starting to add doc of new mqlive version

christophwi · Dec 18, 2019 · 11dfe38 · 11dfe38
1 parent 44824de
commit 11dfe38
Show file tree

Hide file tree

Showing 5 changed files with 10 additions and 10 deletions.
diff --git a/docs/appBoxCar.rst b/docs/appBoxCar.rst
@@ -1,7 +1,7 @@
 BoxCar
 ======
 
-.. figure:: figures/image029.png
+.. image:: figures/image029.png
     :width: 200px
     :align: left
 
@@ -115,7 +115,7 @@ MaxQuant is a software package for quantitative high resolution mass-spectrometr
 3. Set parameter groups for each raw file. BoxCar and shotgun experiments need to be in separate parameter groups. Fractions (if applicable) should not be specified when matching from a fractionated peptide library into single runs is intended.
 4. Set group specific parameters. Select “Type / Standard” for each experiment group containing regular shotgun experiments and “Type / BoxCar” for each group containing BoxCar experiments, respectively. 
 
-.. figure:: figures/image038.png
+.. image:: figures/image038.png
     :width: 100%
     :align: center
 

diff --git a/docs/appEasiTag.rst b/docs/appEasiTag.rst
@@ -1,7 +1,7 @@
 Easitag and TopN
 =================
 
-.. figure:: figures/image031.png
+.. image:: figures/image031.png
     :width: 200px
     :align: left   
 

diff --git a/docs/appTargeting.rst b/docs/appTargeting.rst
@@ -1,7 +1,7 @@
 Targeting
 =========
 
-.. figure:: figures/TargetingApp.png
+.. image:: figures/TargetingApp.png
     :width: 200px
     :align: left   
 
@@ -20,8 +20,8 @@ Steps to setup a targeting run
 2. Set global parameters
 3. Set up targeting action
 
-Peptide ion list
-----------------
+Peptide ions list
+-----------------
 The targeting should comprise a set of peptides of interest and a set of high abundant peptides used for the 
 real-time corrections of mass-to-charge values, expected retention times and peptide intensities. 
 

diff --git a/docs/manageScanProtocol.rst b/docs/manageScanProtocol.rst
@@ -3,7 +3,7 @@ Create and edit Scan Protocols
 
 New scan protocol
 """"""""""""""""""
-.. figure:: figures/AppStore.png
+.. image:: figures/AppStore.png
     :width: 250px
     :align: left
 
@@ -15,7 +15,7 @@ The scan protocol will be saved as file in the scan protocol folder and appear i
 
 Edit scan protocols
 """"""""""""""""""""
-.. figure:: figures/image017.png
+.. image:: figures/image017.png
     :width: 250px
     :align: right
 

diff --git a/docs/runScanProtocol.rst b/docs/runScanProtocol.rst
@@ -22,7 +22,7 @@ method starts.
 
 Xcalibur method setup
 """""""""""""""""""""
-.. figure:: figures/image025.png
+.. image:: figures/image025.png
     :width: 300px
     :align: right
 
@@ -39,7 +39,7 @@ Data acquisition
 3. Open the Xcalibur software and set up a new acquisition sequence. Select the Xcalibur method generated above as the instrument method for your BoxCar runs. Note that different MaxQuant.Live protocols require different Xcalibur methods.
 4. Start the acquisition sequence. MaxQuant.Live will take over control as soon as the trigger signal (full MS scan with a scan range starting at m/z 909, ‘magic scan’) is identified. The home view will indicate that the software is now in Running Mode (Sec. 5.3). Acquisition will stop automatically at the end of the LC-MS run and the Xcalibur sequence will continue with the next run (if applicable). Stop scan protocol stops any running protocol immediately. 
 
-.. figure:: figures/image027.png
+.. image:: figures/image027.png
     :width: 100%
     :align: center