Jones, Andrew R 
ORCID: 0000-0001-6118-9327, Deutsch, Eric W and Vizcaino, Juan Antonio
(2023)
Is DIA proteomics data FAIR? Current data sharing practices, available bioinformatics infrastructure and recommendations for the future.
PROTEOMICS, 23 (7-8).
e2200014-.
Abstract
Data independent acquisition (DIA) proteomics techniques have matured enormously in recent years, thanks to multiple technical developments in, for example, instrumentation and data analysis approaches. However, there are many improvements that are still possible for DIA data in the area of the FAIR (Findability, Accessibility, Interoperability and Reusability) data principles. These include more tailored data sharing practices and open data standards since public databases and data standards for proteomics were mostly designed with DDA data in mind. Here we first describe the current state of the art in the context of FAIR data for proteomics in general, and for DIA approaches in particular. For improving the current situation for DIA data, we make the following recommendations for the future: (i) development of an open data standard for spectral libraries; (ii) make mandatory the availability of the spectral libraries used in DIA experiments in ProteomeXchange resources; (iii) improve the support for DIA data in the data standards developed by the Proteomics Standards Initiative; and (iv) improve the support for DIA datasets in ProteomeXchange resources, including more tailored metadata requirements.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | data independent acquisition, data repositories, data standards, proteomics data, spectral libraries |
| Divisions: | Faculty of Health and Life Sciences Faculty of Health and Life Sciences > Institute of Systems, Molecular and Integrative Biology |
| Depositing User: | Symplectic Admin |
| Date Deposited: | 08 Feb 2023 15:05 |
| Last Modified: | 17 May 2023 10:21 |
| DOI: | 10.1002/pmic.202200014 |
| Open Access URL: | https://doi.org/10.1002/pmic.202200014 |
| Related URLs: | |
| URI: | https://livrepository.liverpool.ac.uk/id/eprint/3168273 |
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