Quercus ilex: Protein Identification Strategies for an Orphan Tree Species

摘要

Substitution-tolerant database searching is a viable tool for shotgun protein identification from partially sequenced organisms. In combination with a GeLC/MS/MS workflow and high resolution mass spectrometry, ～1200 proteins and >7000 distinct peptides could be identified from Quercus ilex leaves at 1% False Discovery Rate. Including amino acid substitutions identified significantly more peptide sequences, but did not significantly impact the number of identified proteins, indicating that the gain in sequence information may be partially offset by the larger search space which would increase False Discovery Rates. The Quercus ilex genome has recently been sequenced. The data is currently being translated into an annotated protein sequence database. Protein identifications obtained against this database will be compared against results obtained by the presented approach to improve the quality of the genome annotation.