. 2013 Oct 11;1(3):180–218. doi: 10.3390/proteomes1030180

Table 4.

Different methods used for the labelling of proteins or peptides in view of off-gel quantification(Peptide based quantification) ^a.

			Advantages	Drawbacks	Robustness for large scale analysis	Exemples of use
Pre-analysis labelling (A single analysis (sample combination after labelling): mass difference between peptide pairs on the same mass spectra)	**In vitro/vivo labelling** (during protein synthesis)	¹⁵N, ¹³C,	Accuracy	Limited to cells in culture,time-consuming	Yes (regardless of the cost and time needed)	Cells in culture
	**In vitro/vivo labelling** (during protein synthesis)	SILAC, CIDTs, superSILAC, SILAM	Accuracy	Limited to cells in culture,time-consuming		Cells in culture
	Pre-digestion labelling	ICPL, iTRAQ, TMT, ICAT, ALICE, dimethyl	Sample complexity	Low sequence recovery		All types of biological sample (regardless of the protein quantity needed)
	In-digestion labelling	H₂¹⁸O	Simplified signal analysis, low cost	Late labelling
	Post-digestion labelling	ICAT, iTRAQ, ICPL, ALICE, TMT	High sequence recovery
	Post-digestion labelling	dimethyl, GIST	High sequence recovery
Direct analysis (Two (or more) analyses carried out independently before their comparison)	Label-free Quantification (without internal standard)	Comparison of mass spectra	Sample number, low cost	Separations normalisation, signal alignment	Yes	All types of biological sample
	Label-free Quantification (without internal standard)	Spectral counting	Sample number, low cost	Separations normalisation, signal alignment	Yes	All types of biological sample
	Absolute Quantification (with internal standard)	AQUA	Easy to use	Cost of internal standard, analysis of one or few proteins	No(too expensive)	Validation of biomarkers
		QconCAT	Enzymatic digestion take into account
		PSAQ	Enzymatic digestion take into account
		SRM / MRM	High sensitivity and reproducibility

^a SILAC, stable isotope labelling by amino acids in cell culture; CDIT, culture-derived isotope tags; SILAM, stable isotope labelling of mammal; ICPL, isotope-coded protein label; TMT, tandem mass tags; ICAT, isotope-coded affinity tags; iTRAQ, isobaric tags for relative and absolute quantification; ALICE, acid-labile isotope-coded extractants; GIST, global internal standard technology; Coomassie brilliant blue; XIC, extracted ion chromatogram; AQUA, absolute quantification of proteins; QconCAT, absolute quantification using artificial proteins of concatenated signature peptides; PSAQ, protein standard for absolute quantification; IMAC, immobilised metal affinity chromatography.