Li, ZiweiHe, BoKou, QiangWang, ZheWu, SiLiu, YunlongFeng, WeixingLiu, Xiaowen2019-07-032019-07-032018-12-28Li, Z., He, B., Kou, Q., Wang, Z., Wu, S., Liu, Y., … Liu, X. (2018). Evaluation of top-down mass spectral identification with homologous protein sequences. BMC bioinformatics, 19(Suppl 17), 494. doi:10.1186/s12859-018-2462-1https://hdl.handle.net/1805/19825BACKGROUND: 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.en-USAttribution-NonCommercial-NoDerivs 3.0 United StatesHomologous protein databaseMass spectrometryTop-downArticle