The OpenMS Proteomics Pipeline (TOPP) is a set of computational tools that can be chained together to tailor problem-specific analysis pipelines for HPLC-MS data. It transforms most of the OpenMS

OpenMS

OpenMS is an open-source C++ library for LC/MS data management and analyses. It offers an infrastructure for the development of mass spectrometry related software. OpenMS is free software available under the LGPL...

 functionality into small command line tools that are the building blocks for more complex analysis pipelines. The functionality of the tools ranges from data preprocessing (file format conversion, baseline reduction, noise reduction, peak picking, map alignment,...) over quantitation (isotope-labeled and label-free) to identification (wrapper tools for Mascot

Mascot (software)

Mascot is a software search engine that uses mass spectrometry data to identify proteins from primary sequence databases.Many research facilities utilize Mascot, either by private or public server for database searching....

, Sequest

SEQUEST

SEQUEST is a tandem mass spectrometry data analysis program used for protein identification. Sequest identifies collections of tandem mass spectra to peptide sequences that have been generated from databases of protein sequences.-Applications:...

, InsPecT and OMSSA).

TOPP is developed in the groups of Prof. Knut Reinert http://www.inf.fu-berlin.de/inst/ag-bio/ at the Free University of Berlin

Free University of Berlin

Freie Universität Berlin is one of the leading and most prestigious research universities in Germany and continental Europe. It distinguishes itself through its modern and international character. It is the largest of the four universities in Berlin. Research at the university is focused on the...

 and in the group of Prof. Kohlbacher http://www-bs.informatik.uni-tuebingen.de/ at the University of Tübingen.

For more detailed information about the TOPP tools, see the TOPP documentation of the latest release and the TOPP publication in the references.