iProX


34871441	iProX in 2021: connecting proteomics data sharing with big data. [PMID: 34871441] Chen T, Ma J, Liu Y, Chen Z, Xiao N, Lu Y, Fu Y, Yang C, Li M, Wu S, Wang X, Li D, He F, Hermjakob H, Zhu Y. Abstract The rapid development of proteomics studies has resulted in large volumes of experimental data. The emergence of big data platform provides the opportunity to handle these large amounts of data. The integrated proteome resource, iProX (https://www.iprox.cn), which was initiated in 2017, has been greatly improved with an up-to-date big data platform implemented in 2021. Here, we describe the main iProX developments since its first publication in Nucleic Acids Research in 2019. First, a hyper-converged architecture with high scalability supports the submission process. A hadoop cluster can store large amounts of proteomics datasets, and a distributed, RESTful-styled Elastic Search engine can query millions of records within one second. Also, several new features, including the Universal Spectrum Identifier (USI) mechanism proposed by ProteomeXchange, RESTful Web Service API, and a high-efficiency reanalysis pipeline, have been added to iProX for better open data sharing. By the end of August 2021, 1526 datasets had been submitted to iProX, reaching a total data volume of 92.42TB. With the implementation of the big data platform, iProX can support PB-level data storage, hundreds of billions of spectra records, and second-level latency service capabilities that meet the requirements of the fast growing field of proteomics. Nucleic Acids Res. 2022:50(D1) \| 272 Citations (from Europe PMC, 2025-03-15)
30252093	iProX: an integrated proteome resource. [PMID: 30252093] Ma J, Chen T, Wu S, Yang C, Bai M, Shu K, Li K, Zhang G, Jin Z, He F, Hermjakob H, Zhu Y. Abstract Sharing of research data in public repositories has become best practice in academia. With the accumulation of massive data, network bandwidth and storage requirements are rapidly increasing. The ProteomeXchange (PX) consortium implements a mode of centralized metadata and distributed raw data management, which promotes effective data sharing. To facilitate open access of proteome data worldwide, we have developed the integrated proteome resource iProX (http://www.iprox.org) as a public platform for collecting and sharing raw data, analysis results and metadata obtained from proteomics experiments. The iProX repository employs a web-based proteome data submission process and open sharing of mass spectrometry-based proteomics datasets. Also, it deploys extensive controlled vocabularies and ontologies to annotate proteomics datasets. Users can use a GUI to provide and access data through a fast Aspera-based transfer tool. iProX is a full member of the PX consortium; all released datasets are freely accessible to the public. iProX is based on a high availability architecture and has been deployed as part of the proteomics infrastructure of China, ensuring long-term and stable resource support. iProX will facilitate worldwide data analysis and sharing of proteomics experiments. Nucleic Acids Res. 2019:47(D1) \| 726 Citations (from Europe PMC, 2025-03-15)

iProX in 2021: connecting proteomics data sharing with big data. [PMID: 34871441]

Chen T, Ma J, Liu Y, Chen Z, Xiao N, Lu Y, Fu Y, Yang C, Li M, Wu S, Wang X, Li D, He F, Hermjakob H, Zhu Y.

The rapid development of proteomics studies has resulted in large volumes of experimental data. The emergence of big data platform provides the opportunity to handle these large amounts of data. The integrated proteome resource, iProX (https://www.iprox.cn), which was initiated in 2017, has been greatly improved with an up-to-date big data platform implemented in 2021. Here, we describe the main iProX developments since its first publication in Nucleic Acids Research in 2019. First, a hyper-converged architecture with high scalability supports the submission process. A hadoop cluster can store large amounts of proteomics datasets, and a distributed, RESTful-styled Elastic Search engine can query millions of records within one second. Also, several new features, including the Universal Spectrum Identifier (USI) mechanism proposed by ProteomeXchange, RESTful Web Service API, and a high-efficiency reanalysis pipeline, have been added to iProX for better open data sharing. By the end of August 2021, 1526 datasets had been submitted to iProX, reaching a total data volume of 92.42TB. With the implementation of the big data platform, iProX can support PB-level data storage, hundreds of billions of spectra records, and second-level latency service capabilities that meet the requirements of the fast growing field of proteomics.

Nucleic Acids Res. 2022:50(D1) | 272 Citations (from Europe PMC, 2025-03-15)

iProX: an integrated proteome resource. [PMID: 30252093]

Ma J, Chen T, Wu S, Yang C, Bai M, Shu K, Li K, Zhang G, Jin Z, He F, Hermjakob H, Zhu Y.

Abstract

Sharing of research data in public repositories has become best practice in academia. With the accumulation of massive data, network bandwidth and storage requirements are rapidly increasing. The ProteomeXchange (PX) consortium implements a mode of centralized metadata and distributed raw data management, which promotes effective data sharing. To facilitate open access of proteome data worldwide, we have developed the integrated proteome resource iProX (http://www.iprox.org) as a public platform for collecting and sharing raw data, analysis results and metadata obtained from proteomics experiments. The iProX repository employs a web-based proteome data submission process and open sharing of mass spectrometry-based proteomics datasets. Also, it deploys extensive controlled vocabularies and ontologies to annotate proteomics datasets. Users can use a GUI to provide and access data through a fast Aspera-based transfer tool. iProX is a full member of the PX consortium; all released datasets are freely accessible to the public. iProX is based on a high availability architecture and has been deployed as part of the proteomics infrastructure of China, ensuring long-term and stable resource support. iProX will facilitate worldwide data analysis and sharing of proteomics experiments.

Nucleic Acids Res. 2019:47(D1) | 726 Citations (from Europe PMC, 2025-03-15)

URL:	http://www.iprox.org
Full name:	Integrated Proteome Resources
Description:	iProX is an integrated proteome resources center in China, which is built to accelerate the worldwide data sharing in proteomics. iProX is composed of a data submission system and a proteome database. The submission system is established under the guidance of the data-sharing policy made by ProteomeXchange consortium.
Year founded:	2019
Last update:	2024-08-27
Version:
Accessibility:	Accessible
Country/Region:	China

Data type:	Protein
Data object:	NA
Database category:	Metadata Raw bio-data
Major species:	NA
Keywords:	proteomics

University/Institution:	National Center for Protein Sciences
Address:	No.38, Life Science Park Road, Changping District, Beijing, 102206, China
City:	Beijing
Province/State:	Beijing
Country/Region:	China
Contact name (PI/Team):	Yunping Zhu
Contact email (PI/Helpdesk):	iprox@iprox.org

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Database Commons a catalog of worldwide biological databases