SuperQuant: a Data Processing Approach to Increase Quantitative Proteome Coverage

SuperQuant is a quantitative proteomics data processing workflow that utilizes fragment ion complementarity to identify multiple co-isolated peptides in tandem mass spectra. Parent ion and label-free quantification method are supported. The performance of the developed approach was tested using dimethyl labeled HeLa lysate sample having artificially created ratio between channels (10(heavy):4(medium):1(light)). Developed software is implemented as a processing node to Thermo Proteome Discoverer 2.x and freely available for the community at https://github.com/caetera/SuperQuantNode.