Difference between revisions of "QuiXoT software package"
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=== What is QuiXoT? === | === What is QuiXoT? === | ||
| − | '''QuiXoT''' is a bioinformatic software package developed especially to provide a set of tools for quantitative proteomics. | + | The '''QuiXoT software package''' is a bioinformatic software package developed especially to provide a set of tools for quantitative proteomics. |
| − | The main program of the package | + | The different programs included in the package are: |
| + | :* '''[[pRatio]]''', a validator of SEQUEST identifications, | ||
| + | :* '''[[RAWToBinStack]]''', to import spectra from Thermo RAW files, | ||
| + | :* '''[[CSVToQuiXML]]''', to convert data from tab-separated files to '''[[QuiXML]]''' files, | ||
| + | :* '''[[QuiXoT]]''', the main program of the package, and the namesake of the whole package, | ||
| + | :* '''[[QuiXtoQuiX]]''', to analyse protein quantifications performed in the MS1-spectra, | ||
| + | :* '''[[MascotToQuiXML]]''' (no longer updated), to convert Mascot's DAT files into QuiXML files, | ||
| + | :* '''[[mgfToBinStack]]''' (no longer updated), to import spectral data from Mascot's MGF files to '''[[binStack]]''', | ||
| + | :* '''[[XMLTool]]''', a lightweight, multi-purpose program to operate with large QuiXML files, or other XML file. | ||
=== Why QuiXoT? === | === Why QuiXoT? === | ||
| − | The tools available to the scientific community to | + | The tools available to the scientific community to quantify and make statistical analyses in ''large scale'' quantitative proteomic experiments were very limited. For this reason we started developing QuiXoT in our laboratory. |
| − | In 2006 we started developing a tool for 18O isotope-labeling experiments able to automatically extract well assigned spectra, | + | In 2006 we started developing a tool for 18O isotope-labeling experiments able to automatically extract well assigned spectra, quantify the data and make a fast statistical analysis. Everything within one hour. |
Later, in February 2009, we decided to expand the software in order to analyze any type of isotopic labeling and to accept data from the most common mass-spectrometres. | Later, in February 2009, we decided to expand the software in order to analyze any type of isotopic labeling and to accept data from the most common mass-spectrometres. | ||
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=== Who is behind QuiXoT? === | === Who is behind QuiXoT? === | ||
| − | QuiXoT has been developed originally by ''' | + | QuiXoT has been developed originally by '''Pedro Navarro''' and afterwards by '''[[User:Mtrevisan|Marco Trevisan-Herraz]]''', at the Cardiovascular Proteomics Lab of Prof. Jesús Vázquez, within the Centro Nacional de Investigaciones Cardiovasculares (CNIC), in Madrid, Spain (originally at the Protein Chemistry and Proteomics Lab, in the Centro de Biología Molecular Severo Ochoa, CBM-CSIC). |
The [[:Image:QuiXoT logo.png|QuiXoT logo]] has been designed by José Pérez Pérez and Pedro Navarro. | The [[:Image:QuiXoT logo.png|QuiXoT logo]] has been designed by José Pérez Pérez and Pedro Navarro. | ||
| + | |||
| + | === Try QuiXoT! === | ||
| + | |||
| + | You can download the executables of the different programs from their corresponding article. The source code is available at [https://github.com/CNIC-Proteomics the Lab's site at GitHub]. | ||
| + | |||
| + | You can start checking the '''[[unit tests for QuiXoT|unit tests]]''' to check the programs run as expected, as well as to get familiarised with the software. | ||
| + | |||
| + | After that, you can start '''[[exploring QuiXoT features]]''', or you can start using your own data (note that depending on your analysis, you may need to change the configuration files). | ||
| + | |||
| + | === Licence === | ||
| + | |||
| + | You can check at '''[[PROTEOMICA:Copyrights]]''' the licence under which all the programs presented here are available. | ||
| + | |||
=== References === | === References === | ||
* {{reference|authors = I. Jorge, P. Navarro, P. Martinez-Acedo, et al.|title = Statistical model to analyze quantitative proteomics data obtained by 18O/16O labeling and linear ion trap mass spectrometry: Application to the study of VEGF-induced angiogenesis in endothelial cells|journal = Mol Cell Proteomics|year = 2009|DOI = 10.1074/mcp.M800260-MCP200}} | * {{reference|authors = I. Jorge, P. Navarro, P. Martinez-Acedo, et al.|title = Statistical model to analyze quantitative proteomics data obtained by 18O/16O labeling and linear ion trap mass spectrometry: Application to the study of VEGF-induced angiogenesis in endothelial cells|journal = Mol Cell Proteomics|year = 2009|DOI = 10.1074/mcp.M800260-MCP200}} | ||
| + | |||
| + | * {{reference|authors = P. Navarro, M. Trevisan-Herraz, E. Bonzon-Kulichenko, et al.|title = General Statistical Framework for Quantitative Proteomics by Stable Isotope Labeling|journal = J Proteome Res|year = 2014|DOI = 10.1021/pr4006958}} | ||
__NOTOC__ <!-- This removes the table of contents --> | __NOTOC__ <!-- This removes the table of contents --> | ||
__NOEDITSECTION__ <!-- This removes the section edit links --> | __NOEDITSECTION__ <!-- This removes the section edit links --> | ||
| + | |||
| + | [[Category:QuiXoT software package]] | ||
Latest revision as of 11:49, 26 May 2017
What is QuiXoT?
The QuiXoT software package is a bioinformatic software package developed especially to provide a set of tools for quantitative proteomics.
The different programs included in the package are:
- pRatio, a validator of SEQUEST identifications,
- RAWToBinStack, to import spectra from Thermo RAW files,
- CSVToQuiXML, to convert data from tab-separated files to QuiXML files,
- QuiXoT, the main program of the package, and the namesake of the whole package,
- QuiXtoQuiX, to analyse protein quantifications performed in the MS1-spectra,
- MascotToQuiXML (no longer updated), to convert Mascot's DAT files into QuiXML files,
- mgfToBinStack (no longer updated), to import spectral data from Mascot's MGF files to binStack,
- XMLTool, a lightweight, multi-purpose program to operate with large QuiXML files, or other XML file.
Why QuiXoT?
The tools available to the scientific community to quantify and make statistical analyses in large scale quantitative proteomic experiments were very limited. For this reason we started developing QuiXoT in our laboratory.
In 2006 we started developing a tool for 18O isotope-labeling experiments able to automatically extract well assigned spectra, quantify the data and make a fast statistical analysis. Everything within one hour.
Later, in February 2009, we decided to expand the software in order to analyze any type of isotopic labeling and to accept data from the most common mass-spectrometres.
Who is behind QuiXoT?
QuiXoT has been developed originally by Pedro Navarro and afterwards by Marco Trevisan-Herraz, at the Cardiovascular Proteomics Lab of Prof. Jesús Vázquez, within the Centro Nacional de Investigaciones Cardiovasculares (CNIC), in Madrid, Spain (originally at the Protein Chemistry and Proteomics Lab, in the Centro de Biología Molecular Severo Ochoa, CBM-CSIC).
The QuiXoT logo has been designed by José Pérez Pérez and Pedro Navarro.
Try QuiXoT!
You can download the executables of the different programs from their corresponding article. The source code is available at the Lab's site at GitHub.
You can start checking the unit tests to check the programs run as expected, as well as to get familiarised with the software.
After that, you can start exploring QuiXoT features, or you can start using your own data (note that depending on your analysis, you may need to change the configuration files).
Licence
You can check at PROTEOMICA:Copyrights the licence under which all the programs presented here are available.
References
- I. Jorge, P. Navarro, P. Martinez-Acedo, et al., «Statistical model to analyze quantitative proteomics data obtained by 18O/16O labeling and linear ion trap mass spectrometry: Application to the study of VEGF-induced angiogenesis in endothelial cells», Mol Cell Proteomics , (2009) (DOI: 10.1074/mcp.M800260-MCP200)
- P. Navarro, M. Trevisan-Herraz, E. Bonzon-Kulichenko, et al., «General Statistical Framework for Quantitative Proteomics by Stable Isotope Labeling», J Proteome Res , (2014) (DOI: 10.1021/pr4006958)
