OpenMS  3.0.0
User Quickstart Guide

Read the User Quickstart guide to gain a brief understanding of key concepts and how to use tools. For more in-depth information, you should consult the entire documentation.

What is OpenMS

OpenMS is a free, open-source C++ library with Python bindings. It is commonly used for liquid chromatography-mass spectrometry (LC-MS) data management and analyses. OpenMS provides an infrastructure for the rapid development of mass spectrometry related software as well as a rich toolset built on top of it. OpenMS is available under the three clause BSD licence and runs under Windows, macOS and Linux operating systems.

Background

Mass spectometry is a sensitive, high-throughput technique used for the quantitative and qualitative measurement of molecules including nucleic acids, proteins and metabolites.

Basic Concepts of OpenMS/TOPP

Before using OpenMS, you need to be familiar with the following terms:
TOPPView: A design tool that is used to view and explore LC-MS data, alignments, groups, peptide identifications and more.
TOPPAS: A graphical workflow design tool that is used to create pipelines from all TOPP tools (and UTILS).
TOPP tools: A set of command line tools. Each of these command line tools is a building block of an analysis pipeline and are chained together in a way that fits the requirements of the user. The TOPP tools are accessible from a command prompt/shell or via TOPPAS. See also: TOPP tutorial and TOPP documentation
UTILS: Similar to TOPP tools, but with more supporting character, which you'd rarely use in a productive pipeline - but rather during pipeline construction or parameter optimization. See also: UTILS documentation

How to run a tool

We'd recommend using TOPPAS. A good start are the example pipelines (see "File" –> "Open example file" within TOPPAS). In parallel you can read the documentation of the tools (see TOPP tutorial, TOPP documentation) and the one of TOPPAS (TOPPAS tutorial).

Alternatively, you can use the command line and call tools directly. In this case you'll probably want to use some type of shell script for automation.

Parameters

The default parameters of each tool can usually be tweaked to fit your data and improve results.

Where do you change them?!

TOPPAS: Double-click the node of which you want to change the parameters. A short docu for each parameter will show up once you select it. All parameters which would be available on the command line and in the INI file are shown here as well.

Command line: Very basic parameters can be set on the command line, e.g. FileFilter -rt 1000:2000 .....
Doing this for all parameters would create a very long list, thus, we use so-called ".ini" files to provide full parameter sets to TOPP tools. If no INI file is given, default parameters are used. To get a default .ini use

<tool> -write_ini <file>

e.g.
FileFilter -write_ini filefilter.ini

Now, you can edit the INI file (which is a XML file) using our INIFileEditor, which is another GUI tool shipped with OpenMS and similar to the one build into TOPPAS.

How do I feed the INI file to a tool?!

TOPPAS: Once you changed the parameters of a node and clicked "Ok", the parameters are in effect. Because they are part of the TOPPAS workflow, they are saved together with the workflow.

Command line: Simply supply the INI file via the -ini flag, e.g.,

<tool> -ini <file>

e.g.
FileFilter -ini filefilter.ini

What parameters need changing and to what value?!

This is tricky and its not possible to give a general answer. In general, you should read the tool description, change the parameters and compare the results using TOPPView if possible. If that does not help try the OpenMS mailing list and ask, but provide us with the details we need in order to help you (see www.openms.de/BUGS).