Clinical Amyloid Typing by Proteomics: Performance Evaluation and Data Sharing between Two Centres
Amyloidosis is a relatively rare human disease caused by the deposition of abnormal protein fibres in the extracellular space of various tissues, impairing their normal function. Proteomic analysis of patients’ biopsies, developed by Dogan and colleagues at the Mayo Clinic, has become crucial for cl...
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| Format: | Article |
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MDPI AG
2021-03-01
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| Series: | Molecules |
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| Online Access: | https://www.mdpi.com/1420-3049/26/7/1913 |
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| author | Diana Canetti Francesca Brambilla Nigel B. Rendell Paola Nocerino Janet A. Gilbertson Dario Di Silvestre Andrea Bergamaschi Francesca Lavatelli Giampaolo Merlini Julian D. Gillmore Vittorio Bellotti Pierluigi Mauri Graham W. Taylor |
| author_facet | Diana Canetti Francesca Brambilla Nigel B. Rendell Paola Nocerino Janet A. Gilbertson Dario Di Silvestre Andrea Bergamaschi Francesca Lavatelli Giampaolo Merlini Julian D. Gillmore Vittorio Bellotti Pierluigi Mauri Graham W. Taylor |
| author_sort | Diana Canetti |
| collection | DOAJ |
| description | Amyloidosis is a relatively rare human disease caused by the deposition of abnormal protein fibres in the extracellular space of various tissues, impairing their normal function. Proteomic analysis of patients’ biopsies, developed by Dogan and colleagues at the Mayo Clinic, has become crucial for clinical diagnosis and for identifying the amyloid type. Currently, the proteomic approach is routinely used at National Amyloidosis Centre (NAC, London, UK) and Istituto di Tecnologie Biomediche-Consiglio Nazionale delle Ricerche (ITB-CNR, Milan, Italy). Both centres are members of the European Proteomics Amyloid Network (EPAN), which was established with the aim of sharing and discussing best practice in the application of amyloid proteomics. One of the EPAN’s activities was to evaluate the quality and the confidence of the results achieved using different software and algorithms for protein identification. In this paper, we report the comparison of proteomics results obtained by sharing NAC proteomics data with the ITB-CNR centre. Mass spectrometric raw data were analysed using different software platforms including Mascot, Scaffold, Proteome Discoverer, Sequest and bespoke algorithms developed for an accurate and immediate amyloid protein identification. Our study showed a high concordance of the obtained results, suggesting a good accuracy of the different bioinformatics tools used in the respective centres. In conclusion, inter-centre data exchange is a worthwhile approach for testing and validating the performance of software platforms and the accuracy of results, and is particularly important where the proteomics data contribute to a clinical diagnosis. |
| first_indexed | 2024-03-10T12:48:40Z |
| format | Article |
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| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-10T12:48:40Z |
| publishDate | 2021-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-c017e28d85fb481d96668e37ce4a88b42023-11-21T13:16:23ZengMDPI AGMolecules1420-30492021-03-01267191310.3390/molecules26071913Clinical Amyloid Typing by Proteomics: Performance Evaluation and Data Sharing between Two CentresDiana Canetti0Francesca Brambilla1Nigel B. Rendell2Paola Nocerino3Janet A. Gilbertson4Dario Di Silvestre5Andrea Bergamaschi6Francesca Lavatelli7Giampaolo Merlini8Julian D. Gillmore9Vittorio Bellotti10Pierluigi Mauri11Graham W. Taylor12Wolfson Drug Discovery Unit and National Amyloidosis Centre, Centre for Amyloidosis and Acute Phase Proteins, Division of Medicine, University College London, London WC1E6BT, UKProteomics and Metabolomics Laboratory, CNR-ITB, Segrate, 20090 Milan, ItalyWolfson Drug Discovery Unit and National Amyloidosis Centre, Centre for Amyloidosis and Acute Phase Proteins, Division of Medicine, University College London, London WC1E6BT, UKWolfson Drug Discovery Unit and National Amyloidosis Centre, Centre for Amyloidosis and Acute Phase Proteins, Division of Medicine, University College London, London WC1E6BT, UKWolfson