Proteome profile of the MCF7 cancer cell line: a mass spectrometric evaluation

Autor: Iulia M. Lazar, Jung H. Yoon, Hetal Sarvaiya
Rok vydání: 2006
Předmět:
Zdroj: Rapid Communications in Mass Spectrometry. 20:3039-3055
ISSN: 1097-0231
0951-4198
DOI: 10.1002/rcm.2677
Popis: The development of novel proteomic technologies that will enable the discovery of disease specific biomarkers is essential in the clinical setting to facilitate early diagnosis and increase survivability rates. We are reporting a shotgun two-dimensional (2D) strong cationic exchange/reversed-phase liquid chromatography/electrospray ionization tandem mass spectrometry (SCX/RPLC/ESI-MS/MS) protocol for the analysis of proteomic constituents in cancerous cells. The MCF7 breast cancer cell line was chosen as a model system. A series of optimization steps were performed to improve the LC/MS experimental setup, sample preparation, data acquisition and database search protocols, and a data filtering strategy was developed to enable confident identification of a large number of proteins and potential biomarkers. This research has resulted in the identification of2000 proteins using multiple filtering and p-value sorting. Approximately 1600-1900 proteins had p0.001, and, of these, approximately 60% were matched byor=2 unique peptides. Alternatively,99% of the proteins identified byor=2 unique peptides had p0.001. When searching the data against a reversed database of proteins, the rate of false positive identifications was 0.1% at the peptide level and 0.4% at the protein level. The typical reproducibility in detecting overlapping proteins across replicate runs exceeded 90% for proteins matched byor=2 unique peptides. According to their biological function, approximately 200 proteins were involved in cancer-relevant cellular processes, and over 25 proteins were previously described in the literature as putative cancer biomarkers, as they were found to be differentially expressed between normal and cancerous cell states. Among these, biomarkers such PCNA, cathepsin D, E-cadherin, 14-3-3-sigma, antigen Ki-67, TP53RK, and calreticulin were identified. These data were generated by subjecting to MS analysis approximately 42 microg of sample, analyzing 16 SCX peptide fractions, and interpreting approximately 55,000 MS2 spectra. Total MS time required for analysis was 40 h.
Databáze: OpenAIRE
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