Version 4 (modified by b.hoekman@…, 4 years ago)

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User Manual

Read this first

The current version of the program offers command line mode execution. A user friendly GUI is currently under development. All enhancements and modifications in the code and the current manual will be announced on the Trac web page of msCompare under the link https://trac.nbic.nl/mscompare/. Human urine LC-MS data are accessible at TRANCHE (link will follow soon) and the annotated parameters file of mzMine and presented in an article submitted to Nature Methods and can be used as an example. Other types of data can be processed as well.

OS and dependency requirements

Execution of msCompare requires a Linux operating system, due to execution of some Linux specific programs, and requires Sun Java version 6. It further requires the installation of the original data processing programs OpenMS (v1.2 and v1.5, for feature quantification and v1.5 for feature matching), Superhirn, and MZmine(v0.60). Minimum RAM requirement is depending on the size of the data. We recommend a minimum of 4 GB, but a PC equipped with 16 or 64GB of RAM is preferable.

Data Analysis

Raw LC-MS data should be converted into mzXML format. This is followed by setting up the workflow xml file, which defines the workflow to analyze the LC-MS data as well as the parameters for the individual modules. msCompare allows the execution of one module or a complete workflow based on the description in the workflow XML file.

Running the program

The workflow, as defined in the workflow xml file, can be run on the command line: java -Xmx3000m -jar msCompare.jar “path to the workflow xml file”. MZmine requires the amount of memory specified for the msCompare program and is using /tmp/… as standard temporary file location. This location can be overridden using standard java settings. Other programs (not java) will allocate memory by themselves, which is depending on the settings used for the concerned module and from the size and type of the analyzed data.

Defining the workflow

The workflow execution including link to data and results is defined in the workflow XML file. The example workflow XML file can be used to run the provided example data set of spiked urine samples at different concentration levels with the mzMine homogenous data processing workflow.