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. The first is to install the LabKey Remote Pipeline Server software on an existing computer with Proteome Discoverer installed. The second is to 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 for more information on the Enterprise Pipeline.

Install JAVA on the computer running Proteome Discoverer 1.1

This software will be installed on the computer running Proteome Discoverer 1.1.

Install the LabKey Remote Pipeline Server Software

Follow the instructions at Configure Remote Pipeline Server to install the LabKey Remote Pipeline Server on the server running Proteome Discover.

Define the Location of the Remote Pipeline Server

In order for the newly installed Remote Pipeline Server to start accepting tasks from the LabKey Server, we will need to define a server location. This is configured in the pipelineConfig.xml. Open the pipelineConfig.xml file you created in the previous step and change

<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

Open the configuration file ms2Config.xml, that was created in the previous step, with your favorite editor. At the bottom of the file, you will want to 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>

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

Follow the instructions at JMS Queue. We recommend installing this software on your LabKey Server.

Configure your LabKey Server to use the Enterprise Pipeline

The changes below will be made on your LabKey Server.

1) Enable Communication with the ActiveMQ JMS Queue:

You will need to uncomment the JMS configuration settings in the LabKey configuration file (labkey.xml). The labkey.xml is normally located in CATALINA_HOME/conf/Catalina/localhost/labkey.xml. Change

<!-- <Resource name="jms/ConnectionFactory" auth="Container"
type="org.apache.activemq.ActiveMQConnectionFactory"
factory="org.apache.activemq.jndi.JNDIReferenceFactory"
description="JMS Connection Factory"
brokerURL="vm://localhost?broker.persistent=false&amp;broker.useJmx=false"
brokerName="LocalActiveMQBroker"/> -->

to

<Resource name="jms/ConnectionFactory" auth="Container"
type="org.apache.activemq.ActiveMQConnectionFactory"
factory="org.apache.activemq.jndi.JNDIReferenceFactory"
description="JMS Connection Factory"
brokerURL="tcp://@@JMSQUEUE@@:61616"
brokerName="LocalActiveMQBroker"/>
  • where @@JMSQUEUE@@ is the hostname or IP address of the server where you installed the ActiveMQ software.
2) Create the Enterprise Pipeline configuration directory

Create the Enterprise Pipeline configuration directory for your server. The recommended location for this directory is LABKEY_HOME/config. Where LABKEY_HOME is the directory where LabKey Server is installed.

3) Enable the Enterprise Pipeline configuration directory

To configure the Enterprise Pipeline configuration directory, open the LabKey configuration file (labkey.xml) and change

<!-- Pipeline configuration -->
<!-- <Parameter name="org.labkey.api.pipeline.config" value="C:\proj\labkey\docs\mule\config-demo"/> -->

to

<!-- Pipeline configuration -->
<Parameter name="org.labkey.api.pipeline.config" value="@@LABKEY_HOME@@\config"/>
  • where @@LABKEY_HOME@@\config is the configuration directory location. The default setting is LABKEY_HOME\config. (i.e., replace @@LABKEY_HOME@@ with the full path to the LABKEY_HOME directory for your installation)
4) Copy the ms2Config.xml file you created and edited above into the Enterprise Pipeline configuration directory

Restart your LabKey Server

All the configuration changes have been made to your LabKey Server. Now restart your LabKey Server and you can start testing.


Install Proteome Discoverer on LabKey Server

In this option, you will install the Proteome Discoverer software on your LabKey Server. NOTE: You can only use this option if your LabKey Server is installed on a Windows XP or Windows 7 computer.

Install Proteome Discoverer 1.1

Install the Proteome Discoverer software on your LabKey Server following the vendor's instructions. Ensure that the directory that contains sequest.exe and makedb.exe is placed on the PATH environment variable for the server.

Download and Expand the Enterprise Pipeline Configuration files

  1. Goto 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 goto the installation directory for your LabKey Server
  2. Create a new directory named config
  3. Write down the full path of this new directory
Install ms2Config.xml file into the configuration directory
  1. Goto 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
Edit the ms2Config.xml file Open the configuration file ms2Config.xml that was created in the previous step, with your favorite editor.

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
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"...
  2. On each line, change the value to be webserver
  3. Save the file

Enable the Enterprise Pipeline configuration directory

To configure the Enterprise Pipeline configuration directory, open the LabKey configuration file (labkey.xml) and change

<!-- Pipeline configuration -->
<!-- <Parameter name="org.labkey.api.pipeline.config" value="C:\proj\labkey\docs\mule\config-demo"/> -->

to

<!-- Pipeline configuration -->
<Parameter name="org.labkey.api.pipeline.config" value="@@LABKEY_HOME@@\config"/>
  • where @@LABKEY_HOME@@\config is the configuration directory location. The default setting is LABKEY_HOME\config. (i.e., replace @@LABKEY_HOME@@ with the full path to the LABKEY_HOME directory for your installation)

Restart your LabKey Server

All the configuration changes have been made to your LabKey Server. Now restart your LabKey Server and you can start testing.

Supported versions of Proteome Discoverer

LabKey currently only supports Proteome Discoverer 1.1. While other versions of Proteome Discoverer may work, they have not been tested by LabKey.

How to Upgrade the Enhanced Sequest MS2 Pipeline

This page is currently under development: If you need assistance with an upgrade, please contact us on the Support Discussion Board

Additional Features

  • The Enhanced MS2 Sequest Pipeline includes the capability of indexing FASTA files using the makedb.exe utility.&nbsp; 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. See the following for more information
  • API for submitting jobs

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