iProX: an integrated proteome resource

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.

NOP2/Sun RNA methyltransferase 2 promotes tumor progression via its interacting partner RPL6 in gallbladder carcinoma

“…The identities of eluted proteins were revealed by liquid chromatography with tandem mass spectrometry (LC‐MS/MS) analysis by Shanghai Applied Protein Technology (Shanghai, China). Two independent biological replicates were performed, of which the mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the iProX partner repository with the dataset identifier PXD013152. Protein candidates are also listed in .…”

Proteomic Analysis Reveals that Odoroside A Triggers G2/M Arrest and Apoptosis in Colorectal Carcinoma Through ROS‐p53 Pathway

“…Ingenuity Pathway Analysis (IPA, Ingenuity Systems, Redwood City, CA, USA) and Cytoscape (version 3.5.1) were used to analyze the differentially expressed proteins (DEPs) as described previously . The MS data have been stored to the ProteomeXchange Consortium via the iProX partner repository …”

Global profiling of megalocytivirus-induced proteins in tongue sole (Cynoglossus semilaevis) spleen identifies cellular processes essential to viral infection

“…For the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, the differentially expressed proteins were mapped to metabolic pathways in KEGG using the KOBAS software (Mao et al, 2005). The mass spectrometry proteomics data have been deposited to ProteomeXchange Consortium (http:// proteomecentral.proteomexchange.org) via the iProX partner repository (Ma et al, 2018) with the dataset identifier PXD011479.…”