Spotlite: A web server for predicting co-complexed proteins from affinity purification – mass spectrometry data

Spotlite is a user-friendly web application for predicting complex co-membership from affinity purification - mass spectrometry data. This web application employs a logistic regression classifier that integrates existing, proven APMS scoring approaches (SAINT, CompPASS, and HGSCore), gene co-expression patterns, functional annotations, domain-domain binding affinity, and homologous interactions, which we have shown outperforms existing APMS scoring methods. Spotlite can be access here.


MSAcquisitionSimulator: data-dependent acquisition simulator for LC-MS shotgun proteomics

MSAcquisitionSimulator is a collection of three command-line tools written in C++ that simulate ground truth LC-MS data and the subsequent application of custom data-dependent acquisition (DDA) algorithms. It provides an opportunity for researchers to test, refine, and evaluate novel DDA algorithms prior to implementation on a mass spectrometer. The project and source code is hosted on GitHub.