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Dowling P, Zweyer M, Swandulla D, Ohlendieck K. Characterization of Contractile Proteins from Skeletal Muscle Using Gel-Based Top-Down Proteomics. Proteomes 2019; 7:proteomes7020025. [PMID: 31226838 PMCID: PMC6631179 DOI: 10.3390/proteomes7020025] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 06/14/2019] [Accepted: 06/17/2019] [Indexed: 12/22/2022] Open
Abstract
The mass spectrometric analysis of skeletal muscle proteins has used both peptide-centric and protein-focused approaches. The term 'top-down proteomics' is often used in relation to studying purified proteoforms and their post-translational modifications. Two-dimensional gel electrophoresis, in combination with peptide generation for the identification and characterization of intact proteoforms being present in two-dimensional spots, plays a critical role in specific applications of top-down proteomics. A decisive bioanalytical advantage of gel-based and top-down approaches is the initial bioanalytical focus on intact proteins, which usually enables the swift identification and detailed characterisation of specific proteoforms. In this review, we describe the usage of two-dimensional gel electrophoretic top-down proteomics and related approaches for the systematic analysis of key components of the contractile apparatus, with a special focus on myosin heavy and light chains and their associated regulatory proteins. The detailed biochemical analysis of proteins belonging to the thick and thin skeletal muscle filaments has decisively improved our biochemical understanding of structure-function relationships within the contractile apparatus. Gel-based and top-down proteomics has clearly established a variety of slow and fast isoforms of myosin, troponin and tropomyosin as excellent markers of fibre type specification and dynamic muscle transition processes.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, Maynooth, W23F2H6 Co. Kildare, Ireland.
- MU Human Health Research Institute, Maynooth University, Maynooth, W23F2H6 Co. Kildare, Ireland.
| | - Margit Zweyer
- Institute of Physiology II, University of Bonn, D-53115 Bonn, Germany.
| | - Dieter Swandulla
- Institute of Physiology II, University of Bonn, D-53115 Bonn, Germany.
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, Maynooth, W23F2H6 Co. Kildare, Ireland.
- MU Human Health Research Institute, Maynooth University, Maynooth, W23F2H6 Co. Kildare, Ireland.
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Kallemeijn MJ, Kavelaars FG, van der Klift MY, Wolvers-Tettero ILM, Valk PJM, van Dongen JJM, Langerak AW. Next-Generation Sequencing Analysis of the Human TCRγδ+ T-Cell Repertoire Reveals Shifts in Vγ- and Vδ-Usage in Memory Populations upon Aging. Front Immunol 2018; 9:448. [PMID: 29559980 PMCID: PMC5845707 DOI: 10.3389/fimmu.2018.00448] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 02/19/2018] [Indexed: 12/20/2022] Open
Abstract
Immunological aging remodels the immune system at several levels. This has been documented in particular for the T-cell receptor (TCR)αβ+ T-cell compartment, showing reduced naive T-cell outputs and an accumulation of terminally differentiated clonally expanding effector T-cells, leading to increased proneness to autoimmunity and cancer development at older age. Even though TCRαβ+ and TCRγδ+ T-cells follow similar paths of development involving V(D)J-recombination of TCR genes in the thymus, TCRγδ+ T-cells tend to be more subjected to peripheral rather than central selection. However, the impact of aging in shaping of the peripheral TRG/TRD repertoire remains largely elusive. Next-generation sequencing analysis methods were optimized based on a spike-in method using plasmid vector DNA-samples for accurate TRG/TRD receptor diversity quantification, resulting in optimally defined primer concentrations, annealing temperatures and cycle numbers. Next, TRG/TRD repertoire diversity was evaluated during TCRγδ+ T-cell ontogeny, showing a broad, diverse repertoire in thymic and cord blood samples with Gaussian CDR3-length distributions, in contrast to the more skewed repertoire in mature circulating TCRγδ+ T-cells in adult peripheral blood. During aging the naive repertoire maintained its diversity with Gaussian CDR3-length distributions, while in the central and effector memory populations a clear shift from young (Vγ9/Vδ2 dominance) to elderly (Vγ2/Vδ1 dominance) was observed. Together with less clear Gaussian CDR3-length distributions, this would be highly suggestive of differentially heavily selected repertoires. Despite the apparent age-related shift from Vγ9/Vδ2 to Vγ2/Vδ1, no clear aging effect was observed on the Vδ2 invariant T nucleotide and canonical Vγ9-Jγ1.2 selection determinants. A more detailed look into the healthy TRG/TRD repertoire revealed known cytomegalovirus-specific TRG/TRD clonotypes in a few donors, albeit without a significant aging-effect, while Mycobacterium tuberculosis-specific clonotypes were absent. Notably, in effector subsets of elderly individuals, we could identify reported TRG and TRD receptor chains from TCRγδ+ T-cell large granular lymphocyte leukemia proliferations, which typically present in the elderly population. Collectively, our results point to relatively subtle age-related changes in the human TRG/TRD repertoire, with a clear shift in Vγ/Vδ usage in memory cells upon aging.
