TY - JOUR
T1 - The ProteomeXchange consortium at 10 years
T2 - 2023 update
AU - Deutsch, Eric W.
AU - Bandeira, Nuno
AU - Perez-Riverol, Yasset
AU - Sharma, Vagisha
AU - Carver, Jeremy J.
AU - Mendoza, Luis
AU - Kundu, Deepti J.
AU - Wang, Shengbo
AU - Bandla, Chakradhar
AU - Kamatchinathan, Selvakumar
AU - Hewapathirana, Suresh
AU - Pullman, Benjamin S.
AU - Wertz, Julie
AU - Sun, Zhi
AU - Kawano, Shin
AU - Okuda, Shujiro
AU - Watanabe, Yu
AU - MacLean, Brendan
AU - MacCoss, Michael J.
AU - Zhu, Yunping
AU - Ishihama, Yasushi
AU - Vizcaíno, Juan Antonio
N1 - Publisher Copyright:
© 2023 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research.
PY - 2023/1/6
Y1 - 2023/1/6
N2 - Mass spectrometry (MS) is by far the most used experimental approach in high-throughput proteomics. The ProteomeXchange (PX) consortium of proteomics resources (http://www.proteomexchange.org) was originally set up to standardize data submission and dissemination of public MS proteomics data. It is now 10 years since the initial data workflow was implemented. In this manuscript, we describe the main developments in PX since the previous update manuscript in Nucleic Acids Research was published in 2020. The six members of the Consortium are PRIDE, PeptideAtlas (including PASSEL), MassIVE, jPOST, iProX and Panorama Public. We report the current data submission statistics, showcasing that the number of datasets submitted to PX resources has continued to increase every year. As of June 2022, more than 34 233 datasets had been submitted to PX resources, and from those, 20 062 (58.6%) just in the last three years. We also report the development of the Universal Spectrum Identifiers and the improvements in capturing the experimental metadata annotations. In parallel, we highlight that data re-use activities of public datasets continue to increase, enabling connections between PX resources and other popular bioinformatics resources, novel research and also new data resources. Finally, we summarise the current state-of-the-art in data management practices for sensitive human (clinical) proteomics data.
AB - Mass spectrometry (MS) is by far the most used experimental approach in high-throughput proteomics. The ProteomeXchange (PX) consortium of proteomics resources (http://www.proteomexchange.org) was originally set up to standardize data submission and dissemination of public MS proteomics data. It is now 10 years since the initial data workflow was implemented. In this manuscript, we describe the main developments in PX since the previous update manuscript in Nucleic Acids Research was published in 2020. The six members of the Consortium are PRIDE, PeptideAtlas (including PASSEL), MassIVE, jPOST, iProX and Panorama Public. We report the current data submission statistics, showcasing that the number of datasets submitted to PX resources has continued to increase every year. As of June 2022, more than 34 233 datasets had been submitted to PX resources, and from those, 20 062 (58.6%) just in the last three years. We also report the development of the Universal Spectrum Identifiers and the improvements in capturing the experimental metadata annotations. In parallel, we highlight that data re-use activities of public datasets continue to increase, enabling connections between PX resources and other popular bioinformatics resources, novel research and also new data resources. Finally, we summarise the current state-of-the-art in data management practices for sensitive human (clinical) proteomics data.
UR - https://www.scopus.com/pages/publications/85145975421
U2 - 10.1093/nar/gkac1040
DO - 10.1093/nar/gkac1040
M3 - Article
C2 - 36370099
AN - SCOPUS:85145975421
SN - 0305-1048
VL - 51
SP - D1539-D1548
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - D1
ER -