Abstract
Here we present a free interactive web tool to process and visualize proteomics data sets with a single click. GiaPronto can process all proteomics quantification methods, i.e. label-free, SILAC and isobaric labeling, and analyze post-translational modifications (PTMs). The software performs normalization and statistics, assists determination of regulated proteins, biomarkers and Gene Ontology (GO) enrichment, and provides high resolution images and tables for further data analysis. We foresee that GiaPronto will become the most rapid and simple tool for assessing data quality and determining most relevant features of proteomic data sets. GiaPronto is available at giapronto.diskinlab.org.
Highlights
Even though MS based proteomics is versatile, most projects are peptide centric, i.e. bottom-up, because of its relatively simpler workflow, higher sensitivity and higher robustness than the other strategies
The quantification method is not as uniform, as the convenience of one method or the other may vary upon type of sample, number of samples and availability of reagents
We present GiaPronto, a software developed in Shiny (4) that uses a protein and/or a post-translational modifications (PTMs) table as input file to process data and plot a variety of common and less common graphs for the analysis of proteomics data sets
Summary
Even though MS based proteomics is versatile, most projects are peptide centric, i.e. bottom-up, because of its relatively simpler workflow, higher sensitivity and higher robustness than the other strategies. The quantification method is not as uniform, as the convenience of one method or the other may vary upon type of sample, number of samples and availability of reagents. Label-free strategies do not require additional labeling steps and maintain a more linear dynamic range of quantifications (3). We present GiaPronto, a software developed in Shiny (4) that uses a protein and/or a PTM table as input file to process data and plot a variety of common and less common graphs for the analysis of proteomics data sets. As compared with existing software that provide excellent support for proteomics data analysis, e.g. Perseus (5), GiaPronto is fully automated and provides both quality control and biological interpretation of protein and PTM level data.
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