Limelight: An Open, Web-Based Tool for Visualizing, Sharing, and Analyzing Mass Spectrometry Data from DDA Pipelines

Liquid chromatography-tandem mass spectrometry employing data-dependent acquisition (DDA) is a mature, widely used proteomics technique routinely applied to proteome profiling, protein-protein interaction studies, biomarker discovery, and protein modification analysis. Numerous tools exist for searching DDA data and myriad file formats are output as results. While some search and post processing tools include data visualization features to aid biological interpretation, they are often limited or tied to specific software pipelines. This restricts the accessibility, sharing and interpretation of data, and hinders comparison of results between different software pipelines. We developed Limelight, an easy-to-use, open-source, freely available tool that provides data sharing, analysis and visualization and is not tied to any specific software pipeline. Limelight is a data visualization tool specifically designed to provide access to the whole "data stack", from raw and annotated scan data to peptide-spectrum matches, quality control, peptides, proteins, and modifications. Limelight is designed from the ground up for sharing and collaboration and to support data from any DDA workflow. We provide tools to import data from many widely used open-mass and closed-mass search software workflows. Limelight helps maximize the utility of data by providing an easy-to-use interface for finding and interpreting data, all using the native scores from respective workflows.