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Table 3 Results from MS searching with the original Ensembl protein database and the reduced database

From: Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations

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

  1. *peptide passing a 1% FDR.