title: Utilization and evaluation of CHO-specific sequence databases for mass spectrometry based proteomics.
abstract: Recently released sequence information on Chinese hamster ovary (CHO) cells promises to not only facilitate our understanding of these industrially important cell factories through direct analysis of the sequence, but also to enhance existing methodologies and allow new tools to be developed. In this article we demonstrate the utilization of CHO specific sequence information to improve mass spectrometry (MS) based proteomic identification. The use of various CHO specific databases enabled the identification of 282 additional proteins, thus increasing the total number of identified proteins by 40-50%, depending on the sample source and methods used. In addition, a considerable portion of those proteins that were identified previously based on inter-species sequence homology were now identified by a larger number of peptides matched, thus increasing the confidence of identification. The new sequence information offers improved interpretation of proteomic analyses and will, in the years to come, prove vital to unraveling the CHO proteome.
authors.affiliation: National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland. paula.meleady@dcu.ie
authors.forename: Paula
authors.initials: P
authors.lastname: Meleady
authors.forename: Raimund
authors.initials: R
authors.lastname: Hoffrogge
authors.forename: Michael
authors.initials: M
authors.lastname: Henry
authors.forename: Oliver
authors.initials: O
authors.lastname: Rupp
authors.forename: Juan Hernandez
authors.initials: JH
authors.lastname: Bort
authors.forename: Colin
authors.initials: C
authors.lastname: Clarke
authors.forename: Karina
authors.initials: K
authors.lastname: Brinkrolf
authors.forename: Shane
authors.initials: S
authors.lastname: Kelly
authors.forename: Benjamin
authors.initials: B
authors.lastname: Müller
authors.forename: Padraig
authors.initials: P
authors.lastname: Doolan
authors.forename: Matthias
authors.initials: M
authors.lastname: Hackl
authors.forename: Tim Frederik
authors.initials: TF
authors.lastname: Beckmann
authors.forename: Thomas
authors.initials: T
authors.lastname: Noll
authors.forename: Johannes
authors.initials: J
authors.lastname: Grillari
authors.forename: Niall
authors.initials: N
authors.lastname: Barron
authors.forename: Alf
authors.initials: A
authors.lastname: Pühler
authors.forename: Martin
authors.initials: M
authors.lastname: Clynes
authors.forename: Nicole
authors.initials: N
authors.lastname: Borth
mesh_terms: D000818:Animals; D016466:CHO Cells; D019295:Computational Biology; D006224:Cricetinae; D003412:Cricetulus; D004847:Epithelial Cells / Q000737:chemistry*; D013058:Mass Spectrometry / Q000379:methods*; D040901:Proteomics