Seeking Effective Combinations of Library Search Methods for Peptide Id: A Study using two Enzymes, three Concentrations and four Methods.

摘要

The key to mass-spectrometry-based proteomics is peptide identification. The major challenge in peptide identification using library search methods is to better attain noise reduction to result in more confident identifications. Because the noise in a spectrum depends on experimental conditions, the instrument used, it cannot be predicted even if the peptide sequence is known. Therefore, different library search methods might be optimized for different conditions and might be complementary to one another when properly combined. To examine whether it is possible to combine different search methods to enhance the accuracy and coverage of peptide identifications, we perform a quantitative study using two enzymes (Trypsin and Glu C), at three different molar concentrations, and using four different library search methods.