Drug Discovery Unit and National Amyloidosis Centre, Centre for Amyloidosis and Acute Phase Proteins, Division of Medicine, University College London, London WC1E6BT, UKProteomics and Metabolomics Laboratory, CNR-ITB, Segrate, 20090 Milan, ItalyProteomics and Metabolomics Laboratory, CNR-ITB, Segrate, 20090 Milan, ItalyAmyloidosis Research and Treatment Centre, Fondazione IRCCS Policlinico San Matteo and University of Pavia, 27100 Pavia, ItalyAmyloidosis Research and Treatment Centre, Fondazione IRCCS Policlinico San Matteo and University of Pavia, 27100 Pavia, ItalyWolfson Drug Discovery Unit and National Amyloidosis Centre, Centre for Amyloidosis and Acute Phase Proteins, Division of Medicine, University College London, London WC1E6BT, UKWolfson Drug Discovery Unit and National Amyloidosis Centre, Centre for Amyloidosis and Acute Phase Proteins, Division of Medicine, University College London, London WC1E6BT, UKProteomics and Metabolomics Laboratory, CNR-ITB, Segrate, 20090 Milan, ItalyWolfson Drug Discovery Unit and National Amyloidosis Centre, Centre for Amyloidosis and Acute Phase Proteins, Division of Medicine, University College London, London WC1E6BT, UKAmyloidosis is a relatively rare human disease caused by the deposition of abnormal protein fibres in the extracellular space of various tissues, impairing their normal function. Proteomic analysis of patients’ biopsies, developed by Dogan and colleagues at the Mayo Clinic, has become crucial for clinical diagnosis and for identifying the amyloid type. Currently, the proteomic approach is routinely used at National Amyloidosis Centre (NAC, London, UK) and Istituto di Tecnologie Biomediche-Consiglio Nazionale delle Ricerche (ITB-CNR, Milan, Italy). Both centres are members of the European Proteomics Amyloid Network (EPAN), which was established with the aim of sharing and discussing best practice in the application of amyloid proteomics. One of the EPAN’s activities was to evaluate the quality and the confidence of the results achieved using different software and algorithms for protein identification. In this paper, we report the comparison of proteomics results obtained by sharing NAC proteomics data with the ITB-CNR centre. Mass spectrometric raw data were analysed using different software platforms including Mascot, Scaffold, Proteome Discoverer, Sequest and bespoke algorithms developed for an accurate and immediate amyloid protein identification. Our study showed a high concordance of the obtained results, suggesting a good accuracy of the different bioinformatics tools used in the respective centres. In conclusion, inter-centre data exchange is a worthwhile approach for testing and validating the performance of software platforms and the accuracy of results, and is particularly important where the proteomics data contribute to a clinical diagnosis.https://www.mdpi.com/1420-3049/26/7/1913amyloid proteomicsproteomics platformsproteomics results validationLC-MS/MS raw data exchange |
| spellingShingle | Diana Canetti Francesca Brambilla Nigel B. Rendell Paola Nocerino Janet A. Gilbertson Dario Di Silvestre Andrea Bergamaschi Francesca Lavatelli Giampaolo Merlini Julian D. Gillmore Vittorio Bellotti Pierluigi Mauri Graham W. Taylor Clinical Amyloid Typing by Proteomics: Performance Evaluation and Data Sharing between Two Centres Molecules amyloid proteomics proteomics platforms proteomics results validation LC-MS/MS raw data exchange |
| title | Clinical Amyloid Typing by Proteomics: Performance Evaluation and Data Sharing between Two Centres |
| title_full | Clinical Amyloid Typing by Proteomics: Performance Evaluation and Data Sharing between Two Centres |
| title_fullStr | Clinical Amyloid Typing by Proteomics: Performance Evaluation and Data Sharing between Two Centres |
| title_full_unstemmed | Clinical Amyloid Typing by Proteomics: Performance Evaluation and Data Sharing between Two Centres |
| title_short | Clinical Amyloid Typing by Proteomics: Performance Evaluation and Data Sharing between Two Centres |
| title_sort | clinical amyloid typing by proteomics performance evaluation and data sharing between two centres |
| topic | amyloid proteomics proteomics platforms proteomics results validation LC-MS/MS raw data exchange |
| url | https://www.mdpi.com/1420-3049/26/7/1913 |
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