TABLE 1.
LC-MS features annotated by DDA and AMT tag approaches
| Parameter | No. of features | No. of peptides | No. of proteins |
|---|---|---|---|
| Monoisotopic features annotated by DDA and/or AMT tags | |||
| DDA | 4,841 | 4,213 | 877 |
| AMT | 6,773 | 5,323 | 2,680 |
| Agreementa | 952 | 808 | 418 |
| LC-MS features annotated by AMT tags alone | |||
| AMT (no DDA available) | 5,618 | 4,714 | 2,514 |
| High confidenceb | 2,220 | 2,220 | 495 |
a
1,155 monoisotopic features were annotated by both DDA and AMT tags; 952 of the 1,155 received identical peptide annotations via both methods.
b
AMT tag annotations were deemed of high confidence if the corresponding proteins were at least identified by DDA (ProteinTeller-predicted error of <3%) or represented by a minimum of three unique peptides.