.. _mzml-guide:

Converting raw data to mzML
===========================

We recommend using `msconvert <http://proteowizard.sourceforge.net/download.html>`_ to convert raw
data generated from the different instruments to mzML format. Files can be converted from a GUI or
from the command line. To convert all the files with names ending in :code:`.RAW` inside a
directory from the command line the following command can be used:

.. code-block:: bat

    msconvert *.RAW -o my_output_dir

If you are using a Waters instrument with lockspray correction, the :code:`scanEvent` filter can
be used to remove the signal from the lockspray.

.. code-block:: bat

    msconvert *.RAW --filter "msEvent 1" -o my_output_dir

To perform feature detection, data must be provided in centroid format. This can be done using
the :code:`peakPicking` filter option:

.. code-block:: bat

    msconvert data.RAW --filter "peakPicking cwt snr=1 peakSpace=0.01"

A :code:`snr=1` is recommended as noisy peaks will be removed during feature detection anyway.
:code:`peakSpacing` should be chosen according to the instrument used. For QTOF instruments a
value of 0.01 is recommended, but for higher resolution instruments, such as orbitrap or FT-ICR,
lower values may be used.