exercise training confers a unique proteome signature characterized by the up-regulation of lipid and organic metabolic processes, vasculogenesis and tissue regeneration. Data retrieved from this analysis also suggested that cardiac mitochondrial proteome is highly dynamic in response to exercise training due, in part, to the action of specific kinases as PKA and PKG. Regarding to the type of exercise, treadmill training seems to have a greater effect on the modulation of cardiac proteome than swimming. Data from the present review will certainly open new perspectives on cardiac proteomics and will help to envisage future studies targeting the identification of the regulatory mechanisms underlying cardiac adaptive and maladaptive remodeling.
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Affiliation(s)
- Rita Ferreira
- Mass Spectrometry Group, QOPNA, Department of Chemistry, University of Aveiro, 3810-193, Aveiro, Portugal,
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