Reverse phase protein array (RPPA) technology is an antibody-based high-throughput assay for protein profiling of biological specim​ens that allows for many measurements with very small amounts of cell lysate. Here, we report the sensitivity, reproducibility, and accuracy of a particular RPPA platform called Zeptosens. We customized the RPPA protocol for our in-house setup, and measured ​more t...

The SPOT(trade mark) technology for highly parallel synthesis of peptides on flat surfaces in array type format has evolved into a versatile toolbox for a variety of applications in proteomics such as mapping protein-protein interactions and profiling the substrate specificity of enzymes such as kinases and proteases. Originally developed for the synthesis of short overlapping peptide sequences...

Background Hydrolysates are complex media supplements composed of many as well as different types of compounds. Within Frieslandcampina Domo’s Quality by Design project, detailed information of these compounds (annotation and quantification) has been generated. This was achieved for soy protein hydrolysates (Proyield Soy SE50MAF-UF) using metabolomics biochemical profiling. Biochemical profilin...

Activity-based protein profiling has emerged as a valuable technology for labeling, enriching, and assessing protein activities from complex mixtures. This is primarily accomplished via a two-step identification and quantification process. Here we show a highly quantitative and streamlined method, termed catch-and-release activity profiling of enzymes (CAPE), which reduces this procedure to a s...

Phylogenetic profiling is a well established method for predicting functional relations and physical interactions between proteins. We present a new method for finding such relations based on phylogenetic profiling of conserved domains rather than proteins, avoiding computationally expensive all versus all sequence comparisons among genomes. The resulting domain interaction map (DIMA) can be ex...

The availability of complete genome sequences for a large number of pathogenic organisms has opened the door for large-scale proteomic studies to dissect both protein expression/regulation and function. This review highlights key proteomic methods including two-dimensional gel electrophoresis, reference mapping, protein expression profiling and recent advances in gel-free separation techniques ...

Emerging evidence suggests Jumonji domain-containing proteins are epigenetic regulators in diverse biological processes including cellular differentiation and proliferation. RNA interference-based analyses combined with gene expression profiling can effectively characterize the cellular functions of these enzymes. We found that the depletion of Jumonji domain-containing protein 6 (JMJD6) and it...