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Channaveerappa D, Ngounou Wetie AG, Darie CC. Bottlenecks in Proteomics: An Update. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:753-769. [PMID: 31347083 DOI: 10.1007/978-3-030-15950-4_45] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Mass spectrometry (MS) is the core for advanced methods in proteomic experiments. When effectively used, proteomics may provide extensive information about proteins and their post-translational modifications, as well as their interaction partners. However, there are also many problems that one can encounter during a proteomic experiment, including, but not limited to sample preparation, sample fractionation, sample analysis, data analysis & interpretation and biological significance. Here we discuss some of the problems that researchers should be aware of when performing a proteomic experiment.
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Affiliation(s)
- Devika Channaveerappa
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, USA
| | - Armand G Ngounou Wetie
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, USA
| | - Costel C Darie
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, USA.
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2
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Abstract
Electrophoretic methodologies for qualitative and preparative purposes are commonly used in biological research and have been well established as an integral analytical tool for a long time in most research laboratories. Listed here are some of the more specialized innovations that have been developed in recent times for special purposes of study. These include micropreparative isoelectric focusing in liquid suspension, accelerated protease digestion by SDS-PAGE, two-dimensional SDS-PAGE for membrane protein resolution, carbon nanotube-modified page for resolution of complement C3, electrophoretic resolution of ultra-acidic proteomes in acidic media, and two-dimensional immunoelectrophoresis of pre-beta/alpha lipoprotein A-I in agarose. All these methods are briefly reviewed in this chapter.
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Affiliation(s)
- James D Fesmire
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA.
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3
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Identification and characterization two isoforms of NADH:ubiquinone oxidoreductase from the hyperthermophilic eubacterium Aquifex aeolicus. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:366-373. [DOI: 10.1016/j.bbabio.2018.02.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 02/18/2018] [Accepted: 02/24/2018] [Indexed: 12/20/2022]
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4
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Duncombe TA, Kang CC, Maity S, Ward TM, Pegram MD, Murthy N, Herr AE. Hydrogel Pore-Size Modulation for Enhanced Single-Cell Western Blotting. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:327-334. [PMID: 26567472 PMCID: PMC4708057 DOI: 10.1002/adma.201503939] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 10/05/2015] [Indexed: 05/18/2023]
Abstract
Pore-gradient microgel arrays enable thousands of parallel high-resolution single-cell protein electrophoresis separations for targets accross a wide molecular mass (25-289 kDa), yet within 1 mm separation distances. Dual crosslinked hydrogels facilitate gel-pore expansion after electrophoresis for efficient and uniform immunoprobing. The photopatterned, light-activated, and acid-expandable hydrogel underpins single-cell protein analysis, here for oncoprotein-related signaling in human breast biopsy.
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Affiliation(s)
- Todd A. Duncombe
- Department of Bioengineering, University of California Berkeley, Berkeley, California, CA 94720, USA
- The UC Berkeley/UCSF Graduate Program in Bioengineering, University of California Berkeley, Berkeley, California, CA 94720, USA
| | - Chi-Chih Kang
- Department of Bioengineering, University of California Berkeley, Berkeley, California, CA 94720, USA
| | - Santanu Maity
- Department of Bioengineering, University of California Berkeley, Berkeley, California, CA 94720, USA
| | - Toby M. Ward
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California, CA 94305, USA
| | - Mark D. Pegram
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California, CA 94305, USA
| | - Niren Murthy
- Department of Bioengineering, University of California Berkeley, Berkeley, California, CA 94720, USA
- The UC Berkeley/UCSF Graduate Program in Bioengineering, University of California Berkeley, Berkeley, California, CA 94720, USA
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5
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Vasconcelos MAD, Alves AC, Carneiro RF, Dias AHS, Martins FWV, Cajazeiras JB, Nagano CS, Teixeira EH, Nascimento KSD, Cavada BS. Purification and primary structure of a novel mannose-specific lectin from Centrolobium microchaete Mart seeds. Int J Biol Macromol 2015; 81:600-7. [PMID: 26321423 DOI: 10.1016/j.ijbiomac.2015.08.059] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 08/24/2015] [Accepted: 08/25/2015] [Indexed: 10/23/2022]
Abstract
This study aimed to purify and characterize a novel mannose-binding lectin from the seeds of Centrolobium microchaete. Centrolobium microchaete lectin (CML) was purified by affinity chromatography in mannose-Sepharose-4B column. CML agglutinated rabbit erythrocytes and was inhibited by D-mannose, α-methyl-D-mannoside, D-glucose, N-Acetyl-D-glucosamine and sucrose. The lectin was stable at pH 7.0 and 8.0 and temperatures up to 60°C. The monomeric form of CML showed approximately 28kDa, and its native form is probably a homodimer, as determined by gel filtration chromatography. The primary structure of CML was determined by tandem mass spectrometry that showed CML as a protein with two distinct forms (isolectins CML-1 and CML-2) with 246 and 247 residues, respectively. CML-2 possesses one residue of Asn more than CML-1 in C-terminal. The primary structure of CML agrees with the molecular weights found by electrospray ionization mass spectrometry: 27,224 and 27,338Da for CML-1 and CML-2, respectively. CML is a metal-dependent glycoprotein. Moreover, the glycan composition of CML and its structure were predicted.
