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

Published in final edited form as: J Proteome Res. 2009 Mar;8(3):1415–1422. doi: 10.1021/pr800774h

Table 3.

Identifications Made in Analysis of a Yeast Lysate Digested with Either Lys-N or Trypsin Using an LTQ-Orbitrap and QSTAR Pulsar I

instrument	enzyme	unique peptides	FDR	proteins with prob >0.9	proteins with 2 or more unique peptides
QSTAR	Lys-N	1747	0.010	364	277
	Trypsin	1733	0.007	385	258
	Combined	3467	0.006	444	382
LTQ-Orbitrap	Lys-N	4653	0.006	1141	700
	Trypsin	6119	0.005	1404	902
	Combined	10696	0.006	1645	1161