Table II.

Summary of methods used in this study

This table lists all methods (column 1), protein prefractionation approaches (column 2), mass spectrometers (column 3), sample quantities (column 4), protein and peptide separation strategies (column 5), number of replicates (column 6), sample throughput (columns 7 and 8), and the number of proteins and peptides identified by each approach (columns 9 and 10).

Method	Protein separation	MS instrument	Sample quantity	Peptide analysis	No. of repetitive analyses	Throughput/ measurement		95% analytical completeness		Total unique peptides identified	Protein identification
						Time	Relative to 2DC	Time	No. of proteins/total measurement days		No. of proteins identified	Relative to 2DC
			μg/run			days		days
2DC	—a	LCQ	150	SCX-RP	10	2	1	14	24	2,916	332	1
GRPC	SDS-PAGE	LCQ	40	RP	5	10	5	50	11	3,883	532	1.6
GRPT	SDS-PAGE	LTQ	40	RP	5	7	3.5	35	40b	5,320	1,110	3.3
G2DC	SDS-PAGE	LCQ	40	SCX-RP	5	14	7	70	19	10,713	1,361	4.1

^aNo further sample purification for this method.

^bCalculated based on four replicates.