Abstract

The subject of this study was to evaluate the impact of dynamic exclusion and protein size on the capability of database search programs to identify protein in tandem mass spectrometry (MS/MS) experiments. Through the two stages of mass fragmentation, MS/MS spectrometry allows for an identification of peptides. Furthermore, the identification of proteins is heightened with the use of dynamic exclusion and fractionation. This bioinformatics study was applied to mass spectra from the brain macrophages of healthy wild type mice and mice exposed to an infection. The database search software PEAKS was used to identify peptides and proteins across protein sizes (fractionations) and exclusion options. Parameter specifications to optimize the identification of proteins and peptides were: parent mass error tolerance (15.0 Da) and fragment mass error tolerance (0.1 Da) specifications. After analysis, proteins such as Beta-globin (A8DUK40) and Actin cytoplasmic 1 (ACTB) were identified.

Original languageEnglish (US)
Title of host publicationProceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014
PublisherInternational Society for Computers and Their Applications
Pages93-96
Number of pages4
ISBN (Print)9781632665140
StatePublished - Jan 1 2014
Event6th International Conference on Bioinformatics and Computational Biology, BICOB 2014 - Las Vegas, NV, United States
Duration: Mar 24 2014Mar 26 2014

Publication series

NameProceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014

Other

Other6th International Conference on Bioinformatics and Computational Biology, BICOB 2014
CountryUnited States
CityLas Vegas, NV
Period3/24/143/26/14

Fingerprint

Fractionation
Proteomics
Proteins
Peptides
Databases
Specifications
beta-Globins
Macrophages
Bioinformatics
Tandem Mass Spectrometry
Computational Biology
Spectrometry
Mass spectrometry
Actins
Brain
Spectrum Analysis
Software
Infection
Experiments

ASJC Scopus subject areas

  • Information Systems
  • Health Informatics

Cite this

Zavala, C., Nixon, S., Southey, B. R., Wu, C., Romanova, E. V., Sweedler, J. V., & Rodriguez-Zas, S. L. (2014). Understanding the impact of fractionation and dynamic exclusion on proteomics. In Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014 (pp. 93-96). (Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014). International Society for Computers and Their Applications.

Understanding the impact of fractionation and dynamic exclusion on proteomics. / Zavala, Cynthia; Nixon, Scott; Southey, Bruce R.; Wu, Cong; Romanova, Elena Vikentievna; Sweedler, Jonathan V; Rodriguez-Zas, Sandra Luisa.

Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014. International Society for Computers and Their Applications, 2014. p. 93-96 (Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014).

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

Zavala, C, Nixon, S, Southey, BR, Wu, C, Romanova, EV, Sweedler, JV & Rodriguez-Zas, SL 2014, Understanding the impact of fractionation and dynamic exclusion on proteomics. in Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014. Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014, International Society for Computers and Their Applications, pp. 93-96, 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014, Las Vegas, NV, United States, 3/24/14.
Zavala C, Nixon S, Southey BR, Wu C, Romanova EV, Sweedler JV et al. Understanding the impact of fractionation and dynamic exclusion on proteomics. In Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014. International Society for Computers and Their Applications. 2014. p. 93-96. (Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014).
Zavala, Cynthia ; Nixon, Scott ; Southey, Bruce R. ; Wu, Cong ; Romanova, Elena Vikentievna ; Sweedler, Jonathan V ; Rodriguez-Zas, Sandra Luisa. / Understanding the impact of fractionation and dynamic exclusion on proteomics. Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014. International Society for Computers and Their Applications, 2014. pp. 93-96 (Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014).
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