mapancsu / icextract

ICExtract

Package for analyzing MS with Python. It provides an ion-chromatogram-extraction method based on Greed Nearest Neighbor algorithm for raw LC-MS dataset (including DDA-MS data and DIA-MS data) effectively and quickly.

Install

Required Dependencies

• Visual Studio Community 2015 with Update 3
• Anaconda Python 3.6.0 64bit
• SWIG 3.0.10
• CMake 3.7.1
• Eigen 3.3.3
• OpenMS 2.3.0

Download

• Download ICExtract.
• Unzip it into ICExtract directory.

Compile

• step 1 Compile OpenMS by OpenMS Guide.

• step 2 Compile ICExtract. Open "VS2015 x64 Native Tools Command Prompt" ; Run following commands in the prompt.

   cd ICExtract
   mkdir build
   cd build
   cmake .. -G "NMake Makefiles" -DCMAKE_BUILD_TYPE=Release
   nmake
   nmake install

Usage

• Download ICExtract_python.zip file from url.

• Upzip ICExtract_python.zip file and go to /python36 directory.

• Run following Python code fragment to extract ion chromatogram from mzXML or mzML file.

   from _ICExtract import DDAMS, DDA_PIC, DIAMS, DIA_PIC, MS2_PIC
   import sys
   ### for DDA-MS data
   mzfile="DDAfile.mzxml" ## dda-ms file
   mzfile=mzfile.encode(sys.getfilesystemencoding())
   ddams=DDAMS()
   ddams.load(mzfile)
   ics_ms1 = DDA_PIC(ddams, 0.025, 300.0, 10.0, 10.0, 5.0)
   
   ### for DIA-MS data
   mzfile="DIAfile.mzxml" ## dia-ms file
   mzfile=mzfile.encode(sys.getfilesystemencoding())
   diams=DIAMS()
   diams.load(mzfile)
   ics_ms1 = DIA_PIC(diams, 0, 0.025, 300.0, 10.0, 10.0, 5.0) ## MS1
   ics_ms2 = MS2_PIC(diams, 1, 0.025, 300.0, 10.0, 10.0, 5.0) ## MS2 

Contact

For any questions, please contact: [email protected]