Web supplement to
B CELL PROTEOME DATABASE
Two-dimensional differential gel electrophoresis (2D-DIGE) and mass spectrometry (MS) based quantitative proteomics were used to study differential protein abundance in various B cell types during B cell maturation. Differential protein expression was studied in eight human cell lines representing various maturation stages from early pre-B cell until terminally differentiated plasma cell (see Supplementary Table 1). Further, B cell antigen receptor (BCR) activation induced proteome profiles were studied in anti-IgM stimulated Ramos cells in a time series. At each maturation stage, expression of proteins affects the commitment to move to the next stage and cellular functions, such as rearrangement and expression of Ig genes. Defects in genes and proteins important for B cell maturation cause primary immunodeficiencies (see IDbase). We have previously studied B cell maturation in anti-IgM stimulated Ramos dataset using traditional two-dimensional gel electrophoresis (2DE) and MS based proteomics (Salonen, J. M., Valmu, L., Rönnholm, G., Kalkkinen, N., Vihinen, M., Proteome analysis of B-cell maturation. Proteomics 2006, 6, 5152-5168 Linkki juttuun tai ainakin Pubmediin). To view our previous 2DE proteomic results, click on Proteome analysis of B cell maturation. To view the latest results, click on 2D-DIGE analysis of B cell maturation.
In the 2D-DIGE method three protein samples differentially labeled with Cy3-, Cy5- and Cy2-dyes can be separated on the same gel. Double image overlays highlight the differences between two samples labeled with Cy3 and Cy5. Triple image overlays enable easy visual comparison between the two samples (labeled with Cy3 and Cy5) in relative to internal standard (Stnd) labeled with Cy2 and run on the same gel. The Stnd is a pooled protein sample prepared by combining protein extracts from the different B cell lines included in the experiment. Here you can compare interactive 2D-DIGE images representing B cell proteomes for different maturation stages. 2063 protein spots across the eight cell lines were clustered on the basis of the relative average protein abundance (see Supplementary Figure 1). Bioinformatic analysis of the proteomic phenotypes revealed shared Gene Ontology (GO) terms and signaling pathways within the clusters of co-expressed proteins (see Tables 1-2). To view all identified proteins (listed in Supplementary Table 2) click on the Reference gel.
Table 1. Enriched GO terms and their p-values for co-expressed proteins
Table 2. Signalling pathways and identified proteins involved.
Supplementary Table 1: Investigated B cell lines
Supplementary Table 2: Proteins in the B cell proteome database