3 0 0 0 OA From Bench to Internet: Sharing Proteomics Data and Methods through the Open Access Journal
- 著者
- Yasushi Ishihama
- 出版者
- Japanese Proteomics Society
- 雑誌
- Journal of Proteome Data and Methods (ISSN:24346454)
- 巻号頁・発行日
- vol.1, pp.1, 2019-09-30 (Released:2020-01-09)
- 著者
- Kosuke Ogata Chih-Hsiang Chang Yasushi Ishihama
- 出版者
- The Mass Spectrometry Society of Japan
- 雑誌
- Mass Spectrometry (ISSN:2187137X)
- 巻号頁・発行日
- pp.A0093, (Released:2020-12-11)
- 参考文献数
- 47
- 被引用文献数
- 13
The insertion of ion mobility spectrometry (IMS) between LC and MS can improve peptide identification in both proteomics and phosphoproteomics by providing structural information that is complementary to LC and MS, because IMS separates ions on the basis of differences in their shapes and charge states. However, it is necessary to know how phosphate groups affect the peptide collision cross sections (CCS) in order to accurately predict phosphopeptide CCS values and to maximize the usefulness of IMS. In this work, we systematically characterized the CCS values of 4,433 pairs of mono-phosphopeptide and corresponding unphosphorylated peptide ions using trapped ion mobility spectrometry (TIMS). Nearly one-third of the mono-phosphopeptide ions evaluated here showed smaller CCS values than their unphosphorylated counterparts, even though phosphorylation results in a mass increase of 80 Da. Significant changes of CCS upon phosphorylation occurred mainly in structurally extended peptides with large numbers of basic groups, possibly reflecting intramolecular interactions between phosphate and basic groups.
- 著者
- Chih-Hsiang Chang Yasushi Ishihama
- 出版者
- Japanese Proteomics Society
- 雑誌
- Journal of Proteome Data and Methods (ISSN:24346454)
- 巻号頁・発行日
- vol.4, pp.3, 2022 (Released:2022-09-17)
- 参考文献数
- 12
Trapped ion mobility spectrometry (TIMS) has been considered as a promising tool in structural biology, proteomics and many other analytical applications. This dataset consists of cell lysates digested with each of seven proteases (trypsin, LysargiNase, Lys-C, Lys-N, Glu-C, Asp-N, and chymotrypsin), fractionated using SCX-StageTip, and analyzed by nanoLC/TIMS/Q/TOF. The data accompanying this paper have been deposited to jPOST with the identifiers JPST000959, JPST001017 and JPST001176.
- 著者
- Yasushi ISHIHAMA
- 出版者
- The Society for Chromatographic Sciences
- 雑誌
- CHROMATOGRAPHY (ISSN:13428284)
- 巻号頁・発行日
- pp.2019.023, (Released:2019-10-10)
- 参考文献数
- 64
- 被引用文献数
- 10
Mass spectrometry-based proteomics platforms have been widely used as ‘proteome sequencers’ to characterize the proteomes of a wide range of organisms. The work-flow generally involves multiple steps of sample preparation, peptide purification/concentration/pre-fractionation, and nanoLC/MS/MS measurement. This review focuses on our contributions to the technical development of current proteomics platforms, and includes a consideration of the limitations of these systems, together with the prospects for developing superior new-generation proteome sequencers.
1 0 0 0 OA Application of Non-negative Matrix Factorization in MassSpectrometry-Based Shotgun Proteomics
- 著者
- Pasrawin Taechawattananant Akiyasu C. Yoshizawa Kazuyoshi Yoshii Yasushi Ishihama
- 出版者
- 日本プロテオーム学会(日本ヒトプロテオーム機構)
- 雑誌
- 日本プロテオーム学会大会要旨集 日本プロテオーム学会2018年大会(MSP2018)
- 巻号頁・発行日
- pp.296, 2018 (Released:2019-03-01)