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Affiliation(s)
- Mayron Alves de Vasconcelos
- Laboratório Integrado de Biomoléculas-LIBS, Departamento de Patologia e Medicina Legal, Universidade Federal do Ceará, Monsenhor Furtado, s/n, 60430-160, Fortaleza, Ceará, Brazil.
| | - Ana Cecília Alves
- Laboratório de Moléculas Biologicamente Ativas - BioMol-Lab, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Campus do Pici, s/n bloco 907, 60440-970, Fortaleza, Ceará, Brazil
| | - Rômulo Farias Carneiro
- Laboratório de Biotecnologia Marinha-BioMar-Lab, Departamento de Engenharia de Pesca, Universidade Federal do Ceará, Campus do Pici s/n, bloco 871, 60440-970, Fortaleza, Ceará, Brazil
| | - Artur Hermano Sampaio Dias
- Laboratório de Moléculas Biologicamente Ativas - BioMol-Lab, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Campus do Pici, s/n bloco 907, 60440-970, Fortaleza, Ceará, Brazil
| | - Francisco William Viana Martins
- Laboratório de Moléculas Biologicamente Ativas - BioMol-Lab, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Campus do Pici, s/n bloco 907, 60440-970, Fortaleza, Ceará, Brazil
| | - João Batista Cajazeiras
- Laboratório de Moléculas Biologicamente Ativas - BioMol-Lab, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Campus do Pici, s/n bloco 907, 60440-970, Fortaleza, Ceará, Brazil
| | - Celso Shiniti Nagano
- Laboratório de Biotecnologia Marinha-BioMar-Lab, Departamento de Engenharia de Pesca, Universidade Federal do Ceará, Campus do Pici s/n, bloco 871, 60440-970, Fortaleza, Ceará, Brazil
| | - Edson Holanda Teixeira
- Laboratório Integrado de Biomoléculas-LIBS, Departamento de Patologia e Medicina Legal, Universidade Federal do Ceará, Monsenhor Furtado, s/n, 60430-160, Fortaleza, Ceará, Brazil
| | - Kyria Santiago do Nascimento
- Laboratório de Moléculas Biologicamente Ativas - BioMol-Lab, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Campus do Pici, s/n bloco 907, 60440-970, Fortaleza, Ceará, Brazil
| | - Benildo Sousa Cavada
- Laboratório de Moléculas Biologicamente Ativas - BioMol-Lab, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Campus do Pici, s/n bloco 907, 60440-970, Fortaleza, Ceará, Brazil.
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6
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Mahboob S, Mohamedali A, Ahn SB, Schulz-Knappe P, Nice E, Baker MS. Is isolation of comprehensive human plasma peptidomes an achievable quest? J Proteomics 2015; 127:300-9. [PMID: 25979773 DOI: 10.1016/j.jprot.2015.05.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 05/06/2015] [Accepted: 05/09/2015] [Indexed: 01/12/2023]
Abstract
The low molecular weight (LMW; <10kDa)* plasma peptidome has been considered a source of useful diagnostic biomarkers and potentially therapeutic molecules, as it contains many cytokines, peptide hormones, endogenous peptide products and potentially bioactive fragments derived from the parent proteome. The small size of the peptides allows them almost unrestricted vascular and interstitial access, and hence distribution across blood-brain barriers, tumour and other vascular permeability barriers. Therefore, the peptidome may carry specific signatures or fingerprints of an individual's health, wellbeing or disease status. This occurs primarily because of the advantage the peptidome has in being readily accessible in human blood and/or other biofluids. However, the co-expression of highly abundant proteins (>10kDa) and other factors present inherently in human plasma make direct analysis of the blood peptidome one of the most challenging tasks faced in contemporary analytical biochemistry. A comprehensive compendium of extraction and fractionation tools has been collected concerning the isolation and micromanipulation of peptides. However, the search for a reliable, accurate and reproducible single or combinatorial separation process for capturing and analysing the plasma peptidome remains a challenge. This review outlines current techniques used for the separation and detection of plasma peptides and suggests potential avenues for future investigation. This article is part of a Special Issue entitled: HUPO 2014.
