A Workflow for Quality Assessment, Quantitation and Statistical Inference of Targeted Proteomics Data using Skyline and Panorama

Skyline and Panorama are integral parts of our data analysis and management system for targeted mass spectrometry experiments. Implemented as a module on the Labkey Server bioinformatics platform, Panorama enables integration of a diverse set of tools such as R programming to create customized workflows. Taking advantage of this feature, we are developing a workflow for post-processing of targeted mass spectrometry Skyline files on the Panorama server. This workflow combines built-in Panorama features with custom R packages (e.g. TargetedMSQC and MSstats) to perform quality control, quantitation and statistical inference. These tests can be performed on Skyline files within Panorama to create a comprehensive and sharable report. This workflow will provide an efficient means for high-throughput analysis of targeted mass spectrometry data, and enable sharing of not only files and final results, but also the processing steps required to generate reports, thus bringing more transparency to the data processing pipeline.