An open-source framework for mass spectrometry and TOPP – The OpenMS Proteomics Pipeline


There are two ways to obtain the OpenMS/TOPP documentation.

  • The documentation is contained in the OpenMS source package and binary packages.
  • The documentation of the latest release is available online.
  • The TOPP documentation can be found here.

The OpenMS tutorial and TOPP tutorial are included in the HTML documentation. For easier printing, we also provide them as PDF:

The OpenMS proteomics pipeline (TOPP)

Any program that is written in OpenMS can easily be made into a TOPPtool by simply using the OpenMS command line parser which is able to parse ParamXML, a powerful XML based description of the tool. Hence most analysis algorithms in OpenMS are available as stand alone tool which can be called on the command line or integrated into workflow engines via the CTD mechanism. A current list of TOPPtools can be found here.

The Common Tool Description (CTD)

The CTD is a format developed from the OpenMS team to allow the user to use TOPPtools also in other workflow engines. Each tool can output a CTD description of itself (the XML scheme for the CTD can be found here), which is then used by node generator program to generate nodes for other work flow engines.

The CTD mechanism is shared by OpenMS with other mature libraries like SeqAn andBALL.


Panning / Zooming (1D View)

Learn how to:

  • Pan a spectrum in 1D View
  • Zoom into a spectrum in 1D View

Panning / Zooming / 3D View

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

Class search engine

You can search the documentation of the latest release for class and struct names through the OpenMS class search engine. For convenience, a Firefox search plugin is available here.

OpenMS XML Formats

Here you can find the most recent XML schemas of the OpenMS formats.

These include:

  • FeatureXML (featureXML)
  • ConsensusXML (consensusXML)
  • IdXML (idXML)
  • ParamXML (ini)
  • TrafoXML (trafoXML)
  • ToolDescriptor (ttd)