Aligning LC peaks by converting gradient retention times to retention index of peptides in proteomic experiments. - Kosaku Shinoda; Masaru Tomita; Yasushi Ishihama (Bioinform., 2008)

emPAI Calc - for the estimation of protein abundance from large-scale identification data by liquid chromatography-tandem mass spectrometry. - Kosaku Shinoda; Masaru Tomita; Yasushi Ishihama (Bioinform., 2010)

Towards the systematic discovery of signal transduction networks using phosphorylation dynamics data. - Haruna Imamura; Nozomu Yachie; Rintaro Saito; Yasushi Ishihama; Masaru Tomita (BMC Bioinform., 2010)

Integrative Features of the Yeast Phosphoproteome and Protein-Protein Interaction Map. - Nozomu Yachie; Rintaro Saito; Naoyuki Sugiyama; Masaru Tomita; Yasushi Ishihama (PLoS Comput. Biol., 2011)

A multi-omic analysis of human naïve CD4+ T cells. - Christopher J. Mitchell; Derese Getnet; Min Sik Kim; Srinivas Manda Srikanth; Praveen Kumar; Tai-Chung Huang; Sneha M. Pinto; Nirujogi Raja Sekhar; Mio Iwasaki; Patrick G. Shaw; Xinyan Wu; Jun Zhong; et al. (BMC Syst. Biol., 2015)

The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition. - Eric W. Deutsch; Attila Csordas; Zhi Sun; Andrew F. Jarnuczak; Yasset Pérez-Riverol; Tobias Ternent; David S. Campbell; Manuel Bernal Llinares; Shujiro Okuda; Shin Kawano; Robert L. Moritz; Jeremy Carver; et al. (Nucleic Acids Res., 2017)

jPOSTrepo: an international standard data repository for proteomes. - Shujiro Okuda; Yu Watanabe; Yuki Moriya; Shin Kawano; Tadashi Yamamoto; Masaki Matsumoto; Tomoyo Takami; Daiki Kobayashi; Norie Araki; Akiyasu C. Yoshizawa; Tsuyoshi Tabata; Naoyuki Sugiyama; et al. (Nucleic Acids Res., 2017)

The jPOST environment: an integrated proteomics data repository and database. - Yuki Moriya; Shin Kawano; Shujiro Okuda; Yu Watanabe; Masaki Matsumoto; Tomoyo Takami; Daiki Kobayashi; Yoshinori Yamanouchi; Norie Araki; Akiyasu C. Yoshizawa; Tsuyoshi Tabata; Mio Iwasaki; et al. (Nucleic Acids Res., 2019)

The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics. - Eric W. Deutsch; Nuno Bandeira; Vagisha Sharma; Yasset Pérez-Riverol; Jeremy Carver; Deepti Jaiswal Kundu; David García-Seisdedos; Andrew F. Jarnuczak; Suresh Hewapathirana; Benjamin S. Pullman; Julie Wertz; Zhi Sun; et al. (Nucleic Acids Res., 2020)

GlycoPOST realizes FAIR principles for glycomics mass spectrometry data. - Yu Watanabe; Kiyoko F. Aoki-Kinoshita; Yasushi Ishihama; Shujiro Okuda (Nucleic Acids Res., 2021)

The ProteomeXchange consortium at 10 years: 2023 update. - Eric W. Deutsch; Nuno Bandeira; Yasset Pérez-Riverol; Vagisha Sharma; Jeremy Carver; Luis Mendoza; Deepti Jaiswal Kundu; Shengbo Wang; Chakradhar Bandla; Selvakumar Kamatchinathan; Suresh Hewapathirana; Benjamin S. Pullman; et al. (Nucleic Acids Res., 2023)