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Pipeline publication

[…] ospray. Quantification experiments were performed using a scheduled LC-MRM mode with MRM detection window of 480 s and cycle time of 1.5 s. Before analysis, samples were spiked with 400 fmol of digested E. coli β-galactosidase (#4465938, SCIEX). Skyline was used to generate extracted ion chromatograms (XICs) of target peptides. Then, peak areas (MRM signals) of XICs were normalized against the geometric mean of the peak areas of two β-galactosidase peptides (FNDDFSR and LNVENPK)., ESP Predictor (http://www.broadinstitute.org/cancer/software/genepattern/esppredictor) was used to predict ionization efficiency of STaLPIR peptides during mass spectrometry. For functional annotation of proteins, DAVID (Database for Annotation, Visualization and Integrated Discovery, http://david.abcc.ncifcrf.gov/) was used (Huang da et al. 2009). Functional annotation charts were generated using each of the following GO terms: Biological Process, Molecular Function, Cellular Component, Uniprot Sequence Feature, and Protein Information Resource. Results were considered significant at P-value < 0.05 and visualized by the Enrichment Map plugin Cytoscape., How to cite this article: Yeom, J. et al. A proteogenomic approach for protein-level evidence of genomic variants in cancer cells. Sci. Rep. 6, 35305; doi: 10.1038/srep35305 (2016)., The study was supported by grants from the National Research Foundation (Multi-omics program: 2012M3A9B9036679; Next-Generation Applied Omics program: 2013M3A9B6076415) funded by the Korean Ministry of Science, ICT and Future Planning, and a grant from the Korea Health Industry Development Institute (Research Hospital program: HI14C3484) funded by the Korean Ministry of Health & Welfare. The study was also supported by an intramural program of the Korea Institute of Science and Technology. We exp […]

Pipeline specifications

Software tools DAVID, Enrichment Map, Cytoscape