Chapter 12: OpenMS: A Modular, Open-Source Workflow System for the Analysis of Quantitative Proteomics Data

OpenMS is a software framework for the analysis and visualisation of proteomics data. It consists of over 100 individual tools which can be combined to simple or more complex analysis workflows. The tools are based on a well-documented, open-source C++ library that can also be accessed via a Python interface. Besides these tools, OpenMS provides wrappers for many popular external software solutions such as search engines and protein inference algorithms. The workflows can be run on simple desktop computers as well as powerful computing clusters. In this chapter, we will discuss four workflows of increasing complexity and thereby introduce new users to the basic concepts of OpenMS.