Table 4.

General comparison of IPG- and NEPHGE- based 2DE methods

Method	IPG	NEPHGE
Characteristics
Preparation of 1st dimension gels	Commercial gels; easy to prepare for IEF	Home-made gels; preparation requires skills
Procedure	Simple, easy to use	Complex, requires skills
Time for analysis	Fast, 2 days	Time-consuming, 5–6 days
Price	Cheap (Invitrogen)	Moderate (WITAvision)
Handling of 1st dimension gels	Handling of IPG strips is safe and easy	Gels are fragile, handling requires serious skills
Reproducibility	Well-reproducible in acidic, poor in a basic zone	Lower in acidic zone, but excellent in basic zone
Possible problems	Poor reproducibility of basic protein spots, protein capacity is limited	Handling difficulties, missing of some highly acidic protein spots
Protein capacity, effect of high protein load	Protein capacity is limited, quality of spots is worse at high protein load	Higher protein capacity, than in IPG gels; quality of spots is good at high load
General characteristic	Simple and easy to use method; ideal for 2-DE of acidic proteins. Drawback is poor reproducibility of basic protein spots.	Method requires skills; excellent for 2-DE of basic proteins. Analysis in acidic zone is satisfactory, but some spots are missed.