openms-doc - library for LC/MS data management and analysis - documentation

Author

This manual page was written by Filippo Rusconi <lopippo@debian.org>. Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 3, published by the Free Software Foundation. On a Debian system the complete text of the GNU General Public License version 3 can be found in the file `/usr/share/common-licenses/GPL-3'. November 2012 OPENMS-DOC(7)

Bibliographical Reference To Be Cited

Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher (2008) OpenMS – an Open- Source Software Framework for Mass Spectrometry. BMCBioinformatics, 9:163. doi:10.1186/1471-2105-9-163.

Description

This manual page documents briefly the openms-doc package that brings a full set of documentation and tutorials to the OpenMS software framework. OpenMS offers an infrastructure for the development of mass spectrometry-related software and powerful 2D and 3D visualization solutions. OpenMS offers analyses for various quantitation protocols, including label-free quantitation, SILAC, iTRAQ, SRM, SWATH… It provides build-in algorithms for de-novo identification and database search, as well as adapters to other state- of-the art tools like X!Tandem, Mascot, OMSSA… OpenMS supports the Proteomics Standard Initiative (PSI) formats for MS data and supports easy integration of tools into workflow engines like Knime, Galaxy, WS- Pgrade, and TOPPAS via the TOPPtools concept and a unified parameter handling.