Sharing of research data is a global trend, and proteome data is no exception. This paper introduces the current status of proteome data sharing globally through the ProteomeXchange Consortium (PXC) and jPOST, a Japanese participant in PXC. However, the datasets collected in PXC currently lack sufficient metadata, which is a barrier to reuse by third parties. Here, I introduce a new way to collect detailed metadata to make the shared datasets easier to reuse. I also report on the objectives and the latest activities of HUPO-PSI, Human Proteome Organization-Proteomics Standards Initiative, which develops standards for effective data sharing. In addition, the current status of the handling of human proteome data will be introduced.

In bottom-up proteomics, sample preparation process, particularly protein digestion, has a significant impact on protein identification and quantification. Although several methods for protein digestion have been developed, it is generally believed that complete protein solubilization with detergent is a critical step for efficient enzymatic digestion. However, since detergent affects subsequent sample preparation and liquid chromatography-mass spectrometry (LC-MS) analysis, they must be completely removed from protein and peptide solution. Especially in multi-sample or very low-quantity sample processing, detergent removal can be a challenge as it can cause sample loss and decrease sample preparation efficiency. Recently, several detergent-free enzymatic digestion methods with incomplete protein solubilization have been reported, and their digestion efficiencies were comparable to that of the conventional method using detergent. In this review, we introduce recently developed methods of enzymatic digestion of proteins without solubilization.

To analyze of endogenous metabolites in diseases is useful for discovering diagnostic biomarkers and elucidating molecular mechanisms of pathogenesis. Niemann-Pick disease type C (NPC) is a autosomal recessive disease with diverse onset times and clinical symptoms, and there were some problems with conventional diagnostic methods. Therefore, we have worked on the developing the biomarkers for NPC using LC-MS/MS analysis. First, we focused on conjugated cholesterol metabolites excreted in large amounts in the urine of NPC patients, and our analysis using LC-MS/MS revealed that several metabolites are useful as diagnostic markers. Next, we aimed to identify the unknown molecule lysosphingomyelin-509, which has been used for screening in Europe and America, and successfully determined its structure using microchemical approaches. In addition, we also developed a novel diagnostic strategy for Niemann-Pick diseases based on simultaneous analysis of two phospholipids in blood. In conclusion, the use of LC-MS/MS analysis for endogenous metabolite analysis was found to be useful in the development of diagnostic biomarkers for NPC.