Table 13.1.2.

Overview of Current Proteome Profiling Technologies

Technology	Labeling required	Detects post-translational modifications?	Proteins that are optimally quantified	Approximate dynamic range	Max. number of proteins or spots quantified	Analytical issues
SELDI or MALDI-MS disease biomarker discovery	None	Yes	Naturally occurring forms of <10 kD proteins	25	Not applicable	Separate experiment required for protein identification
Traditional 2-D gel electrophoresis (2DGE)	None	Yes	Naturally occurring forms of 10- to 200-kD proteins	1,000	3,000	Quantitation and replication difficult
Amersham differential 2-D fluorescence gel electrophoresis (DIGE)	In vitro with Cy-2, -3, or -5 fluorophores at primary amines	Yes	Naturally occurring forms of 10- to 200-kD proteins	10,000a	~3,000b	Detects proteins expressed at the upper 104 to 105 of dynamic range, that have long half-livesa,c and are soluble under 2-D running conditions
Proteome Lab PF 2-D automated 2-D chromatofocusing/ reversed-phase HPLC	None	Yes	Naturally occurring forms of >5 kD peptides and proteins	100d	2,500d	Limited to UV detection unless coupled to MS
Multidimensional LC/MS/MS protein identification (MudPIT)	Not required, but indiscriminate peptide tagging chemistries can be used	Yes	Tryptic peptides from digests of protein extracts	10,000e	872f	Mixture highly complex, requires fractionation prior to MS
Acid-labile isotope coded affinity tag (ICAT) - LC/MS	In vitro with C12/C13 cleavable ICAT reagent at cysteine	No	Cysteine-containing tryptic peptides from digests of protein extracts	10,000	496g	Only detects cysteine-containing proteins; cannot generally detect post-translational modifications

^aTonge et al. (2001).

^bHoving et al. (2000).

^cGygi et al. (1999a).

^dBetgovargez and Simonian (2003).

^eWolters et al. (2001).

^fWashburn et al. (2002).

^gHan et al. (2001).