Browsing by Subject "Top-down"

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    Evaluation of top-down mass spectral identification with homologous protein sequences
    (Biomed Central, 2018-12-28) Li, Ziwei; He, Bo; Kou, Qiang; Wang, Zhe; Wu, Si; Liu, Yunlong; Feng, Weixing; Liu, Xiaowen; Medical and Molecular Genetics, School of Medicine
    BACKGROUND: Top-down mass spectrometry has unique advantages in identifying proteoforms with multiple post-translational modifications and/or unknown alterations. Most software tools in this area search top-down mass spectra against a protein sequence database for proteoform identification. When the species studied in a mass spectrometry experiment lacks its proteome sequence database, a homologous protein sequence database can be used for proteoform identification. The accuracy of homologous protein sequences affects the sensitivity of proteoform identification and the accuracy of mass shift localization. RESULTS: We tested TopPIC, a commonly used software tool for top-down mass spectral identification, on a top-down mass spectrometry data set of Escherichia coli K12 MG1655, and evaluated its performance using an Escherichia coli K12 MG1655 proteome database and a homologous protein database. The number of identified spectra with the homologous database was about half of that with the Escherichia coli K12 MG1655 database. We also tested TopPIC on a top-down mass spectrometry data set of human MCF-7 cells and obtained similar results. CONCLUSIONS: Experimental results demonstrated that TopPIC is capable of identifying many proteoform spectrum matches and localizing unknown alterations using homologous protein sequences containing no more than 2 mutations.
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    A graph-based approach for proteoform identification and quantification using top-down homogeneous multiplexed tandem mass spectra
    (Biomed Central, 2018) Zhu, Kaiyuan; Liu, Xiaowen; BioHealth Informatics, School of Informatics and Computing