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

Cheng Chang; Mansheng Li; Chaoping Guo; Yuqing Ding; Kaikun Xu; Mingfei Han; Fuchu He; Yunping Zhu

doi:10.1093/bioinformatics/bty727

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

Bioinformatics. 2019 Mar 1;35(5):898-900. doi: 10.1093/bioinformatics/bty727.

Authors

Cheng Chang¹, Mansheng Li¹, Chaoping Guo², Yuqing Ding², Kaikun Xu¹, Mingfei Han¹, Fuchu He¹, Yunping Zhu¹

Affiliations

¹ State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (Beijing), Beijing, Peoples Republic of China.
² Beijing Key Laboratory of Human Computer Interactions, Institute of Software Chinese, Academy of Sciences, Beijing, P.R. China.

Abstract

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Data Analysis
Peptides
Proteins
Proteomics*
Software*

Substances

Peptides
Proteins