doi: 10.1093/bioinformatics/btp005.
Epub 2009 Jan 6.
Prequips--an extensible software platform for integration, visualization and analysis of LC-MS/MS proteomics data
Affiliations
- PMID: 19129212
- PMCID: PMC2720692
- DOI: 10.1093/bioinformatics/btp005
Item in Clipboard
Prequips--an extensible software platform for integration, visualization and analysis of LC-MS/MS proteomics data
Bioinformatics.
.
Abstract
Summary: We describe an integrative software platform, Prequips, for comparative proteomics-based systems biology analysis that: (i) integrates all information generated from mass spectrometry (MS)-based proteomics as well as from basic proteomics data analysis tools, (ii) visualizes such information for various proteomic analyses via graphical interfaces and (iii) links peptide and protein abundances to external tools often used in systems biology studies.
Availability: http://prequips.sourceforge.net
Figures
Overview of Prequips' design and functionality. (A) Data model structure. (B) Schematics of data structure and exchange. (C) Spectrum, peptide feature map and table viewers in single sample analysis. (D) Peptide feature maps in multi-sample analysis. (E) Broadcasting to Cytoscape via the Gaggle interface. (F) Network analysis using broadcasted proteins in Cytoscape.
Similar articles
-
Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics.BMC Bioinformatics. 2008 Dec 16;9:542. doi: 10.1186/1471-2105-9-542. BMC Bioinformatics. 2008. PMID: 19087345 Free PMC article.
-
A graphical user interface for RAId, a knowledge integrated proteomics analysis suite with accurate statistics.BMC Res Notes. 2018 Mar 15;11(1):182. doi: 10.1186/s13104-018-3289-6. BMC Res Notes. 2018. PMID: 29544540 Free PMC article.
-
Intellinsity: a tool for visualization and analysis of liquid chromatography/tandem mass spectrometry sampling events.Rapid Commun Mass Spectrom. 2010 Nov 15;24(21):3217-8. doi: 10.1002/rcm.4743. Rapid Commun Mass Spectrom. 2010. PMID: 20941771 No abstract available.
-
Quantitative, high-resolution proteomics for data-driven systems biology.Annu Rev Biochem. 2011;80:273-99. doi: 10.1146/annurev-biochem-061308-093216. Annu Rev Biochem. 2011. PMID: 21548781 Review.
-
Bioinformatics for LC-MS/MS-based proteomics.Methods Mol Biol. 2010;658:61-91. doi: 10.1007/978-1-60761-780-8_4. Methods Mol Biol. 2010. PMID: 20839098 Review.
Cited by
-
MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data.BMC Bioinformatics. 2010 Jul 23;11:395. doi: 10.1186/1471-2105-11-395. BMC Bioinformatics. 2010. PMID: 20650010 Free PMC article.
-
GProX, a user-friendly platform for bioinformatics analysis and visualization of quantitative proteomics data.Mol Cell Proteomics. 2011 Aug;10(8):O110.007450. doi: 10.1074/mcp.O110.007450. Epub 2011 May 20. Mol Cell Proteomics. 2011. PMID: 21602510 Free PMC article.
-
The Prion Disease Database: a comprehensive transcriptome resource for systems biology research in prion diseases.Database (Oxford). 2009;2009:bap011. doi: 10.1093/database/bap011. Epub 2009 Sep 17. Database (Oxford). 2009. PMID: 20157484 Free PMC article.
-
ePlant and the 3D data display initiative: integrative systems biology on the world wide web.PLoS One. 2011 Jan 10;6(1):e15237. doi: 10.1371/journal.pone.0015237. PLoS One. 2011. PMID: 21249219 Free PMC article.
References
-
- Keller A, et al. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 2002;74:5383–5392. - PubMed
-
- Li X-J, et al. A tool to visualize and evaluate data obtained by liquid chromatography-electrospray ionization-mass spectroscopy. Anal. Chem. 2004;76:3856–3860. - PubMed
-
- Saeed A, et al. TM4: a free, open-source system for microarray data management and analysis. Biotechniques. 2003;34:374–378. - PubMed
