. Author manuscript; available in PMC: 2010 May 15.

Published in final edited form as: Anal Chem. 2009 May 15;81(10):4137–4143. doi: 10.1021/ac802605m

Table 2.

Comparison of PQD and ETD-based quantification on iTRAQ–labeled peptides identified from ETD spectra.

Quantification approach		Expected	Average value of 2 biological Replicates analyses
PQD-based Quantification	Peptide ratios	iTRAQ ratio	Average	Absolute error	Standard deviation	CV
	114/115	1	1.01	0.02	0.31	0.30
	114/116	1	0.93	0.07	0.27	0.29
	114/117	1	1.13	0.13	0.34	0.30
ETD-based Quantification	101/102	1	0.54	0.47	0.24	0.45
ETD-based Quantification	101/104	0.50	0.44	0.07	0.20	0.45