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


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:
         - export: svn export SWATHProphet
 Via HTTP:

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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