Tutorial.md

-# In this tutorial we will go through an example of running PeakStrainer, lets start!
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-Start Screen for PeakStrainer
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-![App Main page](/uploads/efa36b03cbd48d4074ae82e7a40514ac/Capture.PNG)
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-On this screen you can select the .raw files by using the **browse **button.  
-You can also choose if [Reorder Scans](ReorderScans) will appear after PeakStrianer is finished
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-Startup Screen for [Reorder Scans](Reorder-Scans)
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-You can also start **reorder scans** without selecting a file or running PeakStrainer
-![Capture1](/uploads/3c5b2b60148c1af927a578fa07e4ad6a/Capture1.PNG)
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-Choose "other" output options
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-You can get the intermediate files that show how the data was processed by selecting the CSV output, if the output directory is empty the files will be created in the same directory as the selected files. 
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-You can also set the logging, to show any issues relevant information, the log file is useful to fix bugs in the program, a high log level means that most if not all messages are stored, alternately a low log level indicates 
-![Capture3](/uploads/f4c5648c3d6ca2c4e3215487a617c848/Capture3.PNG)
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-2Startup Screen for [Reorder Scans](Reorder-Scans)
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-![Capture4](/uploads/1a1ad9909501045b30e45a37d65a1c74/Capture4.PNG)
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-3Startup Screen for [Reorder Scans](Reorder-Scans)
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-![Capture5](/uploads/373a786032413fe03d4496e2f7f44657/Capture5.PNG)
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-4Startup Screen for [Reorder Scans](Reorder-Scans)
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-![Capture6](/uploads/a34aab2992b3c68bd4770e92f5906e0c/Capture6.PNG)
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-5Startup Screen for [Reorder Scans](Reorder-Scans)
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-![Capture7](/uploads/83cececcd09aaafc540fa350b0334896/Capture7.PNG)
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-6Startup Screen for [Reorder Scans](Reorder-Scans)
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-![Capture8](/uploads/6f418e6e06f18a7091cc70800f65f99a/Capture8.PNG)
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+Running with default settings
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+1.  open MSPeakStrainer and select one or more *.raw files
+2.  press Finish
+3.  wait for the process to finish
+4.  close the reorder scans window
 
+new *.mzXML files will be created at the same location where the *.raw files where found
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