Visualization with TOPPView

Visualizing the data is the first step in quality control, an essential tool in understanding the data, and of course an essential step in pipeline development. OpenMS provides a convenient viewer for some of the data: TOPPView. The following screencasts will guide you through some of the basic features of TOPPView which is part of our standalone installer version of OpenMS.

Panning / Zooming (1D View)

Zoom into a spectrum in 1D view

  • All previous zoom levels are stored in a zoom history. The zoom history can be traversed using CTRL+/CTRL- or the mouse wheel (scroll up and down).
  • Zooming into the data: either mark an area in the current view with your mouse while holding the left mouse button plus the CTRL key to zoom to this area or use your mouse wheel to traverse the zoom history.
  • If you have reached the end of the history and keep on pressing CTRL+ or scroll up, the current area will be enlarged by a factor of 1.25
  • Pressing the Backspace key resets the zoom and zoom history.

Pan a spectrum in 1D view

  • Move the mouse while holding the mouse button down to translate the current view (when zoomed in).
  • Arrow keys can be used to translate the view without entering translate mode.

Panning / Zooming / 3D View

Switch into 3D view

  • Right click on your 2D map and select Switch to 3D view to examine your data in 3D mode.

Learn how to:

  • Pan a spectrum in 2D View
  • Zoom into a spectrum in 2D View
  • Switch into 3D View

Data Modes

Learn how to:

  • Switch between different data modes
  • Scale intensity

2D Projections

Learn how to:

  • Use the projections of 2D maps in TOPPView

Command line

OpenMS is a versatile open-source library for mass spectrometry data analysis. Based on this library, we offer a collection of command-line tools ready to be used by end users. These so-called TOPP tools (short for “The OpenMS Proteomics Pipeline”) can be understood as small building blocks of arbitrary complex data analysis workflows.

TOPP INI files
The command line and INI file parameters of the TOPP tools vary due to the different tasks of the TOPP tools. However, all TOPP tools share this common interface:
  • -ini <file> Use the given TOPP INI file
  • -debug <n> Sets the debug level (default: ’0’)
  • -write_ini <file> Writes an example INI file
  • –help Shows a help page for the command line and INI file options
  • –helphelp Shows a more extensive help page including advanced options and algorithm parameters
  • -log <file> Location of the log file (if specified)
  • -no_progress Disables progress logging to command line
Each TOPP tool has its own set of parameters which can be specified at the command line. However, a more convenient (and persistent) way to handle larger sets of parameters is to use TOPP INI files. TOPP INI files are XML-based and can contain the configuration of one or several TOPP tools. The easiest way of creating an INI file is to advise the corresponding TOPP tool to write its default configuration file using the argument ’-write_ini’ on the command line. Now the INI file can be adapted to your needs using the INIFileEditor which is shipped with the other TOPP tools.
Example use cases
General information about peak and feature maps
If you want some general information about a peak or feature map, use the FileInfo tool. See the ’FileInfo –help’ for details.
  • It can print RT, m/z and intensity ranges, the overall number of peaks, and the distribution of MS levels
  • It can print a statistical summary of intensities
  • It can print some meta information
  • It can validate XML files against their schema
  • It can check for corrupt data in peak files

Example:

FileInfo -s -in infile.mzML
Extracting part of the data from a file
If you want to extract part of the data from a mzML file, you can use the FileFilter tool. It allows filtering for RT, m/z, intensity range and for MS level as well as for other criteria. To extract the MS/MS scans between retention time 100 s and 1500 s, you would use the following command:

FileFilter -in myinfile.mzML -levels 2 -rt 100:1500 -out myoutfile.mzML

More Information

You can download a package containing all available command line tools from our Downloads page.

The most convenient way to retrieve the source code is to check it out from https://github.com/OpenMS/OpenMS

The online documentation contains the installation and build instructions.

See the Support page for the documentation of the newest release.