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Affiliation(s)
- Martine J Kallemeijn
- Laboratory for Medical Immunology, Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - François G Kavelaars
- Department of Hematology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Michèle Y van der Klift
- Laboratory for Medical Immunology, Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Ingrid L M Wolvers-Tettero
- Laboratory for Medical Immunology, Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Peter J M Valk
- Department of Hematology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Jacques J M van Dongen
- Laboratory for Medical Immunology, Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Anton W Langerak
- Laboratory for Medical Immunology, Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands
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Kim DW, Yoo WG, Lee MR, Kim YJ, Cho SH, Lee WJ, Ju JW. 2DSpotDB: A Database for the Annotated Two-dimensional Polyacrylamide Gel Electrophoresis of Pathogen Proteins. Genomics Inform 2011. [DOI: 10.5808/gi.2011.9.4.197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Allmer J, Kuhlgert S, Hippler M. 2DB: a Proteomics database for storage, analysis, presentation, and retrieval of information from mass spectrometric experiments. BMC Bioinformatics 2008; 9:302. [PMID: 18605993 PMCID: PMC2475538 DOI: 10.1186/1471-2105-9-302] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2008] [Accepted: 07/07/2008] [Indexed: 11/26/2022] Open
Abstract
Background The amount of information stemming from proteomics experiments involving (multi dimensional) separation techniques, mass spectrometric analysis, and computational analysis is ever-increasing. Data from such an experimental workflow needs to be captured, related and analyzed. Biological experiments within this scope produce heterogenic data ranging from pictures of one or two-dimensional protein maps and spectra recorded by tandem mass spectrometry to text-based identifications made by algorithms which analyze these spectra. Additionally, peptide and corresponding protein information needs to be displayed. Results In order to handle the large amount of data from computational processing of mass spectrometric experiments, automatic import scripts are available and the necessity for manual input to the database has been minimized. Information is in a generic format which abstracts from specific software tools typically used in such an experimental workflow. The software is therefore capable of storing and cross analysing results from many algorithms. A novel feature and a focus of this database is to facilitate protein identification by using peptides identified from mass spectrometry and link this information directly to respective protein maps. Additionally, our application employs spectral counting for quantitative presentation of the data. All information can be linked to hot spots on images to place the results into an experimental context. A summary of identified proteins, containing all relevant information per hot spot, is automatically generated, usually upon either a change in the underlying protein models or due to newly imported identifications. The supporting information for this report can be accessed in multiple ways using the user interface provided by the application. Conclusion We present a proteomics database which aims to greatly reduce evaluation time of results from mass spectrometric experiments and enhance result quality by allowing consistent data handling. Import functionality, automatic protein detection, and summary creation act together to facilitate data analysis. In addition, supporting information for these findings is readily accessible via the graphical user interface provided. The database schema and the implementation, which can easily be installed on virtually any server, can be downloaded in the form of a compressed file from our project webpage.
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Affiliation(s)
- Jens Allmer
- Institute for Plant Biochemistry and Biotechnology, University of Münster, Hindenburgplatz 55, Münster, Germany.
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Muela A, Seco C, Camafeita E, Arana I, Orruño M, López JA, Barcina I. Changes in Escherichia coli outer membrane subproteome under environmental conditions inducing the viable but nonculturable state. FEMS Microbiol Ecol 2008; 64:28-36. [DOI: 10.1111/j.1574-6941.2008.00453.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Lisacek F, Hoogland C, Lescuyer P, Hochstrasser DF, Appel RD. Using bioinformatic resources in the proteomic analysis of biological fluids. Proteomics Clin Appl 2007; 1:900-15. [PMID: 21136743 DOI: 10.1002/prca.200700188] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2007] [Indexed: 12/24/2022]
Abstract
On-line databases targeted towards protein contents in biological fluids are scarce. Consequently, the investigation of proteins identified in a biological fluid most importantly depends on crosschecking information gathered from less specific resources. This review summarises the key databases and tools for collecting information on tissue specificity or expression profiles. It also emphasises the high connectivity between databases fruitfully used to corroborate and piece information together. Finally, selected issues related to appropriate bioinformatics tools in the context of clinical applications are succinctly discussed.
