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Vol 53(2019) N 1 p. 147-155; DOI 10.1134/S0026893319010096  A.V. Lisitsa1,2, N.A. Petushkova1*, L.I. Levitsky3,4, V.G. Zgoda1, O.V. Larina1, Yu.S. Kisrieva1, V.E. Frankevich5, S.I. Gamidov5 Comparative Analysis of the Performance of Mascot and IdentiPy Algorithms on a Benchmark Dataset Obtained by Tandem Mass Spectrometry Analysis of Testicular Biopsies 1Orechovich Institute of Biomedical Chemistry, Moscow, 119121 Russia2East China University of Technology, Nanchang, 330013, China 3Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, 119334 Russia 4Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow oblast, 119334 Russia 5Kulakav Research Center of Obstetrics, Gynecology and Perinatology, Ministry of Health of the Russian Federation, Moscow, 117997 Russia *cyp450@mail.ru Received - 2018-05-29; Revised - 2018-07-03; Accepted - 2018-08-13 Proteome profiling of human testicular biopsies was performed using tandem mass spectrometry with electrospray ionization. Protein identification results were compared for the Mascot commercial search engine, the SearchGUI noncommercial package, and their analog IdentiProt based on the open-source IdentiPy algorithm (http://hg.theorchromo.ru/identipy). A feature of IdentiPy is an automatic optimization of MS/MS search parameters. A set of protein identifications obtained with IdentiPy was consequently greater by one third than the sets with the other search engines. For the first time, an IdentiPy/IdentiProt search was conducted within the Progenesis LC-MS framework, which allows spectrum alignment, and the proteome profile obtained with alignment was compared with that obtained using the ProteoWizard converter. A total of 16 human chromosome 18 proteins were identified, including the myelin basic protein, which is not characteristic of testicular tissue. biopsy, testicular tissue, proteomics, tandem mass spectroscopy, Mascot, SearchGUI, IdentiProt, chromosome 18 |
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