Comparison of tandem mass spectrometry search methods to identify neuropeptides

Abstract

Tools to identify proteins in tandem mass spectrometry experiments are not optimized to identify neuropeptides due to complex processing, post-translational modifications and neuropeptide size. The complementary strengths of three widely-used protein identification tools to identify neuropeptides were assessed. OMSSA, X!Tandem and Crux were applied to identify simulated mass spectra on a database of 7857 mouse neuropeptides from 92 prohormones. For each peptide, spectra was simulated with either +1, +2 and +3 precursor charge states, +1 charged b and y product ions having single water and/or ammonia loss depending on amino acid composition. OMSSA and X!Tandem identified 83% of the peptides with an E-value or P-value < 10−9, while Crux detected 81% and 11% of the peptides with a P-value < 10−1 and < 10−2, respectively. Precursor charge states have minor effect on the detection of neuropeptides. The sensitivity of either tool to detect small neuropeptides (< 10 amino acids in length) was limited. Our results suggest that methods optimized to detect neuropeptides are required.