KPOP: Korea ProteOme rePository for open access proteomics data

With the surge in mass spectrometry (MS)-based proteomics, there is a growing abundance of data from proteomics projects worldwide. Since 2012, the ProteomeXchange (PX) consortium has played a key role in standardizing the submission and dissemination of public MS proteomics data. To promote the global sharing and reuse of proteomic resources, we introduce KPOP repository (https://kbds.re.kr/KPOP), a public platform facilitating open access to a wealth of proteomic resources, encompassing various types of MS data, analysis results, and metadata. KPOP has implemented user-friendly interfaces, accelerated file transfers, and flexible file management, significantly enhancing the usability and value of proteomics data for scientific research.

The primary goal of KPOP is to curate meticulously maintained data sets, supporting prevalent "big data" approaches in proteomics, including machine learning and computational modeling. These approaches enable researchers to decipher complex data patterns and associations from proteomics data, driving innovation in the field. In addition to sample information, KPOP retains metadata related to fractionation, digestion, quantification, modifications, experiment type, and the MS instrument employed. KPOP is a member of K-BDS (Korea BigData Station), which serves as a comprehensive repository for various biological research data, promoting integrated "multi-omics" analyses. This integration is particularly beneficial when datasets, such as whole exome and RNA sequencing data, are simultaneously available, originating from the same project. Researchers can combine proteomics data with other omics data to gain deeper insights into biological processes and disease mechanisms.

KPOP complies with PX Consortium"s guidelines, allowing registered users to submit their proteomics data in public or private modes. Private mode allows sharing with designated users, ideal for pre-publication collaboration or peer review. Public mode offers unrestricted access to datasets. KPOP"s structure is user-centric, organizing data by projects and data sets, with each set encapsulating a distinct experimental setup, such as biological replicates, technical replicates, or clinical samples. In accordance with PX guidelines, KPOP supports two submission workflows, Complete or Partial submission.