xTracker software User Guide
Introduction
xTracker provides a generic, platform-independent pipeline to do proteomics
quantitation. The pipeline is composed of four steps: load identification, load raw spectral
data, quantitation and output, each step is implemented in a specific piece of codes, termed
as a plugin. The various plugins for one step can be interchangeable, which makes xTracker
flexible. It supports the current PSI standards: mzML for raw spectral data, mzIdentML for
identifications and mzQuantML for quantitation result. The project is hosted at http://code.
google.com/p/x-tracker/ where the source codes are available. The software is available at
http://code.google.com/p/x-tracker/downloads/list.
There is a configuration file in the mzQuantML format which tells the software which
plugin to be used for each step in the pipeline along with other information, e.g. the type of
the pipeline (MS2/MS1 based), which level quantitation is needed (feature, peptide or
protein) etc. For most plugins, there are supplementary parameter files with the suffix .xtp or
.xml to configure the plugin specific parameters. For example, the identification plugin needs
the parameter file to describe the relationship between identification files and the
corresponding spectral files. Therefore it is vital to set up the configuration file and parameter
files correctly.
There are two wrappers (Proteo-suite and under Galaxy framework) being developed to
provide GUIs to make these setting easier and error-free. However, it is still important for the
end user to understand the content in these files, which allow them to configure them
manually and use xTracker on its own.
How to configure the pipeline configuration file
The configuration file is actually a mzQuantML file, please refer to its official specification
document at http://code.google.com/p/mzquantml/source/browse/trunk/
documentation/mzQuantML1.0.0-rc.doc. There is also a guideline to mzQuantML
http://code.google.com/p/mzquantml/source/browse/trunk/documentation/TwentyMinuteGuid
eToMzQuantML.docx, which is helpful.
The mandatory elements in the configuration file will be discussed below:
AnalysisSummary section summarize information about the pipeline in terms of the type of
analysis and quantitation levels.
In the above example, it is clearly about an iTraq quantitation pipeline which asks for
three levels of quantitation: feature, peptide and protein.
SoftwareList section lists the software used to acquire and/or process the data in the
mzQuantML file. In this case, it does not need to be changed at all as xTracker will be the
selected software.
DataProcessingList section contains the descriptions of data processing applied to the
data. In xTracker, it is used to define the name of plugins and their corresponding parameter
files.
Please note that the value of software_ref must be equal to “xTRACKER”. The
ProcessingMethod elements under the DataProcessing are used to define the plugins to be
used in the pipeline. Each ProcessingMethod element has three userParam for plugin type,
plugin name and plugin parameter file respectively.
InputFiles section describes all raw spectral files and identification files used in the pipeline.
All the files defined in the load identification plugin parameter file must be listed here.
Otherwise the software reports the error and terminates.
AssayList lists the assays represented by the file, where each assay captures a single
experimental run (e.g. the report ions in iTRAQ used in the example below, heave and light
peptides in the SILAC)
StudyVariableList section describes the experimental conditions used to group results. The
conditions could be wild against treated or time points in a time course.
CvList section reflects the controlled vocabularies (cv) used in the file.
Execution of the software
After downloading the zip file from http://code.google.com/p/x-tracker/downloads/list, unzip it
into a folder (for example, the xtracker folder). In the command shell, enter the xtracker
folder, and then type the command: java –jar xTracker.jar. The usage information will be
displayed. There are two options: one is the mandatory which defines the configuration file in
the mzQuantML format (explained in the section How to configure the pipeline configuration
file), the other one is optional which defines the folder where all plugin-related files locate.