. 2013 Oct 11;1(3):180–218. doi: 10.3390/proteomes1030180

Table 1.

Different methods used for the staining or labelling of proteins in view of in-gel quantification(Protein-based quantification) ^a.

			Advantages	Drawbacks	Robustness for large scale analysis
Pre-electrophoresis staining (Proteins labelled before electrophoresis)	Chromophore-based staining	none
	Fluorophore-based staining	DIGE (cyanine)	Great linearity, sensitivity and reproducibility; MS-compatible	Expensive	Yes
	PTM-specific staining	none
Post-electrophoresis staining (Proteins revealed after electrophoresis)	Chromophore-based staining	Silver staining, Zinc, Copper (metal-based)	Great sensitivity	Low reproducibility, linearity, and accuracy; Low MS compatibility, influenced by external factors	No
	Chromophore-based staining	CBB, ‘blue-silver’ (organic dyes)	Reproducibility, good linearity, good accuracy, MS-compatible	Moderate sensitivity	Yes
	Fluorophore-based staining	Sypro^®, RuBPs, ASCQ_Ru, IrBPS (metal chelates)	Very good reproducibility, good linearity, great sensitivity, non-covalent labelling	Expensive	Yes
	Fluorophore-based staining	Deep Purple^TM, Flamingo^TM, Krypton^TM (Organic dyes)		Expensive	Yes
	PTM-specific staining	ProQdiamond, ProQemerald	Very good linearity, good sensitivity	Expensive	Yes

^a DIGE, Difference gel electrophoresis; PTM, post translational modifications; CBB, Coomassie brilliant blue; RuBPs, Ruthenium (II) tris (4,7-diphenyl-1,10-phenatrolin disulfonate); ASCQ_Ru, ruthenium complex ((bis(2,2'-bipyridine)-4'-methyl-4-carboxybipyridine-ruthenium-N-succidimyl ester-bis(hexafluorophosphate); IrBPS, biscyclometalated iridium(III) complexes with an ancillary bathophenanthroline disulfonate ligand.