Installation Requirements

1. Choose a Windows-based server to run the Conversion Service
2. Install Java
3. Install ProteoWizard. (ReAdW.exe is also supported for backward compatibility for ThermoFinnigan instruments.)
4. Test the Converter Installation

Choose a Server to Run the Conversion Service

The Conversion server must run the Windows Operating System (Vendor software libraries currently only run on the Windows OS).

Install Java

Download the Java version supported by your server. For details see Supported Technologies.

Install the Vendor Software for the Supported Converters

Currently LabKey Server supports the following vendors

• ThermoFinnigan
• Waters

Install ProteoWizard

Download the converter executables from the ProteoWizard project

• ProteoWizard
• Download
• Further Information

Install the executables, and copy them into the directory <LABKEY_HOME>\bin directory

1. Create the directory c:\labkey to be the <LABKEY_HOME> directory
2. Create the binary directory c:\labkey\bin
3. Place the directory <LABKEY_HOME>\bin directory on the PATH System Variable using the System Control Panel
4. Install the downloaded files and copy the executable files to <LABKEY_HOME>\bin

Test the Converter Installation

For the sake of this document, we will use an example of converting a RAW file using the msconvert. Testing for other vendor formats is similar.

1. Choose a RAW file to use for this test. For this example, the file will be called convertSample.RAW
2. Place the file in a temporary directory on the computer. For this example, we will use c:\conversion
3. Open a Command Prompt and change directory to c:\conversion
4. Attempt to convert the sample RAW file to mzXML using msconvert.exe. Note that the first time you perform a conversion, you may need to accept a license agreement.

C:\conversion> dir
Volume in drive C has no label.
Volume Serial Number is 30As-59FG

Directory of C:\conversion

04/09/2008  12:39 PM    <DIR>          .
04/09/2008  12:39 PM    <DIR>          ..
04/09/2008  11:00 AM        82,665,342 convertSample.RAW

C:\conversion>msconvert.exe convertSample.RAW --mzXML
format: mzXML (Precision_64 [ 1000514:Precision_64 1000515:Precision_32 ], ByteOrder_LittleEndian, Compression_None) indexed="true"
outputPath: .
extension: .mzXML
contactFilename:

filters:

filenames:
  convertSample.raw

processing file: convertSample.raw
writing output file: ./convertSample.mzXML

C:\conversion> dir
Volume in drive C has no label.
Volume Serial Number is 20AC-9682

Directory of C:\conversion

04/09/2008  12:39 PM    <DIR>           .
04/09/2008  12:39 PM    <DIR>           ..
04/09/2008  11:15 AM        112,583,326 convertSample.mzXML
04/09/2008  11:00 AM        82,665,342  convertSample.RAW

Resources

Converters.zip