New manuscript accepted
Utilisation and evaluation of CHO-specific sequence databases for mass spectrometry based proteomics
Paula Meleady, Raimund Hoffrogge, Michael Henry, Oliver Rupp, Juan Hernandez Bort, Colin Clarke, Karina Brinkrolf, Shane Kelly, Benjamin Müller, Padraig Doolan, Matthias Hackl, Tim Frederik Beckmann, Thomas Noll, Johannes Grillari, Niall Barron, Alf Pühler, Martin Clynes, Nicole Borth
Biotechnology & Bioengineering, accepted
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 paper we demonstrate the utilisation of CHO specific sequence information to improve mass spectrometry (MS) based proteomic identification. The use of various CHO specific databases increased the 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 unravelling the CHO proteome.