Mass Spectrometry-Based Proteomics in Molecular Diagnostics: Discovery of Cancer Biomarkers Using Tissue Culture

Table 2

Different mass spectrometry-based proteomic approaches with its merits, demerits, and compatibility towards tissue culture.

Proteomic approach	Merits	Demerits	Compatibility with tissue culture^a	References
2-DE	(i) Robust; (ii) Simplistic; (iii) Highly suitable for MS analysis	(i) Involves large amount of sample; (ii) Low throughput; (iii) Poor recovery of hydrophobic proteins	***	[15, 33]
2D-DIGE	(i) Multiplexed; (ii) Better quantitation; (iii) Minimized gel to gel variation	(i) Not suitable for MS analysis; (ii) Expensive Cy dyes; (iii) Poor recovery of hydrophobic proteins	****	[16, 34]
SILAC	(i) High-throughput; (ii) Robust and accurate; (iii) Sensitivity and simplicity	(i) Only suitable for tissue culture model; (ii) Costly reagents; (iii) Not applicable to tissue samples	*****	[25, 48]
Super-SILAC	(i) Better representation of tumor heterogeneity; (ii) Accurate quantitation; (iii) Less error rate	(i) Only suitable to tissue culture model; (ii) Costly reagents; (iii) Internal standard library required	*****	[50]
iTRAQ	(i) Multiplexed; (ii) Applicable to versatile samples; (iii) Better quantitation	(i) Incomplete labelling; (ii) Involves high amount of sample; (iii) Expensive reagents	****	[18, 56]
Label free	(i) Involves less amount of sample; (ii) Broader applicability; (iii) Avoid labelling	(i) High-throughput instrumentation; (ii) Redundancy in detection; (iii) Not suitable for low abundant proteins	****	[61, 64]
SID-MS	(i) Absolute quantitation; (ii) Targeted approach; (iii) Applicable to versatile samples	(i) Applicable to limited number of proteins; (ii) Internal standards are required; (iii) Generally used for validation	***	[65, 68]

^aNumber of “*” indicates extent of compatibility.