Table 1

Overview of selected protein profiling technologies

Technology

Type of labeling required

Ability to detect many post-translational modifications

Biomolecules that are optimally quantified

Approximate dynamic range (and reference)

Number of proteins/spots quantified (and reference)

Two-dimensional gel electrophoresis

Silver staining

Yes

Naturally occurring forms of proteins larger than 10 kDa

10 [9]

1,500 [8]

Differential two-dimensional fluorescence gel electrophoresis (DIGE)

In vitro with Cy2, Cy3 or CY5 fluorophores at primary amines

Yes

Naturally occurring forms of proteins larger than 10 kDa

10,000 [9]

1,100 [51]

SELDI- or MALDI-MS disease biomarker discovery

None

Yes

Naturally occurring forms of proteins smaller than 10 kDa

25

Not applicable

Isotope-coded affinity tag (ICAT) - LC/MS

In vitro with H¹/D or C¹²/C¹³ ICAT reagent at cysteine

No

Cysteine-containing tryptic peptides from digests of protein extracts

10,000*

496 [18]

N¹⁴/N¹⁵ - LC/MS

In vivo at nitrogens in amino acids

Yes

Tryptic peptides from digests of protein extracts

10,000 [19]

872 [20]

*Assumed to be similar to that for multidimensional protein identification. Abbreviations: SELDI-MS, surface-enhanced laser desorption ionization mass spectrometry; MALDI-MS, matrix-assisted laser desorption ionization mass spectrometry; LC/MS, liquid chromatography and mass spectrometry.

Greenbaum et al. Genome Biology 2003 4:117   doi:10.1186/gb-2003-4-9-117