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

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.