TOPP#

TOPP - The OpenMS Proteomics Pipeline is a pipeline for the analysis of HPLC-MS data. It consists of several small applications that can be chained to create analysis pipelines tailored for a specific problem.

The TOPP tools are divided into several subgroups, like graphical tools, file handling, signal processing and preprocessing, quantitation, map alignment, protein/peptide identification, protein/peptide processing, targeted experiments and OpenSWATH, peptide property prediction, cross-linking, quality-control, among a few.

Few of the graphical tools are explained below:

For advanced documentation on every TOPP tool, see the OpenMS TOPP API Reference.

UTILS#

Besides TOPP, OpenMS offers range of other tools. They are not included in TOPP as they are not part of typical analysis pipelines. A set of command line utilities, similar to TOPP tools, mostly used during pipeline construction or parameter optimization.