. Author manuscript; available in PMC: 2010 Jul 1.

Published in final edited form as: J Proteome Res. 2009 Jul;8(7):3746–3751. doi: 10.1021/pr801122b

Table 3.

Excerpt from the Tabulated Results from the CV Optimization Experiment^a

peptide	Q1 m/z	Q3 m/z	default CV	default CV	default CV	AUC def −2 V	AUC default	AUC def +2 V	AUC def +2 V	AUC def +6 V	max AUC	best CV	% AUC gain at best CV
TPHPALTEAK	355.53	448.24	36	1575.0	2621.0	3605.1	3764.7	3552.3	3775.7	3480.7	3775.7	Default +4 V	0.3
TPHPALTEAK	355.53	561.32	36	1359.2	1609.6	1922.3	1702.8	1630.8	1892.5	1481.6	1922.3	Default −2 V	12.9
TPHPALTEAK	355.53	729.41	36	4328.5	5235.2	5102.2	5014.6	4653.8	4927.4	3742.2	5235.2	Default −4 V	4.4
WC[160]TISTHEANK	449.54	461.24	36	1109.8	1010.4	1145.1	1115.9	991.5	822.2	635.9	1145.1	Default −2 V	2.6
WC[160]TISTHEANK	449.54	598.30	36	791.0	507.6	545.3	814.5	828.1	405.2	471.4	828.1	Default +2 V	1.7
WC[160]TISTHEANK	449.54	786.37	36	1037.7	1472.7	1726.9	2283.3	1313.4	1529.4	806.8	2283.3	Default	0.0
AVVQDPALKPLALVYGEATSR	733.41	434.24	36	7249.9	7305.5	8052.4	8030.0	8136.8	5980.1	7246.1	8136.8	Default +2 V	1.3
AVVQDPALKPLALVYGEATSR	733.41	563.28	36	5310.8	5920.4	5729.5	5378.3	6143.5	5195.3	4956.1	6143.5	Default +2 V	14.2
AVVQDPALKPLALVYGEATSR	733.41	620.30	36	23479.0	26911.3	24702.9	27168.1	26404.7	22470.2	24323.1	27168.1	Default	0.0
AVVQDPALKPLALVYGEATSR	733.41	783.36	36	27002.5	27145.7	24043.7	26749.6	25157.1	23732.7	23591.2	27145.7	Default −4 V	1.5
AVVQDPALKPLALVYGEATSR	733.41	882.44	36	6775.5	7654.5	7950.4	7954.0	7068.5	6519.1	5395.6	7954.0	Default	0.0

The AUC calculations were performed by the MRM software package Mr. M, and the CV that produced the largest AUC was taken to be the best-performing CV for the given transition. The percent gain in AUC represents the increase in AUC for the best-performing CV relative to the default CV.