Table 1.
Detection rates of spiked NA modifications at three concentrations in deionized water using different NA adductomic analysis strategies.
| Concentration of multiple types of NA modifications (number of adducts or pairs) | Numbers of the spiked NA modifications detected |
||||
|---|---|---|---|---|---|
| Manual inspection |
DD-NL-MS3 acquisition |
DD-MS2 acquisition |
|||
| MS1 | features in MS2 | by MS3 triggering eventa | With DFBuilder in MZmineb | With FeatureHunter | |
| Level 1 (500 ng/mL each) | |||||
| 2’-dN (23) | 23c (100%)d | 23 (100%) | 23 (100%) | 23 (100%) | 23 (100%) |
| rN (21) | 21 (100%) | 20 (95%) | 20 (95%) | 20 (95%) | 20 (95%) |
| nB (29) | 29 (100%) | 29 (100%) | －e | 29 (100%); 70* | 29 (100%) |
| d0 - d3 peak pair (9) | 9 (100%) | － | － | － | 9 (100%) |
| d0 - d4 peak pair (2) | 2 (100%) | － | － | － | 2 (100%) |
| 14N5 - 15N5 peak pair (4) | 4 (100%) | － | － | － | 4 (100%) |
| Level 2 (5 ng/mL each) | |||||
| 2’-dN (23) | 23 (100%) | 23 (100%) | 22 (96%) | 23 (100%) | 23 (100%) |
| rN (21) | 21 (100%) | 20 (95%) | 18 (86%) | 20 (95%) | 20 (95%) |
| nB (29) | 28 (97%) | 20 (69%) | － | 20 (69%); 50* | 20 (69%) |
| d0 - d3 peak pair (9) | 9 (100%) | － | － | － | 9 (100%) |
| d0 - d4 peak pair (2) | 2 (100%) | － | － | － | 2 (100%) |
| 14N5 - 15N5 peak pair (4) | 4 (100%) | － | － | － | 4 (100%) |
| Level 3 (0.5 ng/mL each) | |||||
| 2’-dN (23) | 23 (100%) | 19 (83%) | 18 (78%) | 16 (70%) | 19 (83%) |
| rN (21) | 20 (95%) | 14 (67%) | 10 (48%) | 13 (62%) | 14 (67%) |
| nB (29) | 18 (62%) | 2 (7%) | － | 2 (7%); 14* | 2 (7%) |
| d0 - d3 peak pair (9) | 9 (100%) | － | － | － | 9 (100%) |
| d0 - d4 peak pair (2) | 2 (100%) | － | － | － | 2 (100%) |
| 14N5 - 15N5 peak pair (4) | 4 (100%) | － | － | － | 4 (100%) |
a
The DD-NL-MS3 acquisition method used was previously reported by Chang et al. (2021)37;
b
Module was developed by Murray et al. (2021)25 within MZmine software;
c
The number of spiked adducts that were successfully extracted;
d
Detection rate is calculated as: (total adducts extracted/spiked adducts) × 100;
e
Not available or not applicable;
*
The total number of extracted adducts, which included both the spiked adducts and the false positive results (derived from the in-source fragmentation of 2’-dN or rN adducts).