These instructions explain how to manually install LabKey Enterprise Pipeline MS2 Conversion service. The Conversion service is used to convert the output of the MS2 machines to the mzXML format which is used by the LabKey Server. (Please note the Conversion Service is optional, and only required if you plan to convert files to mzXML format in your pipeline.)

You may also wish to use the LabKey Server Remote Pipeline Server installer, which will automatically install the prerequisites like the Java Runtime Environment and ProteoWizard.

Installation Requirements

  1. Choose a Windows-based server to run the Conversion Service
  2. Install the Oracle Java Runtime Environment
  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 the Java Runtime Environment

  1. Download the Java Runtime Environment (JRE) 1.7 from
  2. Install the JRE to the chosen directory. On Windows the default installation directory is C:\Program Files\Java.
  • The JDK includes the JRE, so if you have already installed the JDK, you don't need to also install the JRE.

Install the Vendor Software for the Supported Converters

Currently LabKey Server supports the following vendors

  • ThermoFinnigan
  • Waters
Install the Vendor's software following the instructions provided by the vendor.

Install ProteoWizard

Download the converter executables from the ProteoWizard project

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



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



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