ProteoSign: an end-user online differential proteomics statistical analysis platform

Nucleic Acids Research
Georgios EfstathiouIoannis Iliopoulos

Abstract

Profiling of proteome dynamics is crucial for understanding cellular behavior in response to intrinsic and extrinsic stimuli and maintenance of homeostasis. Over the last 20 years, mass spectrometry (MS) has emerged as the most powerful tool for large-scale identification and characterization of proteins. Bottom-up proteomics, the most common MS-based proteomics approach, has always been challenging in terms of data management, processing, analysis and visualization, with modern instruments capable of producing several gigabytes of data out of a single experiment. Here, we present ProteoSign, a freely available web application, dedicated in allowing users to perform proteomics differential expression/abundance analysis in a user-friendly and self-explanatory way. Although several non-commercial standalone tools have been developed for post-quantification statistical analysis of proteomics data, most of them are not end-user appealing as they often require very stringent installation of programming environments, third-party software packages and sometimes further scripting or computer programming. To avoid this bottleneck, we have developed a user-friendly software platform accessible via a web interface in order to enable prote...Continue Reading

References

Dec 13, 2003·Analytical Chemistry·Jue-Liang HsuShu-Hui Chen
Sep 24, 2004·Molecular & Cellular Proteomics : MCP·Philip L RossDarryl J Pappin
Oct 6, 2004·Genome Biology·Robert C GentlemanJianhua Zhang
Jul 18, 2006·Nucleic Acids Research·Johannes RainerZlatko Trajanoski
May 6, 2008·Bioinformatics·Ashoka D PolpitiyaRichard D Smith
Dec 5, 2008·Proteomics·Björn SchwanhäusserMatthias Selbach
Nov 7, 2009·Bioinformatics·Brian CarrilloRobert E Kearney
Sep 2, 2010·Nature Methods·Tommy NilssonJohn J M Bergeron
Aug 24, 2011·Molecular & Cellular Proteomics : MCP·Ruijun TianDaniel Figeys
Jul 24, 2012·Amino Acids·Salvatore CappadonaBas van Breukelen
Dec 4, 2012·Nucleic Acids Research·Juan Antonio VizcaínoHenning Hermjakob
Mar 12, 2013·Nature Methods·Andrew J M HowdenOreste Acuto
May 13, 2014·Bioinformatics·Daniel BroudyBrendan MacLean
May 28, 2014·Nucleic Acids Research·Arnold Kuzniar, Roland Kanaar
Apr 19, 2016·Journal of Proteome Research·Kenneth BryanDavid J Lynn
Jun 28, 2016·Nature Methods·Stefka TyanovaJürgen Cox

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Citations

Nov 22, 2018·Bioinformatics·Gang PengHongyu Zhao
Mar 6, 2019·Journal of Bacteriology·Rachel E BossermanPatricia A Champion
Jan 2, 2019·BMC Systems Biology·Jongsu JunTaesung Park
May 21, 2019·Human Molecular Genetics·Ching-On Wong, Kartik Venkatachalam
Nov 21, 2019·BMC Bioinformatics·Stanislav A Listopad, Trina M Norden-Krichmar
Aug 25, 2018·Scientific Reports·Hendrik NolteMarcus Krüger
Nov 20, 2020·Arteriosclerosis, Thrombosis, and Vascular Biology·Patrick A MurphyRichard O Hynes
Jul 17, 2020·Computational and Structural Biotechnology Journal·George MinadakisGeorge M Spyrou
May 9, 2021·Nucleic Acids Research·Evangelos TheodorakisIoannis Iliopoulos
May 15, 2018·Journal of Proteome Research·Katelyn R LudwigAmanda B Hummon
Oct 24, 2020·Journal of Proteome Research·Maike SperkUjjwal Neogi

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