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].