TABLE 1.

MASS SPECTROMETRY–BASED PROTEOMICS TECHNOLOGY PLATFORMS

	MALDI MS	Two-Dimensional Gel	Tandem MS	MRM MS/MS
Purpose	Profiling	Profiling and ID	Profiling and ID	Quantitation
Sample preparation	± Depletion, fractionation	± Depletion, fractionation	Digestion	Digestion
Analytes	MS Peaks	Spots	MS-MS Spectra	Peak areas
Representative of	Proteins, peptides	Proteins	Peptide sequences	Protein amounts
Depth of analysis	100–300 peaks	100–1,000 proteins	500–3,000 proteins	Single target protein
Analysis compare	Patterns	Patterns	Inventories	Amounts
Protein identification	Difficult	Readily by MS	High-throughput	Quantitative
Information	Correlation to biology	Link to biology	Link to biology	Verification

Definition of abbreviations: MALDI = matrix-assisted laser desorption/ionization; MRM = multiple reaction monitoring; MS = mass spectrometry.