TY - JOUR
T1 - Is DIA proteomics data FAIR? Current data sharing practices, available bioinformatics infrastructure and recommendations for the future
AU - Jones, Andrew R.
AU - Deutsch, Eric W.
AU - Vizcaíno, Juan Antonio
N1 - Publisher Copyright:
© 2022 The Authors. Proteomics published by Wiley-VCH GmbH.
PY - 2023/4/1
Y1 - 2023/4/1
N2 - 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.
AB - 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.
KW - data independent acquisition
KW - data repositories
KW - data standards
KW - proteomics data
KW - spectral libraries
UR - http://www.scopus.com/inward/record.url?scp=85138005401&partnerID=8YFLogxK
U2 - 10.1002/pmic.202200014
DO - 10.1002/pmic.202200014
M3 - Article
C2 - 36074795
AN - SCOPUS:85138005401
SN - 1615-9853
VL - 23
JO - Proteomics
JF - Proteomics
IS - 7-8
M1 - 2200014
ER -