链霉菌基质辅助激光解吸电离飞行时间质谱数据库的建立及测试分析

Establishment and testing of a MALDI-TOF MS database for the identification of Streptomyces

摘要:

链霉菌种类繁多，以盛产抗生素而闻名，是极具研发价值的放线菌类群。然而，商业数据库中收录的链霉菌属菌种数量较少，这限制了基质辅助激光解吸电离飞行时间质谱(matrix-assisted laser desorption/ionization-time of flight mass spectrometry, MALDI-TOF MS)技术在链霉菌鉴定中的应用。目的 基于全基因组测序数据挖掘，建立链霉菌属菌种的MALDI-TOF MS数据库，并测试其准确性。方法 检索基因组数据库，提取已测序的链霉菌属菌种模式菌株的12种核糖体蛋白序列，并计算其理论MALDI质谱峰值，以这12个峰值的组合作为菌种鉴定依据建立数据库。收集模式菌株进行MALDI-TOF MS测试，将实测峰值与数据库中菌种的理论峰值进行比对，以测试建库方法及数据库比对结果的准确性。结果 建立了包含链霉菌属615个菌种的MALDI-TOF MS数据库。测试菌株的质谱均实现了与数据库中目标菌种的准确匹配。本研究还提出了基于数据库比对的菌种鉴定方法。结论 本研究建立的数据库为基于MALDI-TOF MS技术鉴定链霉菌奠定了基础。

Abstract:

Streptomyces is a genus of diverse actinomycetes known for producing antibiotics, showcasing high value for research and development. However, the limited number of Streptomyces species included in commercial databases restricts the application of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in the identification of Streptomyces.Objective To establish a MALDI-TOF MS database for the identification of Streptomyces based on the mining of whole genome sequencing data and test its accuracy.Methods By searching against a genome database, we selected all the genome-sequenced type strains of Streptomyces. Subsequently, the sequences of 12 ribosomal proteins were extracted from their genome sequences and theoretical MALDI mass/charge (m/z) values were calculated. Accordingly, a database was established based on the combination of 12 theoretically calculated m/z values, which can be used as the identification criteria for Streptomyces species. Finally, type strains were randomly collected for MALDI-TOF MS testing. To test the accuracy of the database construction method and comparison results, we matched the experimental m/z values with the theoretically calculated m/z values of the species in the database.Results We established a MALDI-TOF MS database including 615 Streptomyces species. The mass spectra of the tested strains were accurately matched with those of corresponding species in the database. In addition, we proposed a method for the identification of Streptomyces by database comparison.Conclusion The database established in this study laid a foundation for identifying Streptomyces based on MALDI-TOF MS.