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

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

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