1 research outputs found
NucleosâID: A New Search Engine Enabling the Untargeted Identification of RNA Post-transcriptional Modifications from Tandem Mass Spectrometry Analyses of Nucleosides
As RNA post-transcriptional modifications are of growing
interest,
several methods were developed for their characterization. One of
them established for their identification, at the nucleosidic level,
is the hyphenation of separation methods, such as liquid chromatography
or capillary electrophoresis, to tandem mass spectrometry. However,
to our knowledge, no software is yet available for the untargeted
identification of RNA post-transcriptional modifications from MS/MS
data-dependent acquisitions. Thus, very long and tedious manual data
interpretations are required. To meet the need of easier and faster
data interpretation, a new user-friendly search engine, called NucleosâID,
was developed for CE-MS/MS and LCâMS/MS users. Performances
of this new software were evaluated on CE-MS/MS data from nucleoside
analyses of already well-described Saccharomyces cerevisiae transfer RNA and Bos taurus total
tRNA extract. All samples showed great true positive, true negative,
and false discovery rates considering the database size containing
all modified and unmodified nucleosides referenced in the literature.
The true positive and true negative rates obtained were above 0.94,
while the false discovery rates were between 0.09 and 0.17. To increase
the level of sample complexity, untargeted identification of several
RNA modifications from Pseudomonas aeruginosa 70S ribosome was achieved by the NucleosâID search following
CE-MS/MS analysis