Protein array
TCPA v3.0: An Integrative Platform to Explore the Pan-Cancer Analysis of Functional Proteomic DataReverse-phase protein arrays represent a powerful functional proteomics approach. Using this platform, we have characterized ∼8,000 patient samples of 32 cancer types through The Cancer Genome Atlas and built a widely used, open-access bioinformatic resource, The Cancer Proteome Atlas (TCPA). Here we have developed a new module called “TCGA Pan-Cancer Analysis,” which provides comprehensive protein-centric, pan-cancer analyses in rich context of TCGA data. This upgraded TCPA (v3.0) provides a more valuable tool for studying functional proteomics and making translational impacts.
Proteome-wide Tyrosine Phosphorylation Analysis Reveals Dysregulated Signaling Pathways in Ovarian TumorsA systematic, multiplexed approach interrogating enzyme-substrate relationships in context of PTMs is fundamental in understanding the dynamics of these pathways in disease processes. Multiplexed PTM reactions on HuProt arrays were developed and applied to 102 TCGA ovarian tumor samples. Data integration and networks analysis led to the prediction that 19 tyrosine kinases were elevated and potentially responsible for the dysregulated pTyr signaling pathways in ovarian tumors. Elevated kinase activities of PTK2 and PTK2B were confirmed in several ovarian cancer cell lines.
Deciphering Protein Glycosylation by Computational Integration of On-chip Profiling, Glycan-array Data, and Mass SpectrometryA new method is presented to decipher information about the isomeric variants of the glycans attached to purified proteins. The method takes advantage of the specificities of glycosidases and lectins, combined with computational integration of the data with information from glycan arrays and mass spectrometry. The application to microspots of proteins makes it compatible with analyzing low-abundance proteins, providing the potential for studying proteins derived from clinical specimens.