jPOSTrepo: an international standard data repository for proteomes

Abstract

Major advancements have recently been made in mass spectrometry-based proteomics, yielding an increasing number of datasets from various proteomics projects worldwide. In order to facilitate the sharing and reuse of promising datasets, it is important to construct appropriate, high-quality public data repositories. jPOSTrepo (https://repository.jpostdb.org/) has successfully implemented several unique features, including high-speed file uploading, flexible file management and easy-to-use interfaces. This repository has been launched as a public repository containing various proteomic datasets and is available for researchers worldwide. In addition, our repository has joined the ProteomeXchange consortium, which includes the most popular public repositories such as PRIDE in Europe for MS/MS datasets and PASSEL for SRM datasets in the USA. Later MassIVE was introduced in the USA and accepted into the ProteomeXchange, as was our repository in July 2016, providing important datasets from Asia/Oceania. Accordingly, this repository thus contributes to a global alliance to share and store all datasets from a wide variety of proteomics experiments. Thus, the repository is expected to become a major repository, particularly for data collected in the Asia/Oceania region.

SCFFbxw7 ubiquitylates KLF7 for degradation in a manner dependent on GSK‐3‐mediated phosphorylation

“…DiPIUS-NL was performed in mHepa, Neuro2A and C2C12 cells as described previously (Yumimoto et al, 2013(Yumimoto et al, ,2012. All data are available in ProteomeXchange and jPOST (Okuda et al, 2017) under the accession numbers PXD008705 and JPST000373, respectively.…”

Cross‐linked peptide identification: A computational forest of algorithms

“…PRIDE and PeptideAtlas are the most prominent repositories, and these two formed the foundation of the ProteomeXchange consortium that provides a common framework for user‐friendly data deposition and exchange of mass spectrometry based proteomics data . MassIVE (http://massive.ucsd.edu/ProteoSAFe/static/massive.jsp) and jPostrepo have since joined ProteomeXchange. ProteomeXchange has recently also explicitly started to support storage of, and access to, data from cross‐linking experiments.…”

Estimating the Efficiency of Phosphopeptide Identification by Tandem Mass Spectrometry

“…The light and heavy phosphopeptide and peak pairs were identified through the LAXIC algorithm [24]. All of the light and heavy phosphopeptide and peak pairs are listed in the supplementary tables, and the raw data and analysis files for the proteomic analyses have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the jPOST partner repository (http://jpost.org) [25] with the data set identifier PXD005079.…”