Comparative phosphoproteome analysis reveals more ERK activation in MDA-MB-231 than in MCF-7

Protein phosphorylation forms the foundation of many intra-cellular signaling networks. Enrichment is very important to analyze phosphoproteins due to their low abundance in cells. We used TiO2 enrichment and LC–MS/MS to identify phosphopeptides from two breast cancer cells, MCF-7 and MDA-MB-231. The dataset generated were searched using Sequest algorithm with 1% false discovery rate. It was observed that 234 phosphoproteins and 280 phosphopeptides were common from a total of 590 and 455 phosphoproteins and 802 and 599 non-redundant phosphopeptides identified from MCF-7 and MDA-MB-231, respectively. Besides, a total of 843 and 578 non-redundant phosphorylation sites were also identified from these two cell lines. ERK1/ERK2 kinase substrate motif (PX[S/T]#P) was identified in MDA-MB-231 but not in MCF-7, showing that this kinase signal transduction pathway is a key factor during breast cancer progression. Activation of ERK1/ERK2 in MDA-MB-231 was further confirmed by Western blot. Quantitative analysis by spectral counting revealed 31 phosphoproteins were statistically in different levels between the two cells lines. This difference is due to the differences in kinase activities as well as protein expression levels. Since breast cancer research makes extensive use of both of these cell lines, our study's findings will be of value in understanding phosphorylation signal of breast cancer.

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► We analyzed phosphoproteome from two breast cancer cell lines MCF-7 and MDA-MB-231 by mass spectrometry.
► ERK1/ERK2 kinase substrate motif is enriched in MDA-MB-231 compared to MCF-7.
► Differences in phosphoprotein level between MCF-7 and MDA-MB-231 reflect differences in kinase activities as well as protein expression levels.
► Our findings are valuable in breast cancer research due to the wide use of MCF-7 and MDA-MB-231.