TABLE 1.

COMPARISON OF PROTEOMIC APPROACHES IN CANCER BIOMARKER DISCOVERY RESEARCH

	2-D gel separation	MALDI MS	LC-MS/MS	LC-MRM MS	Protein/antibody arrays
Purpose	Profiling, separation and identification	Profiling	Inventory and identification	Targeted protein quantitation	Targeted protein detection
Protein detection and identification	Protein pI and MW. Identification by peptide mapping and sequencing,	Detection of intact peptides and proteins	Identification via peptide sequences.	Peptide specific MS/MS transitions.	Detection using antibodies or ligands
Quantitation	Semi-quantitative	Semiquantitative	Semiquantitative	Quantitative, labeled reference peptides. Label free techniques	Not quantitative
PTM detection	Yes	No	Yes	Yes	Yes
Throughput	Low	High	High	Low	High
Reproducibility	High	High	High	High	High
Sensitivity	Moderate	low	High	High	High
Depth of analysis	100–1,000 proteins	100–300 peaks	500–4,000 proteins	1–100 proteins	0–500 proteins
Major disadvantages	pI and MW range limitations. Contamination by polysaccharides and nucleic acids	Detection of abundant proteins. Limited MW range (2–30 kDa). No identification.	High false discovery rate	Cost of labeled peptides for absolute quantitation	Antibody specificity and availability. Only known proteins can be detected.

Definition of abbreviations: 2-D = two-dimensional; LC-MRM MS = liquid chromatography coupled to multiple reaction monitoring mass spectrometry; LC-MS/MS = liquid chromatography coupled to tandem mass spectrometry; MALDI MS = matrix-assisted laser desorption ionization mass spectrometry; ; MW = molecular weight; pI = isoelectric point; PTM = posttranslational modification.