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Affiliation(s)
- Frédérique Lisacek
- Proteome Informatics Group, Swiss Institute of Bioinformatics, Geneva, Switzerland.
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Ng KW, Garner HR. Nome della Proteina: a protein identification resolution database. IEEE ENGINEERING IN MEDICINE AND BIOLOGY MAGAZINE : THE QUARTERLY MAGAZINE OF THE ENGINEERING IN MEDICINE & BIOLOGY SOCIETY 2007; 26:70-2. [PMID: 17672234 DOI: 10.1109/memb.2007.384099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Affiliation(s)
- Kar-wai Ng
- Eugene McDermott Center for Human Growth and Development, Center for Biomedical Inventions, University of Texas Southwestern Medical Center, Dallas 75390-8591, USA
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Ottens AK, Kobeissy FH, Golden EC, Zhang Z, Haskins WE, Chen SS, Hayes RL, Wang KKW, Denslow ND. Neuroproteomics in neurotrauma. MASS SPECTROMETRY REVIEWS 2006; 25:380-408. [PMID: 16498609 DOI: 10.1002/mas.20073] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Neurotrauma in the form of traumatic brain injury (TBI) afflicts more Americans annually than Alzheimer's and Parkinson's disease combined, yet few researchers have used neuroproteomics to investigate the underlying complex molecular events that exacerbate TBI. Discussed in this review is the methodology needed to explore the neurotrauma proteome-from the types of samples used to the mass spectrometry identification and quantification techniques available. This neuroproteomics survey presents a framework for large-scale protein research in neurotrauma, as applied for immediate TBI biomarker discovery and the far-reaching systems biology understanding of how the brain responds to trauma. Ultimately, knowledge attained through neuroproteomics could lead to clinical diagnostics and therapeutics to lessen the burden of neurotrauma on society.
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Affiliation(s)
- Andrew K Ottens
- Center of Neuroproteomics and Biomarkers Research, McKnight Brain Institute, University of Florida, Gainesville, FL, USA.
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Abstract
In this review, we have summarized our work using combined complex statistical genetics, bioinformatics, and functional genomics to determine the genetic basis of the age-related thymic involution in C57BL/6J X DBA/2J recombinant inbred mice and the parental B6 and D2 mice. We have shown that these mice provided a valuable genetic model that can permit resampling of thymuses from different aged but genetically identical animals and determination of the relative significance of age-associated changes in the thymus. Our results suggest that the quantitative trait loci (QTL) regulating the Con A-induced thymocyte proliferative response were mapped to mouse chromosome Chr 11 (D11Mit51 at 18 cM), a region that harbors the IL-12b gene. The importance of IL-12b in maintaining thymic integrity and function during the aging process was confirmed by a more rapid involution of the thymus in IL-12b knockout (IL-12b-/-) mice compared to wild-type (WT) mice. Functionally, IL-12 provided a strong synergistic effect to augment the IL-7 or IL-2 induced thymocyte proliferative response, especially in both aged WT and IL-12b-/- mice, but not in normal young mice. In contract to the proliferative response, the age-related decline in the total number of thymocytes was determined at different age, and mapped to loci on Chr 9, 62 cM and Chr 10, 32 cM. Using matrix-assisted laser desorption/ionisation-time of flight-mass spectrometry (MALDI-TOF-MS), increased expression of peroxiredoxin was found to be correlated with thymic involution. Our results suggest the possibility to identify the complex molecular network that can be associated with the regulation of thymic involution in aged mice using a high-dimensional functional genomics approach.
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Affiliation(s)
- Hui-Chen Hsu
- Division of Clinical Immunology and Rheumatology, Department of Medicine, The University of Alabama at Birmingham, 701 South 19th Street, LHRB 473, Birmingham, AL 35294, USA
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Meleth S, Deshane J, Kim H. The case for well-conducted experiments to validate statistical protocols for 2D gels: different pre-processing = different lists of significant proteins. BMC Biotechnol 2005; 5:7. [PMID: 15707480 PMCID: PMC553976 DOI: 10.1186/1472-6750-5-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2004] [Accepted: 02/11/2005] [Indexed: 11/15/2022] Open
Abstract
Background The proteomics literature has seen a proliferation of publications that seek to apply the rapidly improving technology of 2D gels to study various biological systems. However, there is a dearth of systematic studies that have investigated appropriate statistical approaches to analyse the data from these experiments. Results Comparison of the effects of statistical pre-processing on the results of two sample t-tests suggests that the results of 2D gel experiments and by extension the conclusions derived from these experiments are not independent of the statistical protocol used. Conclusions This study suggests that there is a need for well-conducted validation studies to establish optimal statistical techniques to be used on such data sets.
