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Coorssen JR, Padula MP. Proteomics-The State of the Field: The Definition and Analysis of Proteomes Should Be Based in Reality, Not Convenience. Proteomes 2024; 12:14. [PMID: 38651373 PMCID: PMC11036260 DOI: 10.3390/proteomes12020014] [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: 03/17/2024] [Revised: 04/17/2024] [Accepted: 04/17/2024] [Indexed: 04/25/2024] Open
Abstract
With growing recognition and acknowledgement of the genuine complexity of proteomes, we are finally entering the post-proteogenomic era. Routine assessment of proteomes as inferred correlates of gene sequences (i.e., canonical 'proteins') cannot provide the necessary critical analysis of systems-level biology that is needed to understand underlying molecular mechanisms and pathways or identify the most selective biomarkers and therapeutic targets. These critical requirements demand the analysis of proteomes at the level of proteoforms/protein species, the actual active molecular players. Currently, only highly refined integrated or integrative top-down proteomics (iTDP) enables the analytical depth necessary to provide routine, comprehensive, and quantitative proteome assessments across the widest range of proteoforms inherent to native systems. Here we provide a broad perspective of the field, taking in historical and current realities, to establish a more balanced understanding of where the field has come from (in particular during the ten years since Proteomes was launched), current issues, and how things likely need to proceed if necessary deep proteome analyses are to succeed. We base this in our firm belief that the best proteomic analyses reflect, as closely as possible, the native sample at the moment of sampling. We also seek to emphasise that this and future analytical approaches are likely best based on the broad recognition and exploitation of the complementarity of currently successful approaches. This also emphasises the need to continuously evaluate and further optimize established approaches, to avoid complacency in thinking and expectations but also to promote the critical and careful development and introduction of new approaches, most notably those that address proteoforms. Above all, we wish to emphasise that a rigorous focus on analytical quality must override current thinking that largely values analytical speed; the latter would certainly be nice, if only proteoforms could thus be effectively, routinely, and quantitatively assessed. Alas, proteomes are composed of proteoforms, not molecular species that can be amplified or that directly mirror genes (i.e., 'canonical'). The problem is hard, and we must accept and address it as such, but the payoff in playing this longer game of rigorous deep proteome analyses is the promise of far more selective biomarkers, drug targets, and truly personalised or even individualised medicine.
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Affiliation(s)
- Jens R. Coorssen
- Department of Biological Sciences, Faculty of Mathematics and Science, Brock University, St. Catharines, ON L2S 3A1, Canada
- Institute for Globally Distributed Open Research and Education (IGDORE), St. Catharines, ON L2N 4X2, Canada
| | - Matthew P. Padula
- School of Life Sciences and Proteomics, Lipidomics and Metabolomics Core Facility, Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia
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Woodland B, Necakov A, Coorssen JR. Optimized Proteome Reduction for Integrative Top–Down Proteomics. Proteomes 2023; 11:proteomes11010010. [PMID: 36976889 PMCID: PMC10059017 DOI: 10.3390/proteomes11010010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/02/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Integrative top–down proteomics is an analytical approach that fully addresses the breadth and complexity needed for effective and routine assessment of proteomes. Nonetheless, any such assessments also require a rigorous review of methodology to ensure the deepest possible quantitative proteome analyses. Here, we establish an optimized general protocol for proteome extracts to improve the reduction of proteoforms and, thus, resolution in 2DE. Dithiothreitol (DTT), tributylphosphine (TBP), and 2-hydroxyethyldisulfide (HED), combined and alone, were tested in one-dimensional SDS-PAGE (1DE), prior to implementation into a full 2DE protocol. Prior to sample rehydration, reduction with 100 mM DTT + 5 mM TBP yielded increased spot counts, total signal, and spot circularity (i.e., decreased streaking) compared to other conditions and reduction protocols reported in the literature. The data indicate that many widely implemented reduction protocols are significantly ‘under-powered’ in terms of proteoform reduction and thus, limit the quality and depth of routine top–down proteomic analyses.
