The Enhanced MS2 Sequest Pipeline allows LabKey Server to use the sequest.exe and makedb.exe utilities that come with Proteome Discoverer 1.1 from Thermo Fisher to perform MS2 searches. The Enhanced MS2 Sequest Pipeline uses the SEQUEST search engine installed with Proteome Discoverer 1.1 to perform the MS2 searches. Proteome Discover can be installed either on LabKey Server or can be installed on a remote computer.

There are 2 ways that the Enhanced Sequest Pipeline can be installed:

1. Install the LabKey Remote Pipeline Server software on an existing computer with Proteome Discoverer installed. (Recommended)
2. Install Proteome Discoverer on the same computer as the LabKey Server

Install the LabKey Remote Pipeline Server on an existing computer with Proteome Discoverer

In this option, you will install LabKey Remote Pipeline Server software on a computer that is currently running Proteome Discoverer software. This is our recommended solution. See Enterprise Pipeline with ActiveMQ for more information on the Enterprise Pipeline.

Install JAVA on the computer running Proteome Discoverer 1.1

• Download the Java Runtime Environment (JRE) from http://www.oracle.com/technetwork/java/javase/downloads/index.html
• Install the JRE to the chosen directory.
• Create the JAVA_HOME environmental variable to point at your installation directory.

Install the LabKey Remote Pipeline Server Software

Define the Location of the Remote Pipeline Server

<property name="remoteServerProperties">
    <bean class="org.labkey.pipeline.api.properties.RemoteServerPropertiesImpl">
         <property name="location" value="mzxmlconvert"/>
    </bean>
</property>

to

<property name="remoteServerProperties">
    <bean class="org.labkey.pipeline.api.properties.RemoteServerPropertiesImpl">
         <property name="location" value="sequest"/>
    </bean>
</property>

Enable Sequest Integration

<!-- Enable Sequest integration and configure it to run on a remote pipeline server (using "sequest" as its location
     property value in its pipelineConfig.xml file). Give pointers to the directory where Sequest is installed,
     and a directory to use for storing FASTA index files. -->
<!--
<bean id="sequestTaskOverride" class="org.labkey.ms2.pipeline.sequest.SequestSearchTask$Factory">
    <property name="location" value="sequest"/>
    <property name="sequestInstallDir" value="C:\Program Files (x86)\Thermo\Discoverer\Tools\Sequest" />
    <property name="indexRootDir" value="C:\FastaIndices" />
</bean>
-->

to

<!-- Enable Sequest integration and configure it to run on a remote pipeline server (using "sequest" as its location
     property value in its pipelineConfig.xml file). Give pointers to the directory where Sequest is installed,
     and a directory to use for storing FASTA index files. -->

<bean id="sequestTaskOverride" class="org.labkey.ms2.pipeline.sequest.SequestSearchTask$Factory">
    <property name="location" value="sequest"/>
    <property name="sequestInstallDir" value="C:\Program Files (x86)\Thermo\Discoverer\Tools\Sequest" />
    <property name="indexRootDir" value="C:\FastaIndices" />
</bean>

Also change the sequestInstallDir property value to be the location of the Sequest binary on your server.

Change the values for all location properties in the file to be webserver

1. Find all places in the file that contain a line that starts with <property name="location"...
1. Do not change location value in the sequestTaskOverride bean, shown above, that should stay as sequest
2. On each line, change the value to be webserver
3. Save the file

Install a JMS Queue for use with the Enterprise Pipeline

Configure your LabKey Server to use the Enterprise Pipeline

1) Enable Communication with the ActiveMQ JMS Queue:

You will need to uncomment the JMS configuration settings in the <LABKEY_HOME>/config/application.properties file. Learn more in this topic:

• Configure the Pipeline with ActiveMQ

Create the Enterprise Pipeline configuration directory for your server. The recommended location for this directory is <LABKEY_HOME>/config.

3) Enable the Enterprise Pipeline configuration directory

To configure the Enterprise Pipeline configuration directory, open the application.properties file and set:

context.pipelineConfig=/path/to/pipeline/config/dir

4) Copy the ms2Config.xml file you created and edited above into the Enterprise Pipeline configuration directory

Restart your LabKey Server

Install Proteome Discoverer on LabKey Server

Install Proteome Discoverer 1.1

Download and Expand the Enterprise Pipeline Configuration files

1. Go to the LabKey Download Page
2. Download the Pipeline Configuration(zip) zip file
3. Expand the downloaded file.

Enable SEQUEST support in LabKey Server

Create the Enterprise Pipeline configuration directory

1. Open Windows Explorer and go to the installation directory for your LabKey Server (<LABKEY_HOME>)
2. Create a new directory named config
3. You will use the full path of this new directory later

1. Go to to the Enterprise Pipeline Configuration files that were downloaded above.
2. Open the webserver directory
3. Copy the ms2Config.xml file to configuration directory created in the previous step

Enable Sequest Integration by going to the bottom of the file and change the text

<!-- Enable Sequest integration and configure it to run on a remote pipeline server (using "sequest" as its location
     property value in its pipelineConfig.xml file). Give pointers to the directory where Sequest is installed,
     and a directory to use for storing FASTA index files. -->
<!--
<bean id="sequestTaskOverride" class="org.labkey.ms2.pipeline.sequest.SequestSearchTask$Factory">
    <property name="location" value="sequest"/>
    <property name="sequestInstallDir" value="C:\Program Files (x86)\Thermo\Discoverer\Tools\Sequest" />
    <property name="indexRootDir" value="C:\FastaIndices" />
</bean>
-->

to

<!-- Enable Sequest integration and configure it to run on a remote pipeline server (using "sequest" as its location
     property value in its pipelineConfig.xml file). Give pointers to the directory where Sequest is installed,
     and a directory to use for storing FASTA index files. -->

<bean id="sequestTaskOverride" class="org.labkey.ms2.pipeline.sequest.SequestSearchTask$Factory">
    <property name="location" value="sequest"/>
    <property name="sequestInstallDir" value="C:\Program Files (x86)\Thermo\Discoverer\Tools\Sequest" />
    <property name="indexRootDir" value="C:\FastaIndices" />
</bean>

in addition:

• change the sequestInstallDir property value to be the installation of the Sequest binary on your server.
• change the location value to be webserver

1. Find all places in the file that contain a line that starts with <property name="location"...
2. On each line, change the value to be webserver
3. Save the file

Set the Enterprise Pipeline configuration directory

To configure the Enterprise Pipeline configuration directory, open the application.properties file and set this to the full path to <LABKEY_HOME>/config/:

context.pipelineConfig=/path/to/pipeline/config/dir

Restart your LabKey Server

Supported versions of Proteome Discoverer

Additional Features

• The Enhanced MS2 Sequest Pipeline includes the capability of indexing FASTA files using the makedb.exe utility. This makes your searches faster. It only works for Sequest. To tell Sequest to use indexed FASTA files, set the appropriate parameter on the MS2 search settings dialog. Learn more:
• Search and Process MS2 Data
• Configure Sequest Parameters
• API for submitting jobs