Table 3.

Results from MS searching with the original Ensembl protein database and the reduced database

Sample	RNA-Seq reads	Mass spectra	Original database		Reduced database
			# entries	Peptide IDs*	# entries	Peptide IDs*	% increase
Jurkat human cells	80 M	500 K	104,310	73,123	82,101	73,436	0.4
B6 mouse islets	94 M	250 K	52,165	30,212	18,052	30,220	0.3
CAST mouse islets	126 M	250 K	52,165	28,902	16,940	28,823	0.2

*peptide passing a 1% FDR.