Table 1:
Table of glycopeptide analysis software versus inputs
| Software name | Uses intact mass to find possible glycopeptide compositions | Uses protein sequence | Uses biological glycosite filter | Incorporates allelic variation | Does not require previous knowledge of glycans | Does not require peptide mass input | Uses tandem data | Uses retention time |
|---|---|---|---|---|---|---|---|---|
| Branch-and-Bound | ✗ | ✗ | ✗ | ✗ | ✓ | ✓ | ✓ | ✗ |
| GlycoMaster | ✗ | ✗ | ✗ | ✗ | ✓ | ✗ | ✓ | ✗ |
| GlycoMiner | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✓ | ✗ |
| GlycoMod | ✓ | ✓ | ✓ | ✗ | ✓ | ✗ | ✗ | ✗ |
| Glycopeakfinder | ✓ | ✗ | ✗ | ✗ | ✓ | ✗ | ✓ | ✗ |
| GlycoPep DB | ✓ | ✓ | ✓ | ✗ | ✓ | ✗ | ✗ | ✗ |
| GlycoPep grader | ✓ | ✓ | ✗ | ✗ | ✗ | ✗ | ✓ | ✗ |
| GlycoPep ID | ✗ | ✓ | ✗ | ✗ | ✗ | ✗ | ✓ | ✗ |
| GlycoSpectrumScan | ✓ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ |
| GlycoX | ✓ | ✓ | ✗ | ✗ | ✓ | ✗ | ✗ | ✗ |
| GlyDB | ✓ | ✓ | ✓ | ✗ | ✓ | ✗ | ✓ | ✗ |
| GlyPID | ✓ | ✗ | unclear | ✗ | ✓ | ✓ | ✓ | ✗ |
| GP finder | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✓ | ✗ |
| Medicel N-glycopeptide library | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✓ | ✗ |
| Peptoonist | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✓ | ✗ |
| Sweet substitute | ✗ | ✗ | ✗ | ✗ | ✓ | ✓ | ✓ | ✗ |
| Ideal software | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |