Software:SWATHProphet
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| - | SWATH Prophet is a software tool for the analysis of SWATH (DIA) data. | + | ==Overview== |
| + | SWATH Prophet is a software tool for the analysis of SWATH (DIA) data. | ||
| - | ==Manuscript == | + | ==Manuscripts == |
| - | ''"Automated Validation of Results and Removal of Fragment Ion Interferences in Targeted Analysis of Data | + | |
| - | Independent Acquisition MS using SWATHProphet"'', Molecular and Cellular Proteomics, in press. | + | ''Automated Validation of Results and Removal of Fragment Ion Interferences in Targeted Analysis of Data Independent Acquisition MS using SWATHProphet'' |
| + | '''Molecular and Cellular Proteomics''', 2015 May;14(5):1411-8. doi: 10.1074/mcp.O114.044917. Epub 2015 Feb 24. PMID: 25713123. | ||
| - | + | ''Opening a SWATH Window on Post-Translational Modifications: Automated Pursuit of Modified Peptides'' | |
| + | |||
| + | '''Molecular and Cellular Proteomics''', 2015 Dec 24. pii: mcp.M115.054478. PMID: 26704149. | ||
| + | |||
| ==Obtaining the software== | ==Obtaining the software== | ||
| - | Via SVN: | + | Via SVN: |
| - website: https://sourceforge.net/p/sashimi/code/HEAD/tree/trunk/SWATHProphet/ | - website: https://sourceforge.net/p/sashimi/code/HEAD/tree/trunk/SWATHProphet/ | ||
| - export: svn export https://svn.code.sf.net/p/sashimi/code/trunk/SWATHProphet SWATHProphet | - export: svn export https://svn.code.sf.net/p/sashimi/code/trunk/SWATHProphet SWATHProphet | ||
| - | Via HTTP: | + | Via HTTP: |
| - https://sourceforge.net/projects/sashimi/files/SWATHProphet/ | - https://sourceforge.net/projects/sashimi/files/SWATHProphet/ | ||
| - | |||
| - | |||
| ==Running the software== | ==Running the software== | ||
| - | There is a tutorial checked into the codebase, which can be obtained as outlined above. The tutorial can also | + | There is a tutorial checked into the codebase, which can be obtained as outlined above. The tutorial can also be downloaded directly [https://sourceforge.net/p/sashimi/code/HEAD/tree/trunk/SWATHProphet/Tutorial.docx here ]. |
| - | be downloaded directly[https://sourceforge.net/p/sashimi/code/HEAD/tree/trunk/SWATHProphet/Tutorial.docx here ]. | + | |
| - | + | ||
| - | The dataset used in the example can be downloaded from SWATH Atlas [http://www.swathatlas.org/etc/20130520_urine_1-1.mzXML.gz here] | + | |
| - | + | ||
| - | + | ||
| - | ==Author== | + | The dataset used in the example can be downloaded from SWATH Atlas [http://www.swathatlas.org/etc/20130520_urine_1-1.mzXML.gz here] |
| - | + | ||
| - | Andy Keller | + | |
Current revision
Contents |
[edit]
Overview
SWATH Prophet is a software tool for the analysis of SWATH (DIA) data.
[edit]
Manuscripts
Automated Validation of Results and Removal of Fragment Ion Interferences in Targeted Analysis of Data Independent Acquisition MS using SWATHProphet
Molecular and Cellular Proteomics, 2015 May;14(5):1411-8. doi: 10.1074/mcp.O114.044917. Epub 2015 Feb 24. PMID: 25713123.
Opening a SWATH Window on Post-Translational Modifications: Automated Pursuit of Modified Peptides
Molecular and Cellular Proteomics, 2015 Dec 24. pii: mcp.M115.054478. PMID: 26704149.
[edit]
Obtaining the software
Via SVN:
- website: https://sourceforge.net/p/sashimi/code/HEAD/tree/trunk/SWATHProphet/
- export: svn export https://svn.code.sf.net/p/sashimi/code/trunk/SWATHProphet SWATHProphet
Via HTTP:
- https://sourceforge.net/projects/sashimi/files/SWATHProphet/
[edit]
Running the software
There is a tutorial checked into the codebase, which can be obtained as outlined above. The tutorial can also be downloaded directly here .
The dataset used in the example can be downloaded from SWATH Atlas here
