Characterization of the Mouse Brain Proteome Using Global Proteomic Analysis Complemented with Cysteinyl-Peptide Enrichment

Journal Article · Wed Feb 01 04:00:00 EST 2006 · Journal of Proteome Research, 5(2):361-369

DOI:https://doi.org/10.1021/pr0503681· OSTI ID:878665

Wang, Haixing H; Qian, Weijun; Chin, Mark H; Petyuk, Vladislav A; Barry, Richard C; Liu, Tao; Gritsenko, Marina A; Mottaz, Heather M; Moore, Ronald J; Camp, David G; Khan, Arshad H; Smith, Desmond; Smith, Richard D

Given the growing interest in applying genomic and proteomic approaches for studying the mammalian brain using mouse models, we hereby present for the first time a comprehensive characterization of the mouse brain proteome. Preparation of the whole brain sample incorporated a highly efficient cysteinyl-peptide enrichment (CPE) technique to complement a global enzymatic digestion method. Both the global and the cysteinyl-enriched peptide samples were analyzed by SCX fractionation coupled with reversed phase LC-MS/MS analysis. A total of 48,328 different peptides were confidently identified (>98% confidence level), covering 7792 non-redundant proteins (~34% of the predicted mouse proteome). 1564 and 1859 proteins were identified exclusively from the cysteinyl-peptide and the global peptide samples, respectively, corresponding to 25% and 31% improvements in proteome coverage compared to analysis of only the global peptide or cysteinyl-peptide samples. The identified proteins provide a broad representation of the mouse proteome with little bias evident due to protein pI, molecular weight, and/or cellular localization. Approximately 26% of the identified proteins with gene ontology (GO) annotations were membrane proteins, with 1447 proteins predicted to have transmembrane domains, and many of the membrane proteins were found to be involved in transport and cell signaling. The MS/MS spectrum count information for the identified proteins was used to provide a measure of relative protein abundances. The mouse brain peptide/protein database generated from this study represents the most comprehensive proteome coverage for the mammalian brain to date, and the basis for future quantitative brain proteomic studies using mouse models.

• Research Organization: Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
• Sponsoring Organization: USDOE
• DOE Contract Number: AC05-76RL01830
• OSTI ID: 878665
• Report Number(s): PNNL-SA-46752; 3567; 400412000
• Journal Information: Journal of Proteome Research, 5(2):361-369, Journal Name: Journal of Proteome Research, 5(2):361-369 Journal Issue: 2 Vol. 5
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
BRAIN
DIGESTION
Environmental Molecular Sciences Laboratory
FRACTIONATION
GENES
MEMBRANE PROTEINS
MOLECULAR WEIGHT
PEPTIDES
PROTEINS
TRANSPORT