RAW to mzXML Converters: /home/

RAW to mzXML Converters

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

Choose a Windows-based server to run the Conversion Service
Install the Oracle Java Runtime Environment
Install ProteoWizard. (ReAdW.exe is also supported for backward compatibility for ThermoFinnigan instruments)
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

Download the Java Runtime Environment (JRE) 1.7 from http://www.oracle.com/technetwork/java/javase/downloads/index.html
Install the JRE to the chosen directory. On Windows the default installation directory is C:\Program Files\Java.

Notes:

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

ProteoWizard

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

Create the directory c:\labkey to be the <LABKEY_HOME> directory
Create the binary directory c:\labkey\bin
Place the directory <LABKEY_HOME>\bin directory on the PATH System Variable using the System Control Panel
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.

Choose a RAW file to use for this test. For this example, the file will be called convertSample.RAW
Place the file in a temporary directory on the computer. For this example, we will use c:\conversion
Open a Command Prompt and change directory to c:\conversion
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

LabKey Support

LabKey Support