Direct Identification of Human Cellular MicroRNAs by Nanoflow Liquid Chromatography High-Resolution Tandem Mass Spectrometry and Database Searching

MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene networks and participate in many physiological and pathological pathways. To date, miRNAs have been characterized mostly by genetic technologies, which have the advantages of being very sensitive and using high-throughput instrumentation; however, these techniques cannot identify most post-transcriptional modifications of miRNAs that would affect their functions. Herein, we report an analytical system for the direct identification of miRNAs that incorporates nanoflow liquid chromatography-high-resolution tandem mass spectrometry and RNA-sequence database searching. By introducing a spray-assisting device that stabilizes negative nanoelectrospray ionization of RNAs and by searching an miRNA sequence database using the obtained tandem mass spectrometry data for the RNA mixture, we successfully identified femtomole quantities of human cellular miRNAs and their 3'-terminal variants. This is the first report of a fully automated, and thus objective, tandem mass spectrometry-based analytical system that can be used to identify miRNAs.