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Yasset Pérez‐Riverol, Chakradhar Bandla, Deepti J Kundu, Selvakumar Kamatchinathan, Jingwen Bai, Suresh Hewapathirana, Nithu Sara John, Ananth Prakash, Mathias Walzer, Shengbo Wang, Juan Antonio Vizcaíno
The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world's leading mass spectrometry (MS)-based proteomics data repository and one of the founding members of the ProteomeXchange consortium. This manuscript summarizes the developments in PRIDE resources and related tools for the last three years. The number of submitted datasets to PRIDE Archive (the archival component of PRIDE) has reached on average around 534 datasets per month. This has been possible thanks to continuous improvements in infrastructure such as a new file transfer protocol for very large datasets (Globus), a new data resubmission pipeline and an automatic dataset validation process. Additionally, we will highlight novel activities such as the availability of the PRIDE chatbot (based on the use of open-source Large Language Models), and our work to improve support for MS crosslinking datasets. Furthermore, we will describe how we have increased our efforts to reuse, reanalyze and disseminate high-quality proteomics data into added-value resources such as UniProt, Ensembl and Expression Atlas.
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Pérez‐Riverol, Y., Bandla, C., Kundu, D. J., Kamatchinathan, S., Bai, J., Hewapathirana, S., John, N. S., Prakash, A., Walzer, M., Wang, S., & Vizcaíno, J. A. (2024). The PRIDE database at 20 years: 2025 update. Nucleic Acids Research, 53(D1), D543–D553. https://doi.org/10.1093/nar/gkae1011
Pérez‐Riverol, Yasset, et al. "The PRIDE database at 20 years: 2025 update." Nucleic Acids Research, vol. 53, no. D1, 2024, pp. D543–D553, https://doi.org/10.1093/nar/gkae1011.
Pérez‐Riverol, Yasset, Chakradhar Bandla, Deepti J Kundu, Selvakumar Kamatchinathan, Jingwen Bai, Suresh Hewapathirana, Nithu Sara John, et al. "The PRIDE database at 20 years: 2025 update." Nucleic Acids Research 53, no. D1 (2024): D543–D553. https://doi.org/10.1093/nar/gkae1011.
Pérez‐Riverol Y., Bandla C., Kundu D. J. [и др.] The PRIDE database at 20 years: 2025 update // Nucleic Acids Research. — 2024. — Vol. 53, № D1. — P. D543–D553. — URL: https://doi.org/10.1093/nar/gkae1011
@article{perezriverol2024pride,
title = {{The PRIDE database at 20 years: 2025 update}},
author = {Yasset Pérez‐Riverol and Chakradhar Bandla and Deepti J Kundu and Selvakumar Kamatchinathan and Jingwen Bai and Suresh Hewapathirana and Nithu Sara John and Ananth Prakash and Mathias Walzer and Shengbo Wang and Juan Antonio Vizcaíno},
journal = {Nucleic Acids Research},
year = {2024},
volume = {53},
number = {D1},
pages = {D543--D553},
doi = {10.1093/nar/gkae1011},
url = {https://doi.org/10.1093/nar/gkae1011}
}TY - JOUR AU - Pérez‐Riverol, Yasset AU - Bandla, Chakradhar AU - Kundu, Deepti J AU - Kamatchinathan, Selvakumar AU - Bai, Jingwen AU - Hewapathirana, Suresh AU - John, Nithu Sara AU - Prakash, Ananth AU - Walzer, Mathias AU - Wang, Shengbo AU - Vizcaíno, Juan Antonio TI - The PRIDE database at 20 years: 2025 update JO - Nucleic Acids Research VL - 53 IS - D1 SP - D543 EP - D553 PY - 2024 DA - 2024/10/16 DO - 10.1093/nar/gkae1011 UR - https://doi.org/10.1093/nar/gkae1011 ER -
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