A novel structural systems biology approach

In a collaboration with Boston University, we developed a new, faster approach in investigating the interactome using mass spectrometry and applied it to reveal and understand mechanisms that drive the malignant cell phenotype formation. This work resulted in two publications in Nature Communications.

In our first publication, we introduced a new multiplex Co-fractionation/Mass Spectrometry (mCF/MS) platform that is more technically efficient, cost-effective and faster than previously reported Co-fractionation/Mass Spectrometry (CF/MS) methods. The mCF/MS approach was applied to compare the global protein interactome of mammary epithelial cells to the Protein Interaction Network (PIN) of two breast cancer cell lines, where many multimolecular complexes that drive malignant cell formation were described and investigated.

In the second publication based on our work, we introduced PAMAF: a Parallelized multidimensional analytic framework that examines 12 modalities: protein abundance in whole-cells, nuclei, exosomes, secretomed and membranes; N-glycosylation, phosphorylation; metabolites; mRNA, miRNA; and, in parallel, single-cell transcriptomes. Using this method, we explored the key proteins in the process of Epithelial to Mesenchymal Transition.