Introducing the CPL/MUW proteome database: interpretation of human liver and liver cancer proteome profiles by referring to isolated primary cells.
Interpretation of proteome data with a focus on biomarker discovery largely relies on comparative proteome analyses. Here, we introduce a database-assisted interpretation strategy based on proteome profiles of primary cells. Both 2-D-PAGE and shotgun proteomics are applied. We obtain high data concordance with these two different techniques. When applying mass analysis of tryptic spot digests from 2-D gels of cytoplasmic fractions, we typically identify several hundred proteins. Using the same protein fractions, we usually identify more than thousand proteins by shotgun proteomics. The data consistency obtained when comparing these independent data sets exceeds 99% of the proteins identified in the 2-D gels. Many characteristic differences in protein expression of different cells can thus be independently confirmed. Our self-designed SQL database (CPL/MUW - database of the Clinical Proteomics Laboratories at the Medical University of Vienna accessible via www.meduniwien.ac.at/proteomics/database) facilitates (i) quality management of protein identification data, which are based on MS, (ii) the detection of cell type-specific proteins and (iii) of molecular signatures of specific functional cell states. Here, we demonstrate, how the interpretation of proteome profiles obtained from human liver tissue and hepatocellular carcinoma tissue is assisted by the Clinical Proteomics Laboratories at the Medical University of Vienna-database. Therefore, we suggest that the use of reference experiments supported by a tailored database may substantially facilitate data interpretation of proteome profiling experiments.
Wimmer
Helge
H
Section Biomedical Laboratory Science, FH Campus Wien, Vienna, Austria.
Gundacker
Nina C
NC
Griss
Johannes
J
Haudek
Verena J
VJ
Stättner
Stefan
S
Mohr
Thomas
T
Zwickl
Hannes
H
Paulitschke
Verena
V
Baron
David M
DM
Trittner
Wolfgang
W
Kubicek
Markus
M
Bayer
Editha
E
Slany
Astrid
A
Gerner
Christopher
C
D022126:Access to Information; D015415:Biomarkers / Q000032:analysis; D003628:Database Management Systems; D030562:Databases, Protein; D015180:Electrophoresis, Gel, Two-Dimensional; D042783:Endothelial Cells / Q000378:metabolism; D006651:Histocytochemistry; D006801:Humans; D016247:Information Storage and Retrieval; D007728:Kupffer Cells / Q000378:metabolism; D008099:Liver / Q000378:metabolism*; D008113:Liver Neoplasms / Q000378:metabolism*; D010449:Peptide Mapping; D020543:Proteome / Q000032:analysis*; D040901:Proteomics / Q000379:methods*; D011786:Quality Control; D014584:User-Computer Interface
D015415:Biomarkers; D020543:Proteome