Dattatreya Mellacheruvu

TL;DR: The contaminant repository for affinity purification (the CRAPome) is presented and its use for scoring protein-protein interactions is described and aggregating negative controls from multiple AP-MS studies can increase coverage and improve the characterization of background associated with a given experimental protocol.

TL;DR: A fragment-ion indexing method, and its implementation in peptide identification tool MSFragger, that enables a more than 100-fold improvement in speed over most existing proteome database search tools.

TL;DR: 'Significance analysis of interactome' (SAINT), a computational tool that assigns confidence scores to protein-protein interaction data generated using affinity purification–mass spectrometry (AP-MS), is presented.

TL;DR: The Philosopher toolkit integrates high-performance algorithms and existing tools and is a dependency-free, fast and comprehensive proteomics pipeline, able to rapidly process even the most complex proteomics datasets with efficient resource management.

TL;DR: It is demonstrated that the mixed-lineage leukemia protein (MLL) complex, a well-known driver of MLL fusion–positive leukemia, acts as a co-activator of AR signaling, and is identified as a potential therapeutic target in advanced prostate cancer.