Poster Presentation HUPO 2019 - 18th Human Proteome Organization World Congress

Promotion of proteomic data sharing through a specialized data journal (#611)

Shin Kawano 1 2 , Shujiro Okuda 3 , Masaki Matsumoto 4 , Yasushi Ishihama 5
  1. Research Organization of Information and Systems, Kashiwa, Japan
  2. Toyama University of International Studies, Toyama, Japan
  3. Niigata University, Niigata, Japan
  4. Kyushu University, Fukuoka, Japan
  5. Kyoto University, Kyoto, Japan


Proteomics is a rapidly growing research area that produces large amounts of data, which has led to complex challenges around data management. Proteomics data and datasets need to become more Findable, Accessible, Interoperable, and Re-usable (FAIR1) to promote data sharing. To address these challenges and facilitate better proteome data management, the field needs to develop formal structures and procedures. To this end, the Japanese Proteomics Society decided to launch a new data journal – the Journal of Proteome Data and Methods (JPDM).


In order to launch JPDM, we prepared the following documents: Publishing plan, Instruction to authors, Guide to reviewers, Ethics policies, License to publish form, and Frequently asked questions. All documents are available at We also prepared a submission system ( using the ScholarOne platform.

Features of JPDM

JPDM is a peer-reviewed and fully open access journal provided via the J-stage platform. JPDM publishes four article types: Data descriptors, Protocols, Data processing notes, and Reviews. The main content of the journal is Data descriptors, which is described detailed metadata of mass-based proteomics datasets. JPDM collaborates with ProteomeXchange2 (PX), which is a consortium of proteome data repositories including jPOST3, PRIDE4, MassIVE, etc. When data producers register their datasets in a PX repository then post detailed metadata in JPDM, the journal sends a feedback to the PX repository. JPDM contributes to add a value for proteome datasets by providing detailed metadata.


We launched the new data journal for proteomics community named JPDM. The journal is peer-reviewed and fully open access, and the website is JPDM realizes the FAIR principal in the proteomics field by providing rich information. JPDM welcomes lots of submission from community members.

  1. Wilkinson MD et al., The FAIR Guiding Principles for scientific data management and stewardship, Sci Data. 3:160018 (2016).
  2. Deutsch EW et al., The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition. Nucleic Acids Res. 45:D1100-D1106 (2017).
  3. Moriya Y et al., The jPOST environment: an integrated proteomics data repository and database. Nucleic Acids Res. 47:D1218-D1224 (2019).
  4. Perez-Riverol Y et al., The PRIDE database and related tools and resources in 2019: improving support for quantification data. Nucleic Acids Res. 47:D442-D450 (2019).