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Chamrád I, Simerský R, Lenobel R, Novák O. Exploring affinity chromatography in proteomics: A comprehensive review. Anal Chim Acta 2024; 1306:342513. [PMID: 38692783 DOI: 10.1016/j.aca.2024.342513] [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: 12/12/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 05/03/2024]
Abstract
Over the past decades, the proteomics field has undergone rapid growth. Progress in mass spectrometry and bioinformatics, together with separation methods, has brought many innovative approaches to the study of the molecular biology of the cell. The potential of affinity chromatography was recognized immediately after its first application in proteomics, and since that time, it has become one of the cornerstones of many proteomic protocols. Indeed, this chromatographic technique exploiting the specific binding between two molecules has been employed for numerous purposes, from selective removal of interfering (over)abundant proteins or enrichment of scarce biomarkers in complex biological samples to mapping the post-translational modifications and protein interactions with other proteins, nucleic acids or biologically active small molecules. This review presents a comprehensive survey of this versatile analytical tool in current proteomics. To navigate the reader, the haphazard space of affinity separations is classified according to the experiment's aims and the separated molecule's nature. Different types of available ligands and experimental strategies are discussed in further detail for each of the mentioned procedures.
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Affiliation(s)
- Ivo Chamrád
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic.
| | - Radim Simerský
- Department of Chemical Biology, Faculty of Science, Palacký University, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
| | - René Lenobel
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
| | - Ondřej Novák
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
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Ignjatovic V, Geyer PE, Palaniappan KK, Chaaban JE, Omenn GS, Baker MS, Deutsch EW, Schwenk JM. Mass Spectrometry-Based Plasma Proteomics: Considerations from Sample Collection to Achieving Translational Data. J Proteome Res 2019; 18:4085-4097. [PMID: 31573204 DOI: 10.1021/acs.jproteome.9b00503] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The proteomic analysis of human blood and blood-derived products (e.g., plasma) offers an attractive avenue to translate research progress from the laboratory into the clinic. However, due to its unique protein composition, performing proteomics assays with plasma is challenging. Plasma proteomics has regained interest due to recent technological advances, but challenges imposed by both complications inherent to studying human biology (e.g., interindividual variability) and analysis of biospecimens (e.g., sample variability), as well as technological limitations remain. As part of the Human Proteome Project (HPP), the Human Plasma Proteome Project (HPPP) brings together key aspects of the plasma proteomics pipeline. Here, we provide considerations and recommendations concerning study design, plasma collection, quality metrics, plasma processing workflows, mass spectrometry (MS) data acquisition, data processing, and bioinformatic analysis. With exciting opportunities in studying human health and disease though this plasma proteomics pipeline, a more informed analysis of human plasma will accelerate interest while enhancing possibilities for the incorporation of proteomics-scaled assays into clinical practice.
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Affiliation(s)
- Vera Ignjatovic
- Haematology Research , Murdoch Children's Research Institute , Parkville , VIC 3052 , Australia.,Department of Paediatrics , The University of Melbourne , Parkville , VIC 3052 , Australia
| | - Philipp E Geyer
- NNF Center for Protein Research, Faculty of Health Sciences , University of Copenhagen , 2200 Copenhagen , Denmark.,Department of Proteomics and Signal Transduction , Max Planck Institute of Biochemistry , 82152 Martinsried , Germany
| | - Krishnan K Palaniappan
- Freenome , 259 East Grand Avenue , South San Francisco , California 94080 , United States
| | - Jessica E Chaaban
- Haematology Research , Murdoch Children's Research Institute , Parkville , VIC 3052 , Australia
| | - Gilbert S Omenn
- Departments of Computational Medicine & Bioinformatics, Human Genetics, and Internal Medicine and School of Public Health , University of Michigan , 100 Washtenaw Avenue , Ann Arbor , Michigan 48109-2218 , United States
| | - Mark S Baker
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences , Macquarie University , 75 Talavera Road , North Ryde , NSW 2109 , Australia
| | - Eric W Deutsch
- Institute for Systems Biology , 401 Terry Avenue North , Seattle , Washington 98109 , United States
| | - Jochen M Schwenk
- Affinity Proteomics, SciLifeLab , KTH Royal Institute of Technology , 171 65 Stockholm , Sweden
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Qundos U, Drobin K, Mattsson C, Hong MG, Sjöberg R, Forsström B, Solomon D, Uhlén M, Nilsson P, Michaëlsson K, Schwenk JM. Affinity proteomics discovers decreased levels of AMFR in plasma from Osteoporosis patients. Proteomics Clin Appl 2015; 10:681-90. [PMID: 25689831 PMCID: PMC5029581 DOI: 10.1002/prca.201400167] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 12/22/2014] [Accepted: 02/11/2015] [Indexed: 12/27/2022]
Abstract
PURPOSE Affinity proteomic approaches by antibody bead arrays enable multiplexed analysis of proteins in body fluids. In the presented study, we investigated blood plasma within osteoporosis to discovery differential protein profiles and to propose novel biomarkers candidates for subsequent studies. EXPERIMENTAL DESIGN Starting with 4608 antibodies and plasma samples from 22 women for an untargeted screening, a set of 72 proteins were suggested for further analysis. Complementing these with targets from literature and other studies, a targeted bead array of 180 antibodies was built to profile for 92 proteins in plasma samples of 180 women from two independent population-based studies. RESULTS Differential profiles between osteoporosis patients and matched controls were discovered for 12 proteins in at least one of the two study sets. Among these targets, the levels of autocrine motility factor receptor (AMFR) were concordantly lower in plasma of female osteoporosis patients. Subsequently, verification of anti-AMFR antibody selectivity was conducted using high-density peptide and protein arrays, and Western blotting. CONCLUSIONS AND CLINICAL RELEVANCE Further validation in additional study sets will be needed to determine the clinical value of the observed decrease in AMFR plasma levels in osteoporosis patients, but AMFR may aid our understanding of disease mechanisms and could support existing tools for diagnosis and monitoring of patient mobility within osteoporosis.
