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.

Original languageEnglish (US)
Title of host publication2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011
Pages982-984
Number of pages3
DOIs
StatePublished - Dec 1 2011
Event2011 IEEE International Conference onBioinformatics and Biomedicine Workshops, BIBMW 2011 - Atlanta, GA, United States
Duration: Nov 12 2011Nov 15 2011

Publication series

Name2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011

Other

Other2011 IEEE International Conference onBioinformatics and Biomedicine Workshops, BIBMW 2011
CountryUnited States
CityAtlanta, GA
Period11/12/1111/15/11

Fingerprint

Tandem Mass Spectrometry
Neuropeptides
Mass spectrometry
Peptides
Amino acids
Proteins
Amino Acids
Post Translational Protein Processing
Ammonia
Databases
Ions
Water
Processing
Chemical analysis
Experiments

Keywords

  • mass spectrometry
  • neuropeptides
  • search algorithms
  • simulation

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics
  • Health Information Management

Cite this

Akhtar, M. N., Southey, B. R., Porter, K. I., Sweedler, J. V., & Rodriguez-Zas, S. L. (2011). Comparison of tandem mass spectrometry search methods to identify neuropeptides. In 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011 (pp. 982-984). [6112530] (2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011). https://doi.org/10.1109/BIBMW.2011.6112530

Comparison of tandem mass spectrometry search methods to identify neuropeptides. / Akhtar, M. N.; Southey, B. R.; Porter, K. I.; Sweedler, Jonathan V; Rodriguez-Zas, Sandra Luisa.

2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011. 2011. p. 982-984 6112530 (2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Akhtar, MN, Southey, BR, Porter, KI, Sweedler, JV & Rodriguez-Zas, SL 2011, Comparison of tandem mass spectrometry search methods to identify neuropeptides. in 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011., 6112530, 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011, pp. 982-984, 2011 IEEE International Conference onBioinformatics and Biomedicine Workshops, BIBMW 2011, Atlanta, GA, United States, 11/12/11. https://doi.org/10.1109/BIBMW.2011.6112530
Akhtar MN, Southey BR, Porter KI, Sweedler JV, Rodriguez-Zas SL. Comparison of tandem mass spectrometry search methods to identify neuropeptides. In 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011. 2011. p. 982-984. 6112530. (2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011). https://doi.org/10.1109/BIBMW.2011.6112530
Akhtar, M. N. ; Southey, B. R. ; Porter, K. I. ; Sweedler, Jonathan V ; Rodriguez-Zas, Sandra Luisa. / Comparison of tandem mass spectrometry search methods to identify neuropeptides. 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011. 2011. pp. 982-984 (2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011).
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