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...

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Detalles Bibliográficos
Autores principales: Chang, Cheng, Li, Mansheng, Guo, Chaoping, Ding, Yuqing, Xu, Kaikun, Han, Mingfei, He, Fuchu, Zhu, Yunping
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6394390/
https://www.ncbi.nlm.nih.gov/pubmed/30816924
http://dx.doi.org/10.1093/bioinformatics/bty727
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author Chang, Cheng
Li, Mansheng
Guo, Chaoping
Ding, Yuqing
Xu, Kaikun
Han, Mingfei
He, Fuchu
Zhu, Yunping
author_facet Chang, Cheng
Li, Mansheng
Guo, Chaoping
Ding, Yuqing
Xu, Kaikun
Han, Mingfei
He, Fuchu
Zhu, Yunping
author_sort Chang, Cheng
collection PubMed
description 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
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spelling pubmed-63943902019-03-05 PANDA: A comprehensive and flexible tool for quantitative proteomics data analysis Chang, Cheng Li, Mansheng Guo, Chaoping Ding, Yuqing Xu, Kaikun Han, Mingfei He, Fuchu Zhu, Yunping Bioinformatics Applications Notes 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 Oxford University Press 2019-03-01 2018-08-23 /pmc/articles/PMC6394390/ /pubmed/30816924 http://dx.doi.org/10.1093/bioinformatics/bty727 Text en © The Author(s) 2018. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Notes
Chang, Cheng
Li, Mansheng
Guo, Chaoping
Ding, Yuqing
Xu, Kaikun
Han, Mingfei
He, Fuchu
Zhu, Yunping
PANDA: A comprehensive and flexible tool for quantitative proteomics data analysis
title PANDA: A comprehensive and flexible tool for quantitative proteomics data analysis
title_full PANDA: A comprehensive and flexible tool for quantitative proteomics data analysis
title_fullStr PANDA: A comprehensive and flexible tool for quantitative proteomics data analysis
title_full_unstemmed PANDA: A comprehensive and flexible tool for quantitative proteomics data analysis
title_short PANDA: A comprehensive and flexible tool for quantitative proteomics data analysis
title_sort panda: a comprehensive and flexible tool for quantitative proteomics data analysis
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6394390/
https://www.ncbi.nlm.nih.gov/pubmed/30816924
http://dx.doi.org/10.1093/bioinformatics/bty727
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