Identification and mapping of post-transcriptional modifications on the HIV-1 antisense transcript Ast in human cells

(A) LC-MS based detection of UA[Am]CAAGp from Ast RNA. Extracted ion chromatogram for m/z 1151.166 (top panel). Tandem mass spectrum of oligonucleotide anion (m/z 1151.166) with all the observed sequence informative fragment ions (bottom panel). The fragment ion, y and w series contain the 3′-end of the oligomer while the a-B and c ion series contain 5′ end of oligomer. Fragmentation pattern of the oligomer is depicted. (B) LC-MS based detection of AA[Gm]AGp from Ast RNA. Extracted ion chromatogram for m/z853.63 (top panel). Tandem mass spectrum of oligonucleotide anion (m/z853.63) with all the observed sequence informative fragment ions (bottom panel). Fragmentation pattern of the oligomer is depicted.