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Affiliation(s)
- Breyer Woodland
- Department of Biological Sciences, Faculty of Mathematics and Science, Brock University, St. Catharines, ON L2S 3A1, Canada
| | - Aleksandar Necakov
- Department of Biological Sciences, Faculty of Mathematics and Science, Brock University, St. Catharines, ON L2S 3A1, Canada
| | - Jens R. Coorssen
- Department of Biological Sciences, Faculty of Mathematics and Science, Brock University, St. Catharines, ON L2S 3A1, Canada
- Ronin Institute, Montclair, NJ 07043, USA
- Correspondence:
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Huang M, Wang Y. GLOBAL AND TARGETED PROFILING OF GTP-BINDING PROTEINS IN BIOLOGICAL SAMPLES BY MASS SPECTROMETRY. MASS SPECTROMETRY REVIEWS 2021; 40:215-235. [PMID: 32519381 PMCID: PMC7725852 DOI: 10.1002/mas.21637] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/04/2020] [Accepted: 05/15/2020] [Indexed: 05/05/2023]
Abstract
GTP-binding proteins are among the most important enzyme families that are involved in a plethora of biological processes. However, owing to the enormous diversity of the nucleotide-binding protein family, comprehensive analyses of the expression level, structure, activity, and regulatory mechanisms of GTP-binding proteins remain challenging with the use of conventional approaches. The many advances in mass spectrometry (MS) instrumentation and data acquisition methods, together with a variety of enrichment approaches in sample preparation, render MS a powerful tool for the comprehensive characterizations of the activities and expression levels of various GTP-binding proteins. We review herein the recent developments in the application of MS-based techniques, together with general and widely used affinity enrichment approaches, for the proteome-wide and targeted capture, identification, and quantification of GTP-binding proteins. The working principles, advantages, and limitations of various strategies for profiling the expression level, activity, posttranslational modifications, and interactome of GTP-binding proteins are discussed. It can be envisaged that future applications of MS-based proteomics will lead to a better understanding about the roles of GTP-binding proteins in different biological processes and human diseases. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Ming Huang
- Environmental Toxicology Graduate Program, University of California Riverside, Riverside, CA 92521, USA
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California Riverside, Riverside, CA 92521, USA
- Department of Chemistry, University of California Riverside, Riverside, CA 92521, USA
- Correspondence author: Yinsheng Wang. Telephone: (951)827-2700;
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Herrmann M, Engelke K, Ebert R, Müller-Deubert S, Rudert M, Ziouti F, Jundt F, Felsenberg D, Jakob F. Interactions between Muscle and Bone-Where Physics Meets Biology. Biomolecules 2020; 10:biom10030432. [PMID: 32164381 PMCID: PMC7175139 DOI: 10.3390/biom10030432] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/27/2020] [Accepted: 03/05/2020] [Indexed: 02/06/2023] Open
Abstract
Muscle and bone interact via physical forces and secreted osteokines and myokines. Physical forces are generated through gravity, locomotion, exercise, and external devices. Cells sense mechanical strain via adhesion molecules and translate it into biochemical responses, modulating the basic mechanisms of cellular biology such as lineage commitment, tissue formation, and maturation. This may result in the initiation of bone formation, muscle hypertrophy, and the enhanced production of extracellular matrix constituents, adhesion molecules, and cytoskeletal elements. Bone and muscle mass, resistance to strain, and the stiffness of matrix, cells, and tissues are enhanced, influencing fracture resistance and muscle power. This propagates a dynamic and continuous reciprocity of physicochemical interaction. Secreted growth and differentiation factors are important effectors of mutual interaction. The acute effects of exercise induce the secretion of exosomes with cargo molecules that are capable of mediating the endocrine effects between muscle, bone, and the organism. Long-term changes induce adaptations of the respective tissue secretome that maintain adequate homeostatic conditions. Lessons from unloading, microgravity, and disuse teach us that gratuitous tissue is removed or reorganized while immobility and inflammation trigger muscle and bone marrow fatty infiltration and propagate degenerative diseases such as sarcopenia and osteoporosis. Ongoing research will certainly find new therapeutic targets for prevention and treatment.
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Affiliation(s)
- Marietta Herrmann
- Orthopedic Department, Bernhard-Heine-Center for Locomotion Research, IZKF Research Group Tissue regeneration in musculoskeletal diseases, University Hospital Würzburg, University of Wuerzburg, 97070 Würzburg, Germany;
| | - Klaus Engelke
- Department of Medicine 3, FAU University Erlangen-Nürnberg and Universitätsklinikum Erlangen, 91054 Erlangen, Germany;
| | - Regina Ebert
- Orthopedic Department, Bernhard-Heine-Center for Locomotion Research, University of Würzburg, IGZ, 97076 Würzburg, Germany; (R.E.)
| | - Sigrid Müller-Deubert
- Orthopedic Department, Bernhard-Heine-Center for Locomotion Research, University of Würzburg, IGZ, 97076 Würzburg, Germany; (R.E.)
| | - Maximilian Rudert
- Orthopedic Department, Bernhard-Heine-Center for Locomotion Research, University of Würzburg, 97074 Würzburg, Germany;
| | - Fani Ziouti
- Department of Internal Medicine II, University Hospital Würzburg, 97080 Würzburg, Germany; (F.Z.); (F.J.)
| | - Franziska Jundt
- Department of Internal Medicine II, University Hospital Würzburg, 97080 Würzburg, Germany; (F.Z.); (F.J.)
| | - Dieter Felsenberg
- Privatpraxis für Muskel- und Knochenkrankheiten, 12163 Berlin Germany;
| | - Franz Jakob
- Orthopedic Department, Bernhard-Heine-Center for Locomotion Research, University of Würzburg, IGZ, 97076 Würzburg, Germany; (R.E.)
- Orthopedic Department, Bernhard-Heine-Center for Locomotion Research, University of Würzburg, 97074 Würzburg, Germany;
- Correspondence:
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Coorssen JR, Padula MP. Special Issue "Top-down Proteomics: In Memory of Dr Alfred Yergey". Alfred Linwood Yergey, III, 17 September 1941-27 May 2018. Proteomes 2020; 8:proteomes8010001. [PMID: 31952104 PMCID: PMC7151663 DOI: 10.3390/proteomes8010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 01/08/2020] [Indexed: 12/03/2022] Open
Affiliation(s)
- Jens R. Coorssen
- Departments of Health Sciences and Biological Sciences, Faculties of Applied Health Sciences and Mathematics & Science, Brock University, St. Catharines, ON L2S 3A1, Canada
- Correspondence: (J.R.C.); (M.P.P.)
| | - Matthew P. Padula
- School of Life Sciences and Proteomics Core Facility, Faculty of Science, The University of Technology, Sydney, Ultimo 2007, Australia
- Correspondence: (J.R.C.); (M.P.P.)
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