@inproceedings{7f27b3c62d184eceb193d5a9ea192911,
title = "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.",
keywords = "mass spectrometry, neuropeptides, search algorithms, simulation",
author = "Akhtar, {M. N.} and Southey, {B. R.} and Porter, {K. I.} and Sweedler, {J. V.} and Rodriguez-Zas, {S. L.}",
year = "2011",
doi = "10.1109/BIBMW.2011.6112530",
language = "English (US)",
isbn = "9781457716133",
series = "2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011",
pages = "982--984",
booktitle = "2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011",
note = "2011 IEEE International Conference onBioinformatics and Biomedicine Workshops, BIBMW 2011 ; Conference date: 12-11-2011 Through 15-11-2011",
}