Table 3.
Molecular masses of tRNA modifications dependent on sulfur metabolism and standards.
| S-Dependent Modifications | |||||
|---|---|---|---|---|---|
| Modification | Name | Monoisotopic Mass (amu) | Observed Molecular Ion (m/z+) | Major Fragment (m/z+) | Standard ** |
| s2C | 2-thiocytidine | 259.063 | 260.071 | 128.028 | 1 |
| s2U | 2-thiouridine | 260.047 | 261.055 | 129.009 * | 1 |
| s4U | 4-thiouridine | 260.047 | 261.055 | 129.009 * | 2 |
| s2Um | 2-thio-2′-O-methyluridine | 274.062 | 275.067 | 129.008 * | |
| m5s2U/s2T | 5-methyl-2-thiouridine/2-thioribothymidine | 274.062 | 275.062 | 143.019 | 1, 2 |
| m2A † | N2-methyladenosine † | 281.112 | 282.114 | 150.071 | |
| nm5s2U | 5-methylaminomethyl-2-thiouridine | 289.073 | 290.081 | 158.038 | |
| mnm5s2U | 5-methylaminomethyl-2-thiouridine | 303.089 | 304.097 | 172.057 * | |
| se2U | 2-selenouridine | 305.992 | 306.999 | 174.956 | |
| ms2m6A | 2-methylthio-N6-methyladenosine | 327.100 | 328.108 | 196.065 | |
| cmnm5s2U | 5-carboxymethylaminomethyl-2-thiouridine | 347.079 | 348.082 | 216.047 * | |
| mnm5se2U | 5-methylaminomethyl-2-selenouridine | 349.034 | 350.034 | 217.991 | |
| inm5s2U | 5-(isopentenylaminomethyl)-2-thiouridine | 357.136 | 358.144 | 226.101 | |
| ms2i6A | 2-methylthio-N6-isopentenyladenosine | 381.147 | 382.155 | 250.108 * | 1 |
| cmnm5se2U | 5-carboxymethylaminomethyl-2-selenouridine | 393.024 | 394.032 | 261.989 | |
| ct6A | cyclic N6-threonylcarbamoyladenosine | 394.124 | 395.128 | 263.089 * | |
| ges2U | 2-geranylthiouridine | 396.172 | 397.180 | 265.137 | |
| ms2io6A | 2-methylthio-N6-(cis-hydroxyisopentenyl) adenosine | 397.142 | 398.150 | 266.107 | |
| Q | queuosine | 409.160 | 410.168 | 278.125 | |
| nm5ges2U | 5-methylaminomethyl-2-geranylthiouridine | 425.198 | 426.206 | 294.163 | |
| mnm5ges2U | 5-methylaminomethyl-2-geranylthiouridine | 439.214 | 440.222 | 308.179 | |
| ms2ct6A | 2-methylthio-cyclic-N6-threonyl carbamoyladenosine | 440.111 | 441.119 | 309.076 | |
| ms2t6A | 2-methylthio-N6-threonyl carbamoyladenosine | 458.112 | 459.130 | 182.049 * | |
| ms2hn6A | 2-methylthio-N6-hydroxynorvalylcarbamoyladenosine | 472.138 | 473.146 | 341.103 | |
| cmnm5ges2U | 5-carboxymethylaminomethyl-2-geranylthiouridine | 483.204 | 484.212 | 352.169 | |
| Precursor and Related Modifications | |||||
| Modification | Name | Monoisotopic Mass (amu) | Observed Molecular Ion (m/z+) | Major Fragment (m/z+) | Standard ** |
| cmnm5Um | 5-carboxymethylaminomethyl-2′-O-methyluridine | 345.117 | 346.117 | 200.058 * | |
| m6A | N6-methyladenosine †,‡ | 281.112 | 282.114 | 150.071 * | 1 |
| mnm5U | 5-methylaminomethyluridine | 287.112 | 288.120 | 156.074 * | |
| i6A | N6-isopentenyladenosine | 335.159 | 336.167 | 204.119 * | 1 |
| inm5U | 5-(isopentenylaminomethyl) uridine | 341.159 | 342.167 | 210.135 | |
| io6A | N6-(cis-hydroxyisopentenyl) adenosine | 351.154 | 352.156 | 220.115 * | |
| inm5Um | 5-(isopentenylaminomethyl)-2′-O-methyluridine | 355.174 | 356.182 | 224.139 | |
| t6A | N6-threonylcarbamoyladenosine | 412.134 | 413.142 | 136.062 * | 3 |
| oQ | epoxyqueuosine | 425.155 | 426.163 | 294.120 | |
| hn6A | N6-hydroxynorvalylcarbamoyl adenosine | 426.150 | 427.158 | 295.115 | |
| Common Internal Standards | |||||
| Modification | Name | Monoisotopic Mass (amu) | Observed Molecular Ion (m/z+) | Major Fragment (m/z+) | Standard ** |
| I | Inosine ‡ | 268.081 | 269.088 | 137.047 * | 2 |
| Ψ | Pseudouridine † | 244.070 | 245.078 | 209.052 * | 2 |
| D | Dihydrouridine † | 246.085 | 247.092 | 115.050 * | 4, 5 |
* major fragment masses have been experimentally validated [151]; ** commercially available standards: 1-Carbosynth Ltd., Berkshire, United Kingdom, 2-Sigma-Aldrich, St Louis, MO, USA, 3-BioLog Life Science Institute, Bremen, Germany, 4-Advanced Technology & Industrial Co., Ltd., Hong Kong, China, 5-Dalton Pharma Services, Toronto, Canada; † Also found in bacterial ribosomal RNA; ‡ Has not been found in bacterial messenger RNA, but occurs in eukaryotic mRNA.