microbeПроблемы особо опасных инфекцийProblems of Particularly Dangerous Infections0370-10692658-719XRussian Research Anti-Plague Institute “Microbe”10.21055/0370-1069-2021-3-40-50microbe-1546Research ArticleОБЗОРЫREVIEWSПрограммные решения для индикации и идентификации патогенных микроорганизмов методом времяпролетной масс-спектрометрииSoftware Solutions for Indication and Identification of Pathogenic Microoranisms Using Time-of-Flight Mass Spectrometryhttps://orcid.org/0000-0001-7754-2201УльшинаД. В.Ul’shinaD. V.

355000, Ставрополь, ул. Советская, 13–15

13–15, Sovetskaya St., Stavropol, 355000, Russian Federation

stavnipchi@mail.ruhttps://orcid.org/0000-0002-9366-5647КовалевД. А.KovalevD. A.

355000, Ставрополь, ул. Советская, 13–15

13–15, Sovetskaya St., Stavropol, 355000, Russian Federation

https://orcid.org/0000-0001-9513-0761КузнецоваИ. В.KuznetsovaI. V.

355000, Ставрополь, ул. Советская, 13–15

13–15, Sovetskaya St., Stavropol, 355000, Russian Federation

https://orcid.org/0000-0001-6338-4476БобрышеваО. В.BobryshevaO. V.

355000, Ставрополь, ул. Советская, 13–15

13–15, Sovetskaya St., Stavropol, 355000, Russian Federation

КрасовскаяТ. Л.KrasovskayaT. L.

355000, Ставрополь, ул. Советская, 13–15

13–15, Sovetskaya St., Stavropol, 355000, Russian Federation

https://orcid.org/0000-0002-9362-3949КуличенкоА. Н.KulichenkoA. N.

355000, Ставрополь, ул. Советская, 13–15

13–15, Sovetskaya St., Stavropol, 355000, Russian Federation

ФКУЗ «Ставропольский научно-исследовательский противочумный институт»РоссияStavropol Research Anti-Plague InstituteRussian Federation202122102021034050Copyright © Ульшина Д.В., Ковалев Д.А., Кузнецова И.В., Бобрышева О.В., Красовская Т.Л., Куличенко А.Н., 20212021Ульшина Д.В., Ковалев Д.А., Кузнецова И.В., Бобрышева О.В., Красовская Т.Л., Куличенко А.Н.Ul’shina D.V., Kovalev D.A., Kuznetsova I.V., Bobrysheva O.V., Krasovskaya T.L., Kulichenko A.N.Данная работа распространяется под лицензией Creative Commons Attribution 4.0.This work is licensed under a Creative Commons Attribution 4.0 License.https://journal.microbe.ru/jour/article/view/1546

Эффективность дифференциации бактериальных патогенов методом MALDI-TOF масс-спектрометрии зависит от качества проведения пробоподготовки, соблюдения параметров анализа и от используемых статистических подходов, реализованных различными современными программными средствами. В обзоре дана краткая характеристика наиболее известного программного обеспечения, используемого при обработке и биоинформационном анализе данных времяпролетной масс-спектрометрии. Представлен перечень компьютерных платформ, программ и сред как коммерческих, так и находящихся в общем доступе. Приведены результаты индикации и идентификации возбудителей особо опасных и природно-очаговых инфекций методом MALDI-TOF массспектрометрии с помощью общедоступного программного обеспечения – язык программирования R, Mass-Up, Microbe MS, лицензированного – MatLab, ClinProTools, а также бесплатных веб-приложений, в том числе Speclust, Ribopeaks. Представлена информация об опыте использования таких известных платформ, как MALDI BioTyper, SARAMIS Vitek-MS и Andromas, для меж- и внутривидовой дифференциации штаммов близкородственных видов патогенных микроорганизмов. Приведены результаты идентификации и дифференциации микроорганизмов методом MALDI-TOF MS на основании выявления специфических белков для перекрестного сравнения – биомаркеров. Показано, что среда языка программирования R представляет собой одну из общедоступных универсальных платформ с оптимальным сочетанием алгоритмов обработки и интерпретации большого массива масс-спектрометрических данных.

The effectiveness of differentiation of bacterial pathogens using MALDI-TOF mass spectrometry depends on the quality of sample preparation, compliance with mass spectrometric analysis parameters and statistical approaches used, implemented by various modern software tools. The review provides a brief description of the most known software used in the processing and bioinformation analysis of time-of-flight mass spectrometry data. A list of computer platforms, programs and environments, both commercial and publicly available, is presented. The results of indication and identification of pathogens of particularly dangerous and natural-focal infections by MALDI-TOF mass spectrometry using publicly available software – programming language R, Mass-Up, MicrobeMS, licensed – MatLab, ClinProTools, as well as free web applications, including, Speclust, Ribopeaksare provided. The data on usage of such well-known platforms as MALDI BioTyper, SARAMIS Vitek-MS and Andromas (Andromas SAS, France) for inter- and intra-specific differentiation of closely related species are presented. Results of identification and differentiation of microorganisms applying MALDI-TOF mass spectrometry based on detection of specific proteins for cross-comparison – biomarkers – are given. The analysis shows that the programming language R environment is one of the publicly available universal platforms with an optimal combination of algorithms for processing and interpreting of a large array of mass spectrometric data.

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The authors declare that there are no conflicts of interest present.