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Beutgen VM, Shinkevich V, Pörschke J, Meena C, Steitz AM, Pogge von Strandmann E, Graumann J, Gómez-Serrano M. Secretome analysis using Affinity Proteomics and Immunoassays: a focus on Tumor Biology. Mol Cell Proteomics 2024:100830. [PMID: 39147028 DOI: 10.1016/j.mcpro.2024.100830] [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: 02/29/2024] [Revised: 07/20/2024] [Accepted: 08/12/2024] [Indexed: 08/17/2024] Open
Abstract
The study of the cellular secretome using proteomic techniques continues to capture the attention of the research community across a broad range of topics in biomedical research. Due to their untargeted nature, independence from the model system employed, historically superior depth of analysis, as well as comparative affordability, mass spectrometry-based approaches traditionally dominate such analyses. More recently, however, affinity-based proteomic assays have massively gained in analytical depth, which together with their high sensitivity, dynamic range coverage as well as high throughput capabilities render them exquisitely suited to secretome analysis. In this review, we revisit the analytical challenges implied by secretomics and provide an overview of affinity-based proteomic platforms currently available for such analyses, using the study of the tumor secretome as an example for basic and translational research.
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Affiliation(s)
- Vanessa M Beutgen
- Institute of Translational Proteomics, Biochemical/Pharmacological Centre, Philipps University, Marburg, Germany; Core Facility Translational Proteomics, Biochemical/Pharmacological Centre, Philipps University, Marburg, Germany
| | - Veronika Shinkevich
- Institute of Pharmacology, Biochemical/Pharmacological Centre, Philipps University, Marburg, Germany
| | - Johanna Pörschke
- Institute for Tumor Immunology, Center for Tumor Biology and Immunology, Philipps University, Marburg, Germany
| | - Celina Meena
- Institute for Tumor Immunology, Center for Tumor Biology and Immunology, Philipps University, Marburg, Germany
| | - Anna M Steitz
- Translational Oncology Group, Center for Tumor Biology and Immunology, Philipps University, Marburg, Germany
| | - Elke Pogge von Strandmann
- Institute for Tumor Immunology, Center for Tumor Biology and Immunology, Philipps University, Marburg, Germany
| | - Johannes Graumann
- Institute of Translational Proteomics, Biochemical/Pharmacological Centre, Philipps University, Marburg, Germany; Core Facility Translational Proteomics, Biochemical/Pharmacological Centre, Philipps University, Marburg, Germany.
| | - María Gómez-Serrano
- Institute for Tumor Immunology, Center for Tumor Biology and Immunology, Philipps University, Marburg, Germany.
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Joshi N, Garapati K, Ghose V, Kandasamy RK, Pandey A. Recent progress in mass spectrometry-based urinary proteomics. Clin Proteomics 2024; 21:14. [PMID: 38389064 PMCID: PMC10885485 DOI: 10.1186/s12014-024-09462-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 02/12/2024] [Indexed: 02/24/2024] Open
Abstract
Serum or plasma is frequently utilized in biomedical research; however, its application is impeded by the requirement for invasive sample collection. The non-invasive nature of urine collection makes it an attractive alternative for disease characterization and biomarker discovery. Mass spectrometry-based protein profiling of urine has led to the discovery of several disease-associated biomarkers. Proteomic analysis of urine has not only been applied to disorders of the kidney and urinary bladder but also to conditions affecting distant organs because proteins excreted in the urine originate from multiple organs. This review provides a progress update on urinary proteomics carried out over the past decade. Studies summarized in this review have expanded the catalog of proteins detected in the urine in a variety of clinical conditions. The wide range of applications of urine analysis-from characterizing diseases to discovering predictive, diagnostic and prognostic markers-continues to drive investigations of the urinary proteome.
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Affiliation(s)
- Neha Joshi
- Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Kishore Garapati
- Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Vivek Ghose
- Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
| | - Richard K Kandasamy
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, 55905, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India.
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, 55905, USA.
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA.
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