. 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 1.

Optimization of PQD conditions for peptide identification and quantification.

	Total identified peptide per analysis	Total unique peptides: identified/quantified	Peptide ratios	Expected iTRAQ reporter ion ratio	Measured iTRAQ reporter ion ratios (average value from 2 MS analyses)
	Total identified peptide per analysis	Total unique peptides: identified/quantified	Peptide ratios	Expected iTRAQ reporter ion ratio	Average	Absolute error	Standard Deviation	CV
PQD27	320	44/13	114/115	1	0.93	0.11	0.14	0.15
			114/116	1	0.93	0.07	0.24	0.26
			114/117	1	1.18	0.19	0.28	0.23
PQD30	1135	148/60	114/115	1	0.93	0.07	0.15	0.16
			114/116	1	0.98	0.04	0.23	0.23
			114/117	1	1.09	0.11	0.23	0.22
PQD35	3379	173/106	114/115	1	0.94	0.06	0.14	0.15
			114/116	1	0.99	0.02	0.23	0.23
			114/117	1	1.07	0.09	0.18	0.17
PQD45	1561	209/87	114/115	1	0.93	0.07	0.23	0.25
			114/116	1	0.93	0.07	0.20	0.21
			114/117	1	1.01	0.03	0.23	0.23