Heron Data Suite: biomedical quantitative analysis applications for Skyline results files v1

This protocol describes the use of the Heron Data Suite application (https://www.herondata.app/). The Heron Data Suite simplifies the analysis of biomedical proteomics results processed in Skyline. Post-data processing, Heron Data organizes results and goes the extra mile to account for technical replicates. Heron Data contains two apps currently: Replicate Absolute Quantification (Heron Quant) and Glycopeptide Area Under the Curve (Heron Glyco). The purpose of Heron Quant is to further analyze 'Peptide Ratio Quantification' .csv exports from the open source proteomics tool Skyline (https://skyline.ms/project/home/software/Skyline/begin.view). Heron Quant improves the rigor and reproducibility of Skyline for biomedical proteomics purposes by averaging replicates of a single sample or standard and plots the averaged calibration curves and outputting concentration averages. Heron Quant will calculate the R-squared value and linear equations of the calibration curves, as well as the coefficient of variance and the standards deviation of replicates. Heron Glyco is designed specifically for analysis of glycopeptide area under the curve CSV files from Skyline. Heron Glyco will organize your Skyline AUC data by glycopeptide into separate worksheets, calculate the percent relative abundance of glycopeptide for each replicate, and plot the percent relative abundance in pie charts of all grouped glycopeptides in each sample. Heron Data Suite will receive future updates and new application additions. Need support? Contact us using the form on our website: https://www.herondata.app/contact