Identification and relative expression of membrane proteins in breast cancer cell lines
EMSL Project ID
2625
Abstract
Overview Phase 1: Protein identification in the ?sub-proteome? mixtures from these cell lines will be accomplished using a combination of separation techniques, LC-ESI-MS/MS, and database search and denovo sequence interpretation of the resulting collision induced disassociation (CID) data. Aside from protein identification, the analysis of complex mixtures extracted from an initial 2 cell-lines will give an idea of: 1. the fractions associated with the highest degree of identification 2. the fractions associated with particular biological relevance (those associated with proteins previously implicated in cancer progression) 3. the proportion of our mixture that can be identified with some certainty 4. the probability can we identify a particular protein from a mixture. Phase 2 of the project involves metabolic labeling of cell lines in N14/N15 media to detect changes in relative protein abundance between 2 distinct cell systems using the high mass accuracy afforded by fourier transform ion cyclotron resonance (FTICR) MS. Relative abundance ratios for individual proteins are calculated by comparing total ion currents occurring among paired (peptide) ion peaks during the initial MS scan. Protein identification will occur using database search and denovo sequencing methods. The biological purposes of this project are: (1) to identify membrane proteins expressed in a subset of these breast cancer cell lines and (2) to quantify their relative expression. In pursuing these goals several informatics objectives include: (1) the systematic identification of proteins and their relative expression in a high-throughput manner (2) the creation of a compendium (database) of protein expression results for a subset of the SPORE panel that may be queried for common expression profiles. (3) comparisons of proteome expression to results from previous gene-expression (microarray) studies
Project Details
Project type
Exploratory Research
Start Date
2002-09-01
End Date
2005-09-04
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members
Related Publications
Patwardhan AJ, EF Strittmatter, DG Camp, RD Smith, and M Pallavicini. 2005. "Comparison of Normal and Breast Cancer Cell lines using Proteome, Genome and Interactome data." Journal of Proteome Research 4(6):1952-1960.