Table 1.
Summary of modifications detected in the HAP1 tRNA data using NASE.
| Search mod. | Represented (isobaric) modification(s) | Spectra with mod. |
|---|---|---|
| t6A | N6-threonylcarbamoyladenosine | 2906 |
| mA | Adenosine monomethylation (base only) | 2429 |
| mU? | Uridine or pseudouridine monomethylation (sugar or base) | 2233 |
| mC? | Cytidine monomethylation (sugar or base) | 1728 |
| mG? | Guanosine monomethylation (sugar or base) | 1512 |
| mcm5s2U | 5-methoxycarbonylmethyl-2-thiouridine | 1185 |
| D | Dihydrouridine | 998 |
| i6A | N6-isopentenyladenosine | 816 |
| m1I | 1-methylinosine | 718 |
| ac4C/f5Cm? | N4-acetylcytidine or 5-formyl-2′-O-methylcytidine | 672 |
| ms2t6A | 2-methylthio-N6-threonylcarbamoyladenosine | 633 |
| acp3U | 3-(3-amino-3-carboxypropyl)uridine or -pseudouridine | 571 |
| I | Inosine | 404 |
| m2,2G | N2,N2-dimethylguanosine | 326 |
| hm5Cm | 2′‐O‐methyl-5-hydroxymethylcytidine | 194 |
| Q | Queuosine | 191 |
| mchm5U | 5-(carboxyhydroxymethyl)uridine methyl ester | 187 |
| mcm5U | 5-methoxycarbonylmethyluridine | 150 |
| mcm5Um | 5-methoxycarbonylmethyl-2′-O-methyluridine | 145 |
| cm5U | 5-carboxymethyluridine | 97 |
| galQ/manQ | Galactosyl- or mannosyl-queuosine | 40 |
| yW | Wybutosine | 37 |
| hm5C | 5-hydroxymethylcytidine | 31 |
Table columns: 1. Short code of the modification specified as a search parameter. 2. The set of modifications implied by the corresponding mass shift, since e.g. positional isomers (Cm, m3C, m5C etc.) generally cannot be distinguished. A question mark in the short code (column 1) indicates that modification of the ribose or the base (implying different masses of “a-B” ions) should both be considered. Forms that are not expected to occur in human tRNA (e.g. Am, Im) are not listed. 3. Number of times identified as part of an oligonucleotide-spectrum match.