TOPP tutorial

This tutorial introduces you to TOPP and TOPPView. We start by describing the intent and concept of TOPP compared to OpenMS. Then we introduce you to the handling of TOPPView which is our central GUI. Apart from viewing data you are also able to analyze it in TOPPView using selected TOPP tools. How do do this is explained in the third part of the Tutorial. Finally we give a complete list and command line interfaces for all TOPP tools contained in the release.

Concepts

This part of the tutorial explains the intent of TOPP and OpenMS .

TOPPView main interface

This part of the tutorial illustrates the main features of TOPPView and shows its basic use.

• Introduction
• The views
• Display modes and view options
• Data analysis
• Data editing
• Hotkeys table

Calling TOPP tools from TOPPView

This part of the tutorial illustrates how to interactively analyse proteomics data using TOPP tools from within TOPPView.

• Smoothing raw data
• Subtracting a baseline from a spectrum
• Picking peaks
• Feature detection on centroided data

Advanced Users: Tips & Tricks

Learn how to use advanced functionalities, increasing productivity in TOPP for Advanced Users .

Scripting with TOPP

This part of the tutorial will give you a detailed overview of the most important TOPP tools. First, some basics that you will need for every TOPP tool are explained, then several example pipelines are shown.

• General introduction
• File Handling
• Profile data processing
• Calibration
• Map alignment
• Feature detection
• Feature grouping
• Consensus peptide identification
• Peptide property prediction
• Quality Control
• Conversion between OpenMS XML formats and text formats