ArticleBioinformatics (Oxford, England)2019
PANDA: A comprehensive and flexible tool for quantitative proteomics data analysis.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Integrated IP-MS and Optoproteomics Reveal Dynamic Remodeling of Protein Interaction Networks During NLRP3 Inflammasome Activation.Molecular & cellular proteomics : MCP · 2026Article
- Comparative Analysis of Lysis Buffers for Enhanced Proteomic and Glycoproteomic Profiling.Biomolecules · 2026Article
- PhyloFunc: phylogeny-informed functional distance as a new ecological metric for metaproteomic data analysis.Microbiome · 2025Article
- A Novel Integrated Pipeline for Site-Specific Quantification of N-glycosylation.Phenomics (Cham, Switzerland) · 2024Article
- cfOmics: a cell-free multi-Omics database for diseases.Nucleic acids research · 2024Article
- DeepRTAlign: toward accurate retention time alignment for large cohort mass spectrometry data analysis.Nature communications · 2023Article
- 6-PlexAnalytical chemistry · 2023Article
- Recent advances in proteomics and metabolomics in plants.Molecular horticulture · 2022Review
- An antibody-based proximity labeling protocol to identify biotinylated interactors of SARS-CoV-2.STAR protocols · 2022Article
- An antibody-based proximity labeling map reveals mechanisms of SARS-CoV-2 inhibition of antiviral immunity.Cell chemical biology · 2022Article
- Proteomics Landscape of Alzheimer's Disease.Proteomes · 2021Review
- Article
- Software Options for the Analysis of MS-Proteomic Data.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Chemical RNA digestion enables robust RNA-binding site mapping at single amino acid resolution.Nature structural & molecular biology · 2020Article
- PANDA-view: an easy-to-use tool for statistical analysis and visualization of quantitative proteomics data.Bioinformatics (Oxford, England) · 2018Article
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
summaryAs 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.
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