MSInspector is a Python program for quality evaluation of the five assay characterization experiments outlined by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) Assay Portal guidance document (https://proteomics.cancer.gov/sites/default/files/assay-characterization-guidance-document.pdf). The CPTAC Assay Portal is a public repository of fit-for-purpose multiplex quantitative mass-spectrometry based proteomic targeted assays.
Following the annotation of each experiment according to the Skyline templates (please refer to Assay Portal User Manual), MSInspector enables researchers to test their Skyline files for statistical calculation and data visualization through the built-in R scripts. The html report file describes the details of the errors and warnings from the data containing discrepancies and displays the statistical images and tables for the non-conflicting data. Please refer to the tutorial document (MSInspector_tutorial.pdf) to install and run MSInspector in Skyline.