Table 1:

Comparison of MS/MS based proteomics and MALDI-TOF protein profiling workflows.

MS/MS Based Proteomics	MALDI-TOF Protein Profiling
Allows for analysis of intact proteins or peptides	Used for analysis of intact proteins
Requires more extensive sample preparation/cleanup	Minimal sample preparation required
Often coupled to online or offline separation/fractionation method	Separation/fractionation is not required
Allows for identification and characterization of proteins/peptides	Only provides putative mass value
Can perform absolute and/or relative quantitation	Can only perform relative quantitation
Sample preparation, cleanup, and separation/fractionation result in lower throughput workflow	Minimal sample preparation results in higher throughput analysis