Table 1–

Numbers of peptide and protein IDs for CZE-ESI-MS/MS

Algorithm	Isolation window	Injection time	Loading amount ng	Peptide IDs	Protein IDs
Effect of algorithm
SPD	0.4 m/z	11 ms	770 ng	14,144	2,963
APD	0.4 m/z	11 ms	770 ng	27,678	4,387
Effect of isolation window width
APD	0.7 m/z	18 ms	386 ng	20,355	3,454
APD	0.4 m/z	18 ms	386 ng	22,433	3,720
Effect of injection time
APD	0.4 m/z	60 ms	220 ng	25,553	3,828
APD	0.4 m/z	11 ms	220 ng	27,113	4,397
Effect of loading amount
APD	0.4 m/z	11 ms	48 ng	19,874	3,566
APD	0.4 m/z	11 ms	95 ng	20,707	3,618
APD	0.4 m/z	11 ms	220 ng	27,113	4,397
APD	0.4 m/z	11 ms	770 ng	27,678	4,387