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Affiliation(s)
- Sreelatha Meleth
- Biostatistics and Bioinformatics Unit, Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jessy Deshane
- Department of Pharmacology, University of Alabama at Birmingham, Birmingham, AL 35924 USA
| | - Helen Kim
- Department of Pharmacology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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Garwood K, McLaughlin T, Garwood C, Joens S, Morrison N, Taylor CF, Carroll K, Evans C, Whetton AD, Hart S, Stead D, Yin Z, Brown AJP, Hesketh A, Chater K, Hansson L, Mewissen M, Ghazal P, Howard J, Lilley KS, Gaskell SJ, Brass A, Hubbard SJ, Oliver SG, Paton NW. PEDRo: a database for storing, searching and disseminating experimental proteomics data. BMC Genomics 2004; 5:68. [PMID: 15377392 PMCID: PMC521486 DOI: 10.1186/1471-2164-5-68] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2004] [Accepted: 09/17/2004] [Indexed: 11/10/2022] Open
Abstract
Background Proteomics is rapidly evolving into a high-throughput technology, in which substantial and systematic studies are conducted on samples from a wide range of physiological, developmental, or pathological conditions. Reference maps from 2D gels are widely circulated. However, there is, as yet, no formally accepted standard representation to support the sharing of proteomics data, and little systematic dissemination of comprehensive proteomic data sets. Results This paper describes the design, implementation and use of a Proteome Experimental Data Repository (PEDRo), which makes comprehensive proteomics data sets available for browsing, searching and downloading. It is also serves to extend the debate on the level of detail at which proteomics data should be captured, the sorts of facilities that should be provided by proteome data management systems, and the techniques by which such facilities can be made available. Conclusions The PEDRo database provides access to a collection of comprehensive descriptions of experimental data sets in proteomics. Not only are these data sets interesting in and of themselves, they also provide a useful early validation of the PEDRo data model, which has served as a starting point for the ongoing standardisation activity through the Proteome Standards Initiative of the Human Proteome Organisation.
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Affiliation(s)
- Kevin Garwood
- Department of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Thomas McLaughlin
- School of Biomolecular Sciences, UMIST, PO Box 88, Manchester M60 1QD, UK
| | - Chris Garwood
- Department of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Scott Joens
- Department of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Norman Morrison
- Department of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK
- School of Biological Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Christopher F Taylor
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Kathleen Carroll
- School of Biomolecular Sciences, UMIST, PO Box 88, Manchester M60 1QD, UK
| | - Caroline Evans
- School of Biomolecular Sciences, UMIST, PO Box 88, Manchester M60 1QD, UK
| | - Anthony D Whetton
- School of Biomolecular Sciences, UMIST, PO Box 88, Manchester M60 1QD, UK
| | - Sarah Hart
- School of Biomolecular Sciences, UMIST, PO Box 88, Manchester M60 1QD, UK
| | - David Stead
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, UK
| | - Zhikang Yin
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, UK
| | - Alistair JP Brown
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, UK
| | - Andrew Hesketh
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | - Keith Chater
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | - Lena Hansson
- Scottish Centre for Genomic Technology & Informatics, University of Edinburgh Medical School, The Chancellor's Building, Little France Crescent, Edinburgh, EH16 4S, UK
| | - Muriel Mewissen
- Scottish Centre for Genomic Technology & Informatics, University of Edinburgh Medical School, The Chancellor's Building, Little France Crescent, Edinburgh, EH16 4S, UK
| | - Peter Ghazal
- Scottish Centre for Genomic Technology & Informatics, University of Edinburgh Medical School, The Chancellor's Building, Little France Crescent, Edinburgh, EH16 4S, UK
| | - Julie Howard
- University of Cambridge, Department of Biochemistry, Downing Site, Cambridge, CB2 1QW, UK
| | - Kathryn S Lilley
- University of Cambridge, Department of Biochemistry, Downing Site, Cambridge, CB2 1QW, UK
| | - Simon J Gaskell
- Department of Chemistry, UMIST, PO Box 88, Manchester M60 1QD, UK
| | - Andy Brass
- Department of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK
- School of Biological Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Simon J Hubbard
- School of Biomolecular Sciences, UMIST, PO Box 88, Manchester M60 1QD, UK
| | - Stephen G Oliver
- School of Biological Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Norman W Paton
- Department of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK
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