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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.
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