Table 2.

Comparison of different technologies for functional proteomics

	ORF Phage Display	Y2H	MS-based approach
Capacity of the technologies
Protein-protein interaction	Yes	Yes	Yes
Protein-polysaccharide interaction	Yes	No	Yes
Protein-lipid interaction	Yes	No	Yes
Protein-antibody interaction	Yes	No	Yes
Protein-RNA interaction	Yes	No	Yes
Protein-DNA interaction	Yes	Yesa	Yes
Protein-virus interaction	Yes	No	Nob
Protein-cell interaction	Yes	No	Nob
Protein-tissue interaction	Yes	No	Nob
In vivo selection	Yes	No	No
Protease substrate identification	Yes	No	Yes
Eat-me signal identification	Yes	No	No
Features of the technologies
Required time	~2–7 daysc	~1–4 monthsb	~4–6 daysb, d
Screening scale	≥1011 pfu	~106−107 clones	Entire proteomeb
Sensitivity	Single clone	Single clone	Subfemtomole
Re-verification
Binding activity	Convenient	Convenient	Difficultb
Binding specificity	Convenient	Difficultb	Difficultb
cDNA for identified proteins	Available	Available	Not available
Instrument requirement	Minimal	Minimal	Demanding
Subcloning	Not required	Required	Requiredb
Skill required	Minimal	Demanding	Demandingb
Cost	Minimal	Costly	Costlyb

^aYeast one-hybrid system.

^bOpen to interpretation.

^cA fully-automated system of ORF phage display could identify unknown bait-binding proteins in as fast as ~2 days.

^dEstimated time for MS-TAP with ectopic gene expression in mammalian cells.