PNNL

Abstract

Over the last five years proteogenomics has emerged as a promising approach to identifying cleavable N-terminal signals in a high-throughput manner. To establish the potential and limitation of proteogenomics, we present here the analysis of signal peptides discovered with the help of protegenomics in Escherichia coli K12, the classical bacterial model organism. We demonstrate that after appropriate filtering more than 90% of N-terminal cleaved sequences represent signal peptides. In a single run proteogenomics recovered one third of all signal peptides that have been experimentally confirmed during the past three decades. Although E. coli is the most extensively studied bacterium, proteogenomics reported at least thirty signal peptides not known before. Based on a comparison of proteogenomics data with the wealth of experimentally verified and predicted signal peptides, we argue here that the percentage of proteins containing signal peptides in gram-negative bacteria is in the order of 10%, much lower than reported before.