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Affiliation(s)
- S Mahboob
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, NSW 2109, Australia
| | - A Mohamedali
- Department of Chemistry and Biomolecular Sciences, Faculty of Science, Macquarie University, NSW 2109, Australia
| | - S B Ahn
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, NSW 2109, Australia
| | | | - E Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - M S Baker
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, NSW 2109, Australia.
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8
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Carneiro RF, de Melo AA, de Almeida AS, Moura RDM, Chaves RP, de Sousa BL, do Nascimento KS, Sampaio SS, Lima JPMS, Cavada BS, Nagano CS, Sampaio AH. H-3, a new lectin from the marine sponge Haliclona caerulea: Purification and mass spectrometric characterization. Int J Biochem Cell Biol 2013; 45:2864-73. [DOI: 10.1016/j.biocel.2013.10.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 09/19/2013] [Accepted: 10/10/2013] [Indexed: 11/30/2022]
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9
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Papasotiriou DG, Markoutsa S, Gorka J, Schleiff E, Karas M, Meyer B. MALDI analysis of proteins after extraction from dissolvable ethylene glycol diacrylate cross-linked polyacrylamide gels. Electrophoresis 2013; 34:2484-94. [DOI: 10.1002/elps.201300132] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 04/20/2013] [Accepted: 05/12/2013] [Indexed: 12/23/2022]
Affiliation(s)
- Dimitrios G. Papasotiriou
- Institute of Pharmaceutical Chemistry; Cluster of Excellence “Macromolecular Complexes”, Goethe University; Frankfurt am Main Germany
| | - Stavroula Markoutsa
- Institute of Pharmaceutical Chemistry; Cluster of Excellence “Macromolecular Complexes”, Goethe University; Frankfurt am Main Germany
| | - Jan Gorka
- Institute of Pharmaceutical Chemistry; Cluster of Excellence “Macromolecular Complexes”, Goethe University; Frankfurt am Main Germany
| | - Enrico Schleiff
- Molecular Cell Biology of Plants; Cluster of Excellence “Macromolecular Complexes”, Goethe University; Frankfurt am Main Germany
| | - Michael Karas
- Institute of Pharmaceutical Chemistry; Cluster of Excellence “Macromolecular Complexes”, Goethe University; Frankfurt am Main Germany
| | - Bjoern Meyer
- Institute for Instrumental Analysis and Bioanalysis; Mannheim University of Applied Sciences; Mannheim Germany
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10
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Liu F, Ye M, Wang C, Hu Z, Zhang Y, Qin H, Cheng K, Zou H. Polyacrylamide Gel with Switchable Trypsin Activity for Analysis of Proteins. Anal Chem 2013; 85:7024-8. [DOI: 10.1021/ac4017693] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Fangjie Liu
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingliang Ye
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Chunli Wang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhengyan Hu
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongqiang Qin
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Cheng
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Hanfa Zou
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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11
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Ortiz A, Richa L, Defer C, Dernis D, Huart JJ, Tokarski C, Rolando C. Proteomics applied to transfusion plasma: the beginning of the story. Vox Sang 2013; 104:275-91. [PMID: 23438183 DOI: 10.1111/j.1423-0410.2012.01663.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
'Safe blood' is and has always been the major concern in transfusion medicine. Plasma can undergo virus inactivation treatments based on physicochemical, photochemical or thermal methodologies for pathogen inactivation. The validation of these treatments is essentially based on clottability assays and clotting factors' titration; however, their impact on plasma proteins at the molecular level has not yet been evaluated. Proteomics appears as particularly adapted to identify, to localize and, consequently, to correlate these modifications to the biological activity change. At the crossroads of biology and analytical sciences, proteomics is the large-scale study of proteins in tissues, physiological fluids or cells at a given moment and in a precise environment. The proteomic strategy is based on a set of methodologies involving separative techniques like mono- and bidimensional gel electrophoresis and chromatography, analytical techniques, especially mass spectrometry, and bioinformatics. Even if plasma has been extensively studied since the very beginning of proteomics, its application to transfusion medicine has just begun. In the first part of this review, we present the principles of proteomics analysis. Then, we propose a state of the art of proteomics applied to plasma analysis. Finally, the use of proteomics for the evaluation of the impact of storage conditions and pathogen inactivation treatments applied to transfusion plasma and for the evaluation of therapeutic protein fractionated is discussed.
