TOPP Tutorial

The following tutorial is an introduction to TOPP and TOPPView. Let’s start with understanding the intent and concept of TOPP compared to OpenMS. Later, we will move to the handling of TOPPView which is our central GUI. Apart from viewing data, TOPPView can also be used to analyze it using selected TOPP tools; how-to is explained in the third part of the tutorial.

Finally, the tutorial lists the command line interfaces for all TOPP tools contained in the release.

Concepts

Let’s understand the intent of TOPP and OpenMS.

• TOPP and OpenMS

TOPPView Main Interface

In the following section, we will learn about the main features of TOPPView and its basic uses.

• TOPPView Introduction
• Views in TOPPView
• Display Modes and View Options in TOPPView
• Data Analysis in TOPPView
• Data Editing in TOPPView
• TOPPView Hotkeys

Calling TOPP tools from TOPPView

The following 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

Read TOPP for Advanced Users to know more about how to use advanced functionalities, increasing productivity.

• TOPP for Advanced Users

Scripting with TOPP

This part of the tutorial gives a detailed overview of the most important TOPP tools. First, some basics needed 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