Masaru Miyagi, PhD

Department of Pharmacology
School of Medicine
Cancer Metabolism Shared Resource
Case Comprehensive Cancer Center
Molecular Oncology Program
Case Comprehensive Cancer Center
Center for Proteomics and Bioinformatics
School of Medicine
Cleveland Center for Membrane & Structural Biology


Research Information

Research Interests

We are motivated to develop mass spectrometry-based analytical methods for studying protein post-translational modifications, protein structural dynamics, and proteome dynamics. Mass spectrometry is the pre-eminent technology in analytical protein chemistry. However, current methods on the front end of mass spectrometry analysis are not fully utilizing the potential of modern mass spectrometry technologies. Development of advanced analytical methods on the front end of mass spectrometry analysis is, therefore, critical to advancing the study of proteins. We have innovated diverse mass spectrometry-based methodologies for protein/proteome analysis, resulting in over 120 peer-reviewed articles. Our current research interests include: 1) Identifying isoaspartic acid (isoAsp) residues in proteins involved in neurodegenerative diseases and understanding the consequences of isoAsp formation, and 2) Developing an analytical platform for identifying the targets of drugs.


View All Publications


1. Miyagi, M.; Tanaka, K.; Watanabe, S.; Kondo, J.; Kishimoto, T. Identifying Protein-Drug Interactions in Cell Lysates Using Histidine Hydrogen Deuterium Exchange. Anal. Chem. 2021, 93 (45), 14985–14995. PMCID: 34735131

2. Miyagi, M.; Kiesel, E.; Neumbo, K.; Nakazawa K. Deuterium Labeling of Isoaspartic and Isoglutamic Acids for Mass Spectrometry Analysis, Anal. Chem, 2024, 96 (7), 3077–3086 PMID: 38344941

3. Yamada, K. D.; Omori, S.; Nishi, H.; Miyagi, M. Identification of the Sequence Determinants of Protein N-Terminal Acetylation through a Decision Tree Approach. BMC Bioinformatics 2017, 18 (1), 289. PMCID: PMC5457594

4. Vukoti, K.; Yu, X.; Sheng, Q.; Saha, S.; Feng, Z.; Hsu, A.-L.; Miyagi, M. Monitoring Newly Synthesized Proteins over the Adult Life Span of Caenorhabditis Elegans. J. Proteome Res. 2015, 14 (3), 1483–1494. PMCID: PMC4440835

5. Miyagi, M.; Nakazawa, T. Determination of PKa Values of Individual Histidine Residues in Proteins Using Mass Spectrometry. Anal Chem 2008, 80 (17), 6481–6487. PMID: 18665614


Doctor of Philosophy
Osaka University, Osaka, Japan
Master of Science
University of the Ryukyus, Okinawa, Japan
Bachelor of Science
University of the Ryukyus, Okinawa, Japan

Additional Information


  1. U.S. Patent 6,194,190 (Issued February 27, 2001), titled “Amino-terminal deblocking enzyme”, Inventors: Yukiko Izu, Tetsuki Tanaka, Masaru Miyagi, Tetsuo Tanigawa, Jun Tomono, Susumu Tsunasawa, Ikunoshin Kato
  2. U.S. Patent 7,476,546 (Issued January 13, 2009), titled “Method for single oxygen atom incorporation into digested peptides using peptidases”, Inventors: Masaru Miyagi and K. C. Sekhar Rao
  3. U.S. Patent 8,580,534 (Issued November 12, 2013), titled “Method for incorporation of two oxygen atoms into digested peptides using peptidases”, Inventors: Masaru Miyagi
  4. U.S. Patent 8,921,515 B2 (Issued December 30, 2015), titled “Methods and compositions of preparation for proteome analysis”, Inventors: Masaru Miyagi and Chandra Sekhar Rao Kadiyala