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Affiliation(s)
- A Ortiz
- USR CNRS 3290, Miniaturisation pour la Synthèse, l'Analyse et la Protéomique (MSAP), Université de Lille 1, Sciences et Technologie, Villeneuve d'Ascq, France
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12
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Bouchal P, Dvorakova M, Scherl A, Garbis SD, Nenutil R, Vojtesek B. Intact protein profiling in breast cancer biomarker discovery: protein identification issue and the solutions based on 3D protein separation, bottom-up and top-down mass spectrometry. Proteomics 2013; 13:1053-8. [PMID: 23303686 DOI: 10.1002/pmic.201200121] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 10/31/2012] [Accepted: 12/17/2012] [Indexed: 11/07/2022]
Abstract
Proteomics profiling of intact proteins based on MALDI-TOF MS and derived platforms has been used in cancer biomarker discovery studies. This approach suffers from a number of limitations such as low resolution, low sensitivity, and that no knowledge is available on the identity of the respective proteins in the discovery mode. Nevertheless, it remains the most high-throughput, untargeted mode of clinical proteomics studies to date. Here we compare key protein separation and MS techniques available for protein biomarker identification in this type of studies and define reasons of uncertainty in protein peak identity. As a result of critical data analysis, we consider 3D protein separation and identification workflows as optimal procedures. Subsequently, we present a new protocol based on 3D LC-MS/MS with top-down at high resolution that enabled the identification of HNRNP A2/B1 intact peptide as correlating with the estrogen receptor expression in breast cancer tissues. Additional development of this general concept toward next generation, top-down based protein profiling at high resolution is discussed.
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Affiliation(s)
- Pavel Bouchal
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic.
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13
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Drabik A, Bodzon-Kulakowska A, Suder P. Application of the ETD/PTR reactions in top-down proteomics as a faster alternative to bottom-up nanoLC-MS/MS protein identification. JOURNAL OF MASS SPECTROMETRY : JMS 2012; 47:1347-1352. [PMID: 23019167 DOI: 10.1002/jms.3086] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Our goal was to compare two popular analytical techniques used nowadays in proteomic investigations for proteins/peptides sequencing and identification, a widely used nanoLC-MS/MS approach applied in the bottom-up proteomics and electron transfer dissociation/proton transfer reaction fragmentation preferably used when top-down strategy is applied. Comparison was carried out with the aid of the ESI-quadrupole ion-trap instrument using the following criteria: total time of analysis including sample preparation, sequence coverage, Mascot scoring, capability to detect modifications, quality of the results as a function of protein molecular weight and sample consumption.
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14
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Abstract
DNA damage detection and repair take place in the context of chromatin, and histone proteins play important roles in these events. Post-translational modifications of histone proteins are involved in repair and DNA damage signalling processes in response to genotoxic stresses. In particular, acetylation of histones H3 and H4 plays an important role in the mammalian and yeast DNA damage response and survival under genotoxic stress. However, the role of post-translational modifications to histones during the plant DNA damage response is currently poorly understood. Several different acetylated H3 and H4 N-terminal peptides following X-ray treatment were identified using MS analysis of purified histones, revealing previously unseen patterns of histone acetylation in Arabidopsis. Immunoblot analysis revealed an increase in the relative abundance of the H3 acetylated N-terminus, and a global decrease in hyperacetylation of H4 in response to DNA damage induced by X-rays. Conversely, mutants in the key DNA damage signalling factor ATM (ATAXIA TELANGIECTASIA MUTATED) display increased histone acetylation upon irradiation, linking the DNA damage response with dynamic changes in histone modification in plants.
