INKA, an integrative analysis pipeline for inference of hyperactive phosphokinases in mass spectrometry-based phosphoproteomics data: CRC Organoids

CRC Organoid and corresponding PDX data are part of a larger project that includes proteomeXchange accessions PXD006616, PXD008032, and PXD009995. We present a computational pipeline called Integrative Inferred Kinase Activity (INKA) scoring that integrates the observed abundance of phosphopeptides derived from (i) kinases as a whole, (ii) their kinase activation loop segments, (iii) proteins deduced to be kinase substrates based on prior experimental knowledge of kinase-substrate relationships, and/or (iv) kinase substrates predicted by the sequence motif- and network-based NetworKIN algorithm.