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Utilization and evaluation of CHO‐specific sequence databases for mass spectrometry based proteomics
Author(s) -
Meleady Paula,
Hoffrogge Raimund,
Henry Michael,
Rupp Oliver,
Bort Juan Hernandez,
Clarke Colin,
Brinkrolf Karina,
Kelly Shane,
Müller Benjamin,
Doolan Padraig,
Hackl Matthias,
Beckmann Tim Frederik,
Noll Thomas,
Grillari Johannes,
Barron Niall,
Pühler Alf,
Clynes Martin,
Borth Nicole
Publication year - 2012
Publication title -
biotechnology and bioengineering
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.136
H-Index - 189
eISSN - 1097-0290
pISSN - 0006-3592
DOI - 10.1002/bit.24476
Subject(s) - chinese hamster ovary cell , proteome , proteomics , computational biology , mass spectrometry , sequence database , sequence (biology) , protein sequencing , identification (biology) , isobaric labeling , biology , peptide sequence , database , bioinformatics , chemistry , tandem mass spectrometry , computer science , biochemistry , genetics , chromatography , protein mass spectrometry , cell culture , gene , botany
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. Biotechnol. Bioeng. 2012; 109:1386–1394. © 2012 Wiley Periodicals, Inc.