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OpenSwath

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Hannes Roest edited this page Mar 7, 2022 · 28 revisions

This page is intended to document how OpenSwath works on a technical level

Executable

OpenSwathWorkflow is an executable that is most commonly used to run OpenSwath: https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/UTILS_OpenSwathWorkflow.html

Algorithm

The executable uses the OpenSwathWorkflow Algorithm to perform its job: https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/classOpenMS_1_1OpenSwathWorkflow.html

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OpenSwathWorkflow

Introduction

Workflow

  1. Chromatogram Extraction

    1. Mapping Transitions To SWATHs
    2. Preparing the Batches
    3. Perform Extraction
    4. Write Out Chromatogram

  2. Peak Group Identification

    1. Pick Peaks in Each Chromatogram
    2. Create Peak Groups

  3. Scoring

    1. Chromatographic Scoring
    2. Library Scores
    3. Single Spectrum Scores
    4. Sonar Scores
    5. Unique Ion Signature Scores
    6. Intensity Score
    7. Elution Model Score

Extras

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