pyOpenMS
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Introduction

  • Background

Getting started

  • Installation
  • Import pyopenms
  • Getting help
  • First look at data

Mass Spectrometry Concepts

  • MS Data
  • Chemistry
  • Peptides and Proteins
  • Oligonucleotides: RNA
  • Fragment spectrum generation
  • Spectrum alignment
  • Digestion
  • Identification Data
  • Quantitative Data

OpenMS Algorithms

  • Parameter Handling
  • Algorithms
  • Smoothing
  • Centroiding
  • Spectrum normalization
  • Charge and Isotope Deconvolution
  • Feature Detection
  • Map Alignment
  • Feature Linking
  • Peptide Search
  • Chromagraphic Analysis
  • Quality Control
  • Mass Decomposition
  • Export files for GNPS

Example Workflows

  • Identification by Accurate Mass
  • Untargeted Metabolomics Pre-Processing

How to contribute

  • Contribute

Advanced Topics

  • Reading Raw MS data
  • Other MS data formats
  • mzML files
  • Export to pandas DataFrame
  • Query MSExperiment with MassQL
  • Memory management
  • pyOpenMS in R
  • Build from source
  • Wrapping Workflow and wrapping new Classes
  • Interactive plots
  • Interfacing with ML libraries

Full API documentation

  • Full API documentation

Support

  • Support
  • Frequently Asked Questions
  • OpenMS Glossary
pyOpenMS
  • Search

© Copyright 2022, OpenMS Team. Revision a3643ead.

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