Combining phenotypic and proteomic approaches to identify membrane targets in a ‘triple negative’ breast cancer cell type

Table 2 Comparison of the advantages and disadvantages of membranome target discovery techniques

Protein profiling using LPI™ FlowCells and LC-MS/MS		Hybridoma-based phenotypic antibody screening		Phage display-based phenotypic antibody screening
Advantages	Disadvantages	Advantages	Disadvantages	Advantages	Disadvantages
Direct comparison with normal matched tissue can be performed	Extremely reliant on quality of membrane preparation and extraction of membrane proteins	Screening antibodies can assign a potential mechanism of action	High cell requirement	Reduced cell requirement compared to hybridoma approach	Isolation of relatively low affinity antibodies and poor target identification success rate- requirement for complementary techniques for success of target identification
Sample fractionation possible and total survey of the membranome	Reliant on database annotations	Isolation of high affinity antibodies	Dominance of single targets and antibodies	Ability to perform initial screen against multiple cell types with relative ease
	No function or mechanism of action associated with antigens identified	Functional in phenotypic screens	No ability to deselect against abundant antigens or comparator cell types	Screening can assign a potential mechanism of action
		High target identification success rate		Ability to avoid dominance – can deselect against abundant antigens and comparator cell types
		Isolation of antibodies that can be used for target validation or as a therapeutic candidates		Isolation of antibodies that can be used for target validation
				Potential to identify target and therapeutic candidate

Comparing LPI™. FlowCells and LC-MS/MS with hybridoma-based phenotypic antibody screening and phage display-based antibody screening.