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

Yusuke Kawashima

出版者

Japanese Proteomics Society

雑誌

Journal of Proteome Data and Methods (ISSN:24346454)

巻号頁・発行日

vol.5, pp.2, 2023 (Released:2023-03-08)

参考文献数

8

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We established a deep proteome analysis method of cell-derived proteins in fetal bovine serum-containing culture supernatants and successfully detected more than 3500 cell-derived proteins.

著者

Tsuyoshi Tabata Akiyasu C. Yoshizawa Ishihama Yasushi

出版者

Japanese Proteomics Society

雑誌

Journal of Proteome Data and Methods (ISSN:24346454)

巻号頁・発行日

vol.2, pp.4, 2020 (Released:2020-12-16)

参考文献数

5

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For the analysis of mass spectrometry data from proteome samples, several steps must be paid attention to, the first of which is the generation of peak list. Although programs distributed by mass spectrometer vendors, or mscovert.exe by ProteoWizard [1] are commonly used to generate peak lists; these may not be suitable for the purpose. Herein, we have implemented single function tools to solve these problems. For example, raw data files generated by modern high-performance mass spectrometers may result in huge .mgf files of more than 500 MB, which are time-consuming to perform database search and may cause communication errors to the computational server; e.g. the Mascot server. Our PeaklistSplit splits the files to reduce the search time per search. As the precursor ion for each product ion spectrum, the mass spectrometer tends to select the peak with the greatest intensity in the isotope cluster of interest, not necessarily the monoisotopic ion, and the m/z of the precursor ion may not be properly recorded, especially in the case of high molecular weight ions. We have thus created two tools to address this issue: ProteoWizardPlist and ProteoWizardPlistW. In addition, for use in the ongoing proteome database jPOST [2,3], multiple peak lists are generated from a single raw data in some cases. We developed PeakListMerge, a tool to merge multiple peak lists into a single list to control the false discovery rate based on target-decoy search [4,5].

著者

Daisuke Nakajima Yusuke Kawashima Osamu Ohara

出版者

Japanese Proteomics Society

雑誌

Journal of Proteome Data and Methods (ISSN:24346454)

巻号頁・発行日

vol.5, pp.8, 2023 (Released:2023-04-29)

参考文献数

4

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To analyse deep protein profiling of dried blood spot (DBS). We developed a simple method using sodium carbonate precipitation (SCP). SCP enriches hydrophobic proteins from DBS, allowing substantial removal of soluble proteins. In combination with SCP, we used quantitative LC-MS/MS proteome analysis in a data-independent acquisition mode (DIA) to enhance the sensitivity and quantification limits of proteome analysis.

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

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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

Byron Baron

出版者

Japanese Proteomics Society

雑誌

Journal of Proteome Data and Methods (ISSN:24346454)

巻号頁・発行日

vol.3, pp.1, 2021 (Released:2021-06-29)

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Protein methylation has been studies for over two decades, mainly in histones but more recently also in non-histone proteins. Despite the great advances in technologies, particularly the application of Orbitrap technology, proteomic analysis of methylation still remains a challenge. This is mainly due to the small size of methylations, their position on fragmented peptides and issue of incorrect identification. A number of different methods have been developed or modified to varying degrees of success in order to enrich for protein methylation prior to mass spectrometric analysis. Despite the availability of different techniques, it is important to understand the underlying strategy employed, the type of sample being analysed and the methylation-related question being investigated. Without such knowledge it is very easy to become lost analysing large volumes of insignificant data or misinterpret the data output.

著者

Yu Watanabe Shujiro Okuda

出版者

Japanese Proteomics Society

雑誌

Journal of Proteome Data and Methods (ISSN:24346454)

巻号頁・発行日

vol.2, pp.1, 2020 (Released:2020-06-29)

参考文献数

4

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The jPOST repository has been managed since 2016. Here, we summarize the contents of the registered projects and the newly developed functions implemented in the repository.