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Update mainWindow.rst
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christophwi committed Oct 29, 2018
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Expand Up @@ -29,10 +29,9 @@ Scan Protocol Library
^^^^^^^^^^^^^^^^^^^^^
.. figure:: figures/image014.jpg
:align: left
Scan protocols implement various the acquisition strategies supported by our software. Every scan proto-col has a certain type (BoxCar, EasiTag…), a unique four-digit identification number and a short experiment description. All scan protocols are stored in a library.

.. figure:: figures/image011.png
:align: right
Scan protocols implement various the acquisition strategies supported by our software. Every scan proto-col has a certain type (BoxCar, EasiTag…), a unique four-digit identification number and a short experiment description. All scan protocols are stored in a library.
In the scan protocol section of the software you can manage the library.

New scan protocol:
Expand Down Expand Up @@ -67,6 +66,7 @@ There are three operation modes:
Setup Mode
^^^^^^^^^^
.. figure:: figures/image019.png
:width: 250px
:align: right
This is the initial operation mode after software startup. In this modus, three parts of MaxQuant.Live (Sec. 4) can be configured.
After loading the log-directory, the scan protocol library and connecting the instru-ment,
Expand All @@ -75,6 +75,7 @@ MaxQuant.Live switches to the Listening Mode.
Listening Mode
^^^^^^^^^^^^^^
.. figure:: figures/image021.png
:width: 250px
:align: right
In this mode, the software receives all the spectra acquired by the instrument but does not send any commands
to the mass spectrometer. MaxQuant.Live is therefore not affecting the data acquisition of the mass spectrometer.
Expand All @@ -84,6 +85,7 @@ MaxQuant.Live switches to the Running Mode.
Running Mode
^^^^^^^^^^^^
.. figure:: figures/image023.png
:width: 250px
:align: right
This operation mode is active during the execution of a scan protocol.
Afterwards, the software automati-cally switches back to the listening mode.

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