Proteomics Methods
Dr. Rui Branca

In our group, we are developing and applying mass spectrometry (MS)-based methods with an aim to improve human proteome analysis. We have developed a prefractionation method known as high-resolution peptide isoelectric focusing (HiRIEF) (Branca, Nature Methods 2014). This method allows reproducible fractionation leading to a reduction of sample complexity prior to MS-analysis. This improves analytical depth, increases peptide and protein sequence coverage, improves overlap of detected peptides and proteins between samples, and provides an additional data point to each peptide, the peptide isoelectric point, allowing novel applications. One such novel application is using MS-data in an unbiased genome-wide search for protein coding DNA sequences in the human genome (proteogenomics) (Branca, Nature Methods 2014; Boekel Nature Biotechnology 2015). We are also developing methods to improve tissue and plasma proteome analysis, detection and quantification of post-translational modifications (most notably phosphorylations, glycosylations, and redox related cysteine modifications), and targeted analysis of proteins. To interpret the vast amounts of information generated by proteomics technologies, we are actively working on development and use of bioinformatics tools. We have recently developed novel tools for splice variant specific quantification at protein level (Zhu, Mol. Cell. Prot. 2014), a galaxy based proteogenomics pipeline (Boekel, Nature Biotechnology), and methods to improve quantification accuracy in proteomics (Forshed, Mol. Cell. Prot. 2011; Hultin-Rosenberg Mol. Cell. Prot. 2013; Sandberg J. Proteomics 2014).