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15
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Wang D, Baudys J, Rees J, Marshall KM, Kalb SR, Parks BA, Nowaczyk L, Pirkle JL, Barr JR. Subtyping botulinum neurotoxins by sequential multiple endoproteases in-gel digestion coupled with mass spectrometry. Anal Chem 2012; 84:4652-8. [PMID: 22577857 DOI: 10.1021/ac3006439] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Botulinum neurotoxin (BoNT) is one of the most toxic substances known. BoNT is classified into seven distinct serotypes labeled A-G. Among individual serotypes, researchers have identified subtypes based on amino acid variability within a serotype and toxin variants with minor amino acid sequence differences within a subtype. BoNT subtype identification is valuable for tracing and tracking bacterial pathogens. A proteomics approach is useful for BoNT subtyping since botulism is caused by botulinum neurotoxin and does not require the presence of the bacteria or its DNA. Enzymatic digestion and peptide identification using tandem mass spectrometry determines toxin protein sequences. However, with the conventional one-step digestion method, producing sufficient numbers of detectable peptides to cover the entire protein sequence is difficult, and incomplete sequence coverage results in uncertainty in distinguishing BoNT subtypes and toxin variants because of high sequence similarity. We report here a method of multiple enzymes and sequential in-gel digestion (MESID) to characterize the BoNT protein sequence. Complementary peptide detection from toxin digestions has yielded near-complete sequence coverage for all seven BoNT serotypes. Application of the method to a BoNT-contaminated carrot juice sample resulted in the identification of 98.4% protein sequence which led to a confident determination of the toxin subtype.
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Affiliation(s)
- Dongxia Wang
- National Center for Environmental Health, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia 30341, United States
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16
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Perfusion reversed-phase high-performance liquid chromatography for protein separation from detergent-containing solutions: An alternative to gel-based approaches. Anal Biochem 2012; 424:97-107. [DOI: 10.1016/j.ab.2012.02.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Revised: 02/15/2012] [Accepted: 02/16/2012] [Indexed: 11/19/2022]
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17
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Abstract
The use of electrophoretic methodologies for use in qualitative and preparative purposes are commonly used in biological research and have been well established as an integral analytical tool for a long time in most research laboratories. Listed here are some of the more specialized innovations that have been developed in recent times for special purposes of study. These include micropreparative isoelectric focusing in liquid suspension, accelerated protease digestion by SDS-PAGE, two-dimensional SDS-PAGE for membrane protein resolution, carbon nanotube-modified page for resolution of complement C3, electrophoretic resolution of ultra-acidic proteomes in acidic media, and two-dimensional immunoelectrophoresis of pre-beta/alpha lipoprotein A-I in agarose. All these methods are briefly reviewed in this chapter.
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Affiliation(s)
- James D Fesmire
- Oklahoma Medical Research Foundation, Oklahoma City, OK, USA.
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18
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Biosa G, Addis MF, Tanca A, Pisanu S, Roggio T, Uzzau S, Pagnozzi D. Comparison of blood serum peptide enrichment methods by Tricine SDS-PAGE and mass spectrometry. J Proteomics 2011; 75:93-9. [PMID: 21757041 DOI: 10.1016/j.jprot.2011.06.025] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Revised: 05/30/2011] [Accepted: 06/25/2011] [Indexed: 11/18/2022]
Abstract
Characterisation of blood serum peptides can provide valuable information on physiological and pathological processes. However, the analysis of raw serum samples by MS results in the identification of a limited number of peptides. In order to improve sensitivity, many peptide enrichment methods have been proposed during the last ten years. Here, we present a comparison of fractionation methods aimed to simplify analysis of small proteins and peptides in blood serum, one of the most promising sources of putative biomarkers. Specifically, three methods based on ultrafiltration, differential precipitation, and peptide ligand libraries (ProteoMiner) were evaluated for the enrichment of peptides and low molecular weight proteins, as demonstrated by Tricine SDS-PAGE and subsequent LC-MS/MS (GeLC-MS/MS). As a result, differential solubilisation (DS) allowed the identification of the highest number of peptides. Moreover, the DS method enabled also the quantitative comparison of samples, producing fundamental information in biomarker discovery approaches.
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Affiliation(s)
- Grazia Biosa
- Porto Conte Ricerche Srl, Tramariglio, Alghero Sassari, Italy
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19
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Ainseba-Chirani N, Dembahri Z, Tokarski C, Rolando C, Benmouna M. Newly designed polyacrylamide/dextran gels for electrophoresis protein separation: synthesis and characterization. POLYM INT 2011. [DOI: 10.1002/pi.3035] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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20
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Meyer B, Papasotiriou DG, Karas M. 100% protein sequence coverage: a modern form of surrealism in proteomics. Amino Acids 2010; 41:291-310. [DOI: 10.1007/s00726-010-0680-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Accepted: 06/25/2010] [Indexed: 01/11/2023]
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