imzMLConverter

Tool for converting mass spectrometry data to the imzML format.

If you find this useful please cite: Alan M. Race, Iain B. Styles, Josephine Bunch, Journal of Proteomics, 75(16):5111-5112, 2012. http://dx.doi.org/10.1016/j.jprot.2012.05.035

How do I get set up?

Download the latest version of imzMLConverter
Install Java SE 8 JRE
Install ProteoWizard
[Optional] Install MS Data Converter (SCIEX) to enable conversion of data from AB SCIEX data instruments

Converting data

imzMLConverter is currently a command line tool. To use this tool, open the folder where jimzMLConverter-2.0.2.jar is stored, hold the shift button and right click in the folder. Select Open command window here from the drop-down menu.

To see a full list of options for the converter run the command:

java -jar jimzMLConverter-2.0.2.jar

Converting Waters data

Modify the following command:

java -jar jimzMLConverter-2.0.2.jar imzML -p "C:\Path\To\Data\my_data.pat" "C:\Path\To\Data\my_data.raw"

Converting ION-TOF data

Export the data to GRD, ensuring that the properties.txt file is generated
Modify the following command:

java -jar jimzMLConverter-2.0.2.jar imzML -p "C:\Path\To\Data\my_data.properties.txt" "C:\Path\To\Data\my_data.grd"

Converting SCIEX data

Install MS Data Converter (SCIEX)
Modify the following command:

java –jar jimzMLConverter-2.0.2.jar imzML "C:\Path\To\Data\my_data.wiff"

Converting AP-SMALDI data

Modify the following command:

java -jar jimzMLConverter-2.0.2.jar imzML -p "C:\Path\To\Data\my_data.udp" "C:\Path\To\Data\my_data.RAW"