.. _pyms-demo:

**************
Introduction
**************

Examples of PyMassSpec use given in the User Guide.

Further examples can be found at https://github.com/domdfcoding/PyMassSpec/tree/master/pyms-demo/jupyter


Chapter 1 -- GC-MS Raw Data Model
-----------------------------------

:ref:`20e -- Reading of GC-MS raw data in the mzML format, and some properties of raw data object. There isn't yet an example mzML file so this demo doesn't yet do anything. <demo-20e>`


Chapter 2 -- GC-MS data derived objects
-----------------------------------------

:ref:`32 -- Saving IonChromatogram and IntensityMatrix information.  <demo-32>`

.. TODO: 55 and 56

Chapter 5 -- Peak alignment by dynamic programming.
------------------------------------------------------

:ref:`64 -- Peak alignment with the "common ion" filtering. <demo-64>`

.. TODO: Parallel processing with PyMassSpec.
.. TODO: :ref:`x10 -- An example of parallel processing of data. Shows how to loop over all ICs in an intensity matrix, and perform noise smoothing on each IC (in parallel). Please see User Guide for instructions how to run this example on multiple CPUs. <demo-x10>