- 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
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
- Yasumi Uchida Yasuto Uchida Takanobu Kobayashi Seiichiro Shirai Nobuyuki Hiruta Ei Shimoyama Tsuyoshi Tabata
- 出版者
- The Japanese Circulation Society
- 雑誌
- Circulation Journal (ISSN:13469843)
- 巻号頁・発行日
- vol.81, no.12, pp.1886-1893, 2017-11-24 (Released:2017-11-24)
- 参考文献数
- 21
- 被引用文献数
- 15
Background:The presence of ceramide in human coronary plaques is a risk factor for ischemic heart disease, but its visualization in the human vessel wall is currently beyond the scope of any available imaging techniques.Methods and Results:Deposition of ceramide was examined by fluorescent angioscopy (FA) and microscopy (FM) using golden fluorescence (Go) as a specific marker of ceramide in yellow plaques, which were obtained from 23 autopsy subjects and classified by conventional angioscopy and histology. Ceramide was observed by FM in 34 of the 41 yellow plaques with a necrotic core (NC) but rarely in the 28 without. Ceramide and macrophages/foam cells co-deposited mainly in the border zone of the NC and fibrous cap (FC). The Go of ceramide was seen when the fibrous cap thickness was ≤100 µm. FA was performed to detect coronary plaques exhibiting Go in patients with coronary artery disease. Ceramide was also detected by FA in 6 of 18 yellow plaques (33.3%) in 8 patients with stable angina and in 18 of 24 yellow plaques (75.0%, P<0.05 vs. stable angina) in 8 patients with old myocardial infarction.Conclusions:The Go of ceramide in human coronary plaques is detectable by FA and Go could be used as a marker of vulnerable plaque (i.e., thin FC with NC).