Table 3.

Different strategies for the addition of reference peptides

Source of the peptide	Level of labeling	Type of label	Method of quantification	Abbreviation	References
Reference peptide	Chemical synthesis using labeled amino acids	Heavy isotope labeled amino acids	Amino acid analysis Frank et al. 100, Arsene et al. 142	AQUA (absolute quantification)	Gerber et al. 63
	Chemical postsynthesis tagging	Isotope‐labeled tags	Weighing	ICPL	Hochleitner et al. 70
Reference concatamer	Metabolic labeling	15N label	Not necessary for stoichiometries	QconCAT	Beynon et al. 92
	Enzymatic labeling in vivo	Heavy isotope labeled amino acids	Not necessary for stoichiometries	PCS (peptide concatenated standard)	Kito et al. 77
	In vitro translation incorporating labeled amino acids	Heavy isotope labeled amino acids: K	Not necessary for stoichiometries	polySIS	Anderson et al. 93
	Chemical synthesis, trypsination, labeling	mTRaq	Equalization using a concatenated reporter peptide	EtEP (equimolarity through equalizer peptide)	Holzmann et al. 72
Reference protein	In vitro translation (E. coli extract) incorporating labeled amino acids	Heavy isotope labeled amino acids: R/K	Amino acid analysis	PSAQ (protein standard for absolute quantification)	Brun et al. 94 Protein synthesis: Torizawa et al. 95
	In vitro translation (wheat germ extract) incorporating labeled amino acids	Heavy isotope labeled amino acids: R/K	Quantification of a tag peptide after digestion using the AQUA approach	Flexiquant	Singh et al. 96 Protein synthesis: Endo and Sawasaki 97
	In vitro translation (E. coli extract) incorporating labeled amino acids	Heavy isotope labeled amino acids: R/K+ selenomethionine	ICPMS quantification of selenomethionine	RISQ	Zinn et al. 98
	Metabolic labeling in vivo (auxotrophic E. coli strain) or upon in vitro translation	Heavy isotope labeled amino acids: R/K	Amino acid analysis	Absolute SILAC	Hanke et al. 99