Table 3.

Predicted Ψ-fragments from endonuclease digested E. coli tRNAs. Endonucleases include RNase A and RNase T1. tRNA sequences were obtained from the tRNA database.²⁸ Pseudouridines are highlighted for emphasis only. Sequences are only shown for RNase digestion products greater than m/z 1000 due to MALDI-MS background interferences present at lower masses. N.D. - not detected in this study.

tRNA	Ψ-sequence	Base compositions detected in this work
Arg III	Ψ – 55	TΨCGp (RNase T1)
Arg V	Ψ – 55	TΨCGp (RNase T1)
Gln II	Ψ – 38 Ψ – 55	[m2A]ΨACCGp (RNase T1); G[m2A]Ψp (RNase A) TΨCGp (RNase T1)
Glu I	Ψ – 13 Ψ – 55	UCΨAGp (RNase T1) TΨCGp (RNase T1)
Glu II	Ψ – 13 Ψ – 55	UCΨAGp (RNase T1) TΨCGp (RNase T1)
Glu III	Ψ – 13 Ψ – 55	UCΨAGp (RNase T1) TΨCGp (RNase T1)
Gly I	Ψ – 55	TΨCGp (RNase T1)
Gly II	Ψ – 55	TΨCGp (RNase T1)
His	Ψ – 38 Ψ – 39 Ψ – 55	G[m2A]Ψp (RNase A) N.D. TΨCGp (RNase T1)
Leu II	Ψ – 38 Ψ – 40 Ψ - 55	AGGΨp (RNase A) ΨUAGp (RNase T1) TΨCGp (RNase T1)
Leu III	Ψ – 38 Ψ - 55	GAGGΨp (RNase A) TΨCGp (RNase T1)
Met	Ψ – 39 Ψ - 55	N.D. TΨCGp (RNase T1)
Phe	Ψ – 32 Ψ – 39 Ψ – 55	AΨUGp (RNase T1); AGGGGAΨp (RNase A) AA[ms2i6A]AΨCCCCGp (RNase T1); GAA[ms2i6A]AΨp (RNase A) TΨCGp (RNase T1)
Ser I	Ψ – 55	TΨCGp (RNase T1)
Ser II	Ψ – 55	TΨCGp (RNase T1)
Ser III	Ψ – 40 Ψ – 55	GGAAAGΨp (RNase A) TΨCGp (RNase T1)
Ser IV	Ψ – 40 Ψ – 55	GGAAAGΨp (RNase A) TΨCGp (RNase T1)
Ser V	Ψ – 55	TΨCGp (RNase T1)
Thr I	Ψ – 55	TΨCGp (RNase T1)
Thr II	Ψ – 55	TΨCGp (RNase T1)
Trp	Ψ – 55	TΨCGp (RNase T1)
Tyr I	Ψ – 39 Ψ - 55	A[ms2i6A]AΨp (RNase A) TΨCGp (RNase T1)
Tyr II	Ψ – 39 Ψ - 55	A[ms2i6A]AΨp (RNase A) TΨCGp (RNase T1)
Val III	Ψ – 55	TΨCGp (RNase T1)