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Affiliation(s)
- Ulrika Qundos
- Affinity Proteomics, SciLifeLab, KTH-Royal Institute of Technology, Solna, Sweden
| | - Kimi Drobin
- Affinity Proteomics, SciLifeLab, KTH-Royal Institute of Technology, Solna, Sweden
| | - Cecilia Mattsson
- Affinity Proteomics, SciLifeLab, KTH-Royal Institute of Technology, Solna, Sweden
| | - Mun-Gwan Hong
- Affinity Proteomics, SciLifeLab, KTH-Royal Institute of Technology, Solna, Sweden
| | - Ronald Sjöberg
- Affinity Proteomics, SciLifeLab, KTH-Royal Institute of Technology, Solna, Sweden
| | - Björn Forsström
- Affinity Proteomics, SciLifeLab, KTH-Royal Institute of Technology, Solna, Sweden
| | - David Solomon
- Affinity Proteomics, SciLifeLab, KTH-Royal Institute of Technology, Solna, Sweden
| | - Mathias Uhlén
- Affinity Proteomics, SciLifeLab, KTH-Royal Institute of Technology, Solna, Sweden
| | - Peter Nilsson
- Affinity Proteomics, SciLifeLab, KTH-Royal Institute of Technology, Solna, Sweden
| | - Karl Michaëlsson
- Department of Surgical Sciences, Section of Orthopedics, Uppsala University, Uppsala, Sweden.,Uppsala Clinical Research Centre, Uppsala University, Uppsala, Sweden
| | - Jochen M Schwenk
- Affinity Proteomics, SciLifeLab, KTH-Royal Institute of Technology, Solna, Sweden
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Flores-Nascimento MC, Paes-Leme AF, Mazetto BM, Zanella JL, De Paula EV, Annichino-Bizzacchi JM. Inflammatory, immune and lipid transportation proteins are differentially expressed in spontaneous and proximal deep vein thrombosis patients. Thromb Res 2012; 130:e246-50. [DOI: 10.1016/j.thromres.2012.08.306] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 08/11/2012] [Accepted: 08/21/2012] [Indexed: 12/25/2022]
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A fully integrated multi-column system for abundant protein depletion from serum/plasma. J Chromatogr B Analyt Technol Biomed Life Sci 2012; 902:35-41. [DOI: 10.1016/j.jchromb.2012.06.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 05/30/2012] [Accepted: 06/01/2012] [Indexed: 10/28/2022]
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Schwenk JM, Igel U, Neiman M, Langen H, Becker C, Bjartell A, Ponten F, Wiklund F, Grönberg H, Nilsson P, Uhlen M. Toward next generation plasma profiling via heat-induced epitope retrieval and array-based assays. Mol Cell Proteomics 2010; 9:2497-507. [PMID: 20682762 DOI: 10.1074/mcp.m110.001560] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
There is a need for high throughput methods for screening patient samples in the quest for potential biomarkers for diagnostics and patient care. Here, we used a combination of undirected target selection, antibody suspension bead arrays, and heat-induced epitope retrieval to allow for protein profiling of human plasma in a novel and systematic manner. Several antibodies were found to reveal altered protein profiles upon epitope retrieval at elevated temperatures with limits of detection improving into lower ng/ml ranges. In a study based on prostate cancer patients, several proteins with differential profiles were discovered and subsequently validated in an independent cohort. For one of the potential biomarkers, the human carnosine dipeptidase 1 protein (CNDP1), the differences were determined to be related to the glycosylation status of the targeted protein. The study shows a path of pursuit for large scale screening of biobank repositories in a flexible and proteome-wide fashion by utilizing heat-induced epitope retrieval and using an antibody suspension bead array format.
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Affiliation(s)
- Jochen M Schwenk
- Science for Life Laboratory, Royal Institute of Technology (KTH), Stockholm, Sweden.
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