Software:SWATHProphet

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-==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 2015''', 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''
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 +'''Molecular and Cellular Proteomics''', 2015 Dec 24. pii: mcp.M115.054478. PMID: 26704149.
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==Obtaining the software== ==Obtaining the software==
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==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 be downloaded directly[https://sourceforge.net/p/sashimi/code/HEAD/tree/trunk/SWATHProphet/Tutorial.docx here ].+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 ].
The dataset used in the example can be downloaded from SWATH Atlas [http://www.swathatlas.org/etc/20130520_urine_1-1.mzXML.gz 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]
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-==Author== 
-  
-Andy Keller 

Current revision

Contents

Overview

SWATH Prophet is a software tool for the analysis of SWATH (DIA) data.


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.

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/


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

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