Table 5:

Required components for high-throughput glycopeptide analysis programs

Programming areas	Requirements
Input	Match experimental intact masses to possible glycopeptides
	Employs biologically relevant protein sequences
	Provides biological filter for glycosite determination
	Incorporates allelic variation
	Does not require input of known glycans or peptide sequences
	Employs tandem MS/MS data
	Employs retention time
Data handling	Performs internal deconvoluting and deisotoping
	Compatible with multiple data input types
	Performs batch processing
	Retains biological context, such as position in protein sequence
Output	Solves peptide and glycan composition and glycosite for N- and O-linked glycopeptides
	Solves glycopeptide compositions in single protein, cocktail and complex biological samples
	Determines glycan structure
	Has low false positive and false negative rates
	Provides preliminary comparison of results from multiple samples
Flexibility	Provides options for different enzymatic cleavage types
	Open source
Portability	Works on Linux, Mac and Windows or web-interface
Availability	Freely available