PANDA: A comprehensive and flexible tool for quantitative proteomics data analysis.

SUMMARY: As the experiment techniques and strategies in quantitative proteomics are improving rapidly, the corresponding algorithms and tools for protein quantification with high accuracy and precision are continuously required to be proposed. Here, we present a comprehensive and flexible tool named PANDA for proteomics data quantification. PANDA, which supports both label-free and labeled quantifications, is compatible with existing peptide identification tools and pipelines with considerable flexibility. Compared with MaxQuant on several complex datasets, PANDA was proved to be more accurate and precise with less computation time. Additionally, PANDA is an easy-to-use desktop application tool with user-friendly interfaces. AVAILABILITY AND IMPLEMENTATION: PANDA is freely available for download at https://sourceforge.net/projects/panda-tools/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PANDA-view: an easy-to-use tool for statistical analysis and visualization of quantitative proteomics data.

Summary: Compared with the numerous software tools developed for identification and quantification of -omics data, there remains a lack of suitable tools for both downstream analysis and data visualization. To help researchers better understand the biological meanings in their -omics data, we present an easy-to-use tool, named PANDA-view, for both statistical analysis and visualization of quantitative proteomics data and other -omics data. PANDA-view contains various kinds of analysis methods such as normalization, missing value imputation, statistical tests, clustering and principal component analysis, as well as the most commonly-used data visualization methods including an interactive volcano plot. Additionally, it provides user-friendly interfaces for protein-peptide-spectrum representation of the quantitative proteomics data. Availability and implementation: PANDA-view is freely available at https://sourceforge.net/projects/panda-view/. Supplementary information: Supplementary data are available at Bioinformatics online.