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Eric W. Deutsch, Nuno Bandeira, Yasset Pérez‐Riverol, Vagisha Sharma, Jeremy Carver, Luis Mendoza, Deepti J Kundu, Shengbo Wang, Chakradhar Bandla, Selvakumar Kamatchinathan and 12 more
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.
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Deutsch, E. W., Bandeira, N., Pérez‐Riverol, Y., Sharma, V., Carver, J., Mendoza, L., Kundu, D. J., Wang, S., Bandla, C., Kamatchinathan, S., Hewapathirana, S., Pullman, B. S., Wertz, J., Sun, Z., Kawano, S., Okuda, S., Watanabe, Y., MacLean, B., MacCoss, M. J., … Vizcaíno, J. A. (2022). The ProteomeXchange consortium at 10 years: 2023 update. Nucleic Acids Research, 51(D1), D1539–D1548. https://doi.org/10.1093/nar/gkac1040
Deutsch, Eric W., et al. "The ProteomeXchange consortium at 10 years: 2023 update." Nucleic Acids Research, vol. 51, no. D1, 2022, pp. D1539–D1548, https://doi.org/10.1093/nar/gkac1040.
Deutsch, Eric W., Nuno Bandeira, Yasset Pérez‐Riverol, Vagisha Sharma, Jeremy Carver, Luis Mendoza, Deepti J Kundu, et al. "The ProteomeXchange consortium at 10 years: 2023 update." Nucleic Acids Research 51, no. D1 (2022): D1539–D1548. https://doi.org/10.1093/nar/gkac1040.
Deutsch E. W., Bandeira N., Pérez‐Riverol Y. [и др.] The ProteomeXchange consortium at 10 years: 2023 update // Nucleic Acids Research. — 2022. — Vol. 51, № D1. — P. D1539–D1548. — URL: https://doi.org/10.1093/nar/gkac1040
@article{deutsch2022proteomexchange,
title = {{The ProteomeXchange consortium at 10 years: 2023 update}},
author = {Eric W. Deutsch and Nuno Bandeira and Yasset Pérez‐Riverol and Vagisha Sharma and Jeremy Carver and Luis Mendoza and Deepti J Kundu and Shengbo Wang and Chakradhar Bandla and Selvakumar Kamatchinathan and Suresh Hewapathirana and Benjamin S Pullman and Julie Wertz and Zhi Sun and Shin Kawano and Shujiro Okuda and Yu Watanabe and Brendan MacLean and Michael J. MacCoss and Yunping Zhu and Yasushi Ishihama and Juan Antonio Vizcaíno},
journal = {Nucleic Acids Research},
year = {2022},
volume = {51},
number = {D1},
pages = {D1539--D1548},
doi = {10.1093/nar/gkac1040},
url = {https://doi.org/10.1093/nar/gkac1040}
}TY - JOUR AU - Deutsch, Eric W. AU - Bandeira, Nuno AU - Pérez‐Riverol, Yasset AU - Sharma, Vagisha AU - Carver, Jeremy 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 TI - The ProteomeXchange consortium at 10 years: 2023 update JO - Nucleic Acids Research VL - 51 IS - D1 SP - D1539 EP - D1548 PY - 2022 DA - 2022/10/23 DO - 10.1093/nar/gkac1040 UR - https://doi.org/10.1093/nar/gkac1040 ER -
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