Table 3:

Table of glycopeptide analysis software versus outputs

Software name	Solves peptide, glycan and glycosite of N- and O-linked glycopeptides	Solves glycopeptides from single protein, protein cocktails and complex biosystems	Determines glycan structure	Provides match score	Calculates false positive and false negative rate
Branch-and-Bound	✗	✓	✓ (in some cases	✓	✗
GlycoMaster	✗	✗	✓	✓	✗
GlycoMiner	✗	✗	✗	✓	✓
GlycoMod	✗	✗	✗	✗	✗
Glycopeakfinder	✓	✗	✗	✗	✗
GlycoPep DB	✗	✗	✗	✗	✗
GlycoPep Grader	✗	✗	✗	✓	✗
GlycoPep ID	✗	✗	✗	✗	✗
GlycoSpectrumScan	✓	✗	✗	✗	✗
GlycoX	✓	✗	✗	✗	✗
GlyDB	✗	✗	✓ (for simple biantennary glycans)	✓	✗
GlyPID	✗	✗	✗	✓	✗
GP finder	✓	✓ (for pronase digested glycopeptides)	✗	✓	✗
Medicel N-glycopeptide library	✗	✓	✗	✓	✗
Peptoonist	✗	✗	✗	✓	✗
Sweet substitute	✗	✗	✓ (in some cases)	✗	✗
Ideal software	✓	✓	✓	✓	✓