The jPOST (Japan ProteOme STandard Repository/Database) project is working to build an integrated proteome database by standardizing, integrating, and managing various types of experimental proteome data from the world based on FAIR (Findable, Accessible, Interoperable, and Re-usable) data principles. In 2016, the jPOST repository, a proteome data repository compliant with international standards provided by the ProteomeXchange (PX) consortium, was established. The jPOST repository is used by many researchers because of its unique features, including an easy-to-use web interface and a fast file upload system that can be completed using only a web browser. In addition, a new data journal called the Journal of Proteome Data and Methods (JPDM) was launched to manage technical and methodological information to accelerate reuse of the proteome data at the initiative of the Japanese Society for Proteomics in 2019. In this manuscript, we would like to discuss the current status of the repository and the data journal promoted by the jPOST project.

The immunoprecipitation-mass spectrometry (IP-MS) method, in which protein complexes are immunoprecipitated from extracts of biological samples and the precipitates are analyzed by mass spectrometry after enzymatic digestion, is useful to elucidate biological functions of target proteins. IP-MS can globally identify and quantify various post-translational modifications and interacting proteins of the target proteins. We have performed numerous IP-MS experiments on various types of proteins, including cytoplasmic, nuclear, membrane, and extracellular proteins, and have optimized the experimental protocols. As a result, it has become clear that the conditions of various steps of immunoprecipitation should be changed for IP-MS compared to conventional Western blot analysis of immunoprecipitates. Here, this report focuses on the steps from the immunoprecipitation to the preparation of digested peptides, which are important for researchers who are not experts in proteomics.

Proteomics has advanced over the past 25 years with a primary focus on mass spectrometry. Shotgun LC/MS, in particular, has enabled the identification of a vast number of proteins, regardless of species, as long as a database of amino acid sequences and other information is available. However, LC/MS quantification has not been very well managed in terms of validation, and several issues remain, especially in the field of plasma proteomics. This is where the Proximity Extension Assay (PEA) was introduced. This is a method combining antibody and oligonucleotide amplification, which is called immuno-PCR. PEA method facilitates the analysis of cytokines and other substances in blood that are difficult to detect by LC/MS while ensuring specificity, and is designed to guarantee reliability in quantitation. It has been applied to the measurement of plasma and serum samples from more than 1,000 subjects, and more than 3,000 types of proteins have recently been quantified. In the future, LC/MS may be used for the search and identification of plasma proteins, while PEA may be used for quantitative analysis.