Table 2: Different mass spectrometry-based proteomic approaches with its merits, demerits, and compatibility towards tissue culture.

Proteomic approachMeritsDemeritsCompatibility with tissue cultureaReferences

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.