User guide
==========

This guide is for users that want to use pyopenms to develop and/or prototype scripts and
programs for mass spectrometry data analysis and visualization.

You can find the full table of contents in the following. On every page, you can also
navigate this table by using the left sidebar. The right sidebar shows the page's
headings and structure.

.. toctree::
   :maxdepth: 2

   background

.. toctree::
   :maxdepth: 2
   :caption: Getting started

   installation
   first_steps

.. toctree::
   :maxdepth: 2
   :caption: Mass Spectrometry Concepts

   ms_data
   chemistry
   peptides_proteins
   oligonucleotides_rna
   fragment_spectrum_generation
   spectrum_alignment
   digestion
   identification_data
   quantitative_data

.. toctree::
   :maxdepth: 2
   :caption: OpenMS Algorithms

   parameter_handling
   algorithms
   smoothing
   centroiding
   spectrum_normalization
   spectrum_merging
   charge_isotope_deconvolution
   feature_detection
   map_alignment
   adduct_detection
   feature_linking
   peptide_search
   chromatographic_analysis
   quality_control
   mass_decomposition
   export_files_GNPS

.. toctree::
   :maxdepth: 2
   :caption: Example Workflows

   identification_accurate_mass
   untargeted_metabolomics_preprocessing

.. toctree::
   :maxdepth: 2
   :caption: Advanced Topics

   logging
   reading_raw_ms_data
   other_ms_data_formats
   mzml_files
   scoring_spectra_hyperscore
   export_pandas_dataframe
   query_msexperiment_massql
   memory_management
   pyopenms_in_r
   interactive_plots
   interfacing_ml_libraries

.. toctree::
   :maxdepth: 2
   :caption: Support

   support
   faq
   glossary


Indices and Tables
==================

* :ref:`genindex`