PDV: an integrative proteomics data viewer

Bioinformatics
Kai LiBo Wen

Abstract

Data visualization plays critical roles in proteomics studies, ranging from quality control of MS/MS data to validation of peptide identification results. Herein, we present PDV, an integrative proteomics data viewer that can be used to visualize a wide range of proteomics data, including database search results, de novo sequencing results, proteogenomics files, MS/MS data in mzML/mzXML format and data from public proteomics repositories. PDV is a lightweight visualization tool that enables intuitive and fast exploration of diverse, large-scale proteomics datasets on standard desktop computers in both graphical user interface and command line modes. PDV software and the user manual are freely available at http://pdv.zhang-lab.org. The source code is available at https://github.com/wenbostar/PDV and is released under the GPL-3 license. Supplementary data are available at Bioinformatics online.

References

Apr 30, 2005·Analytical Chemistry·Ari Frank, Pavel Pevzner
Dec 31, 2005·Nucleic Acids Research·Frank DesiereRuedi Aebersold
Dec 31, 2005·Nucleic Acids Research·Philip JonesRolf Apweiler
May 12, 2009·Journal of Proteome Research·Marc Sturm, Oliver Kohlbacher
Mar 10, 2011·BMC Bioinformatics·Harald BarsnesLennart Martens
Feb 10, 2012·Nature Biotechnology·Rui WangJuan Antonio Vizcaíno
Mar 1, 2012·Molecular & Cellular Proteomics : MCP·Andrew R JonesDavid Creasy
Jan 1, 2013·Journal of Proteome Research·Hao ChiMeng-Qiu Dong
Dec 4, 2013·Journal of Proteome Research·Thilo MuthHarald Barsnes
Mar 5, 2014·Molecular & Cellular Proteomics : MCP·Peter R Baker, Robert J Chalkley
Dec 17, 2014·Proteomics·Eystein OvelandHarald Barsnes
Jul 1, 2015·Journal of the American Society for Mass Spectrometry·Bin Ma
Jun 17, 2016·Journal of Proteome Research·Dmitry M AvtonomovAlexey I Nesvizhskii
Jul 20, 2017·Proceedings of the National Academy of Sciences of the United States of America·Ngoc Hieu TranMing Li
Dec 10, 2017·Molecular & Cellular Proteomics : MCP·Xiaojing WangBing Zhang

❮ Previous
Next ❯

Citations

Oct 8, 2018·Molecular & Cellular Proteomics : MCP·Zhe RenAndrew R Jones
Oct 9, 2019·Molecular & Cellular Proteomics : MCP·Korrawe KarunratanakulSira Sriswasdi
Jul 4, 2020·Molecular & Cellular Proteomics : MCP·Fengchao YuAlexey I Nesvizhskii
Jun 28, 2020·Molecular & Cellular Proteomics : MCP·Jana ZechaBernhard Kuster
Jul 17, 2020·Nature Methods·Felipe da Veiga LeprevostAlexey I Nesvizhskii
Oct 7, 2020·Nature Methods·Daniel A PolaskyAlexey I Nesvizhskii
Jul 11, 2020·Cell·Michael A GilletteUNKNOWN Clinical Proteomic Tumor Analysis Consortium
Jan 9, 2021·Cancer Cell·Chen HuangUNKNOWN Clinical Proteomic Tumor Analysis Consortium
Jan 23, 2021·Current Biology : CB·Takashi HottaRyoma Ohi
Dec 1, 2019·Molecular & Cellular Proteomics : MCP·Korrawe KarunratanakulSira Sriswasdi
Jan 17, 2021·Molecular & Cellular Proteomics : MCP·Jana ZechaBernhard Kuster
Jan 1, 2019·Molecular & Cellular Proteomics : MCP·Zhe RenAndrew R Jones
Jan 17, 2021·Molecular & Cellular Proteomics : MCP·Fengchao YuAlexey I Nesvizhskii
Feb 16, 2020·Cell·Yongchao DouUNKNOWN Clinical Proteomic Tumor Analysis Consortium
Mar 30, 2021·Journal of the American Society for Mass Spectrometry·In Kwon ChoiXiaowen Liu
Jul 2, 2021·Expert Review of Vaccines·Nasim EbrahimiMichael R Hamblin
Aug 7, 2021·Cell·Shankha SatpathyUNKNOWN Clinical Proteomic Tumor Analysis Consortium
May 6, 2020·Journal of Proteome Research·Haifen LiXuanqiang Liang
Dec 13, 2018·Journal of Proteome Research·Mingqiang RongZhonghua Liu
Aug 28, 2021·International Journal of Molecular Sciences·Sarah C AtkinsonNatalie A Borg

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.