LipidXplorer Tutorial - Revision history

B.hossen at 13:21, 17 August 2026

2026-08-17T13:21:12Z

Nils.hoffmann: /* Specify the import settings */

2019-10-13T09:29:34Z

Specify the import settings

Falmachot: /* Specify the import settings */

2019-09-13T10:57:03Z

Specify the import settings

Falmachot: /* Specify the import settings */

2019-09-13T10:56:16Z

Specify the import settings

Falmachot: /* Specify the import settings */

2019-09-13T10:55:16Z

Specify the import settings

Falmachot: /* Specify the import settings */

2019-09-12T09:47:21Z

Specify the import settings

Falmachot: /* The LipidXplorer graphical user interface */

2019-09-12T09:43:16Z

The LipidXplorer graphical user interface

Falmachot: /* The LipidXplorer graphical user interface */

2019-09-12T09:42:04Z

The LipidXplorer graphical user interface

Falmachot: /* The LipidXplorer graphical user interface */

2019-09-12T09:41:14Z

The LipidXplorer graphical user interface

Falmachot: /* The LipidXplorer graphical user interface */

2019-09-12T09:40:54Z

The LipidXplorer graphical user interface

@@ Line 10: / Line 10: @@
 *[[File:Spectra tutorial.zip]]
-Open the *.zip file and store the content of <tt>spectra_tutorial\spectra_Ecoli_negative\*</tt> to a place of your choice. LipidXplorer cames with a suggested folder structure. You can store the spectra under <tt>LipidXplorer\spectra\negative\</tt>
+Unzip the *.zip file in your desired location. Inside you will find a mzML folder which contains mzML data files that are converted from raw data using MSConvert.
 ===The LipidXplorer workflow===
@@ Line 33: / Line 33: @@
 [[Image:lx128_source_1.png|400px|right|LipidXplorer Import Source panel]]
-Open LipidXplorer and you will see the 'Import Source' panel. Click on the green 'Browse' button and select the folder
+Open LipidXplorer and you will see the 'Import Source' panel. Click on the 'Browse' button and select the mzML folder in unzipped Spectra tutorial file.
-*<tt>LipidXplorer\spectra\negative\spectra_EColi_negative\spec_neg_100000</tt> or
+This folder contains 12 acquisitions of mice lung tissue on Q Exactive Orbitrap Mass Spectrometers (MS) in both positive and negative mode.
-This folder contains 4 acquisitions of E.coli on an LTQ Orbitrap with high resolution MS and low resolution MS/MS spectra in negative mode.
+Now the input folder with the spectra is selected. Make sure to have 'mzML' selected next to the 'Browse' button, because the spectra are in mzML format.
 <br clear = "all"/>
@@ Line 51: / Line 48: @@
 For every import, machine-specific settings have to be set.
-'''LipidXplorer 1.2.8''' offers new import settings which are the MSFilter and MSMSFilter.
+From '''LipidXplorer 1.2.8''', it offers new import settings which are the MSFilter and MSMSFilter.
 The MSFilter and MSMSFilter take a value between  0 and 1 that can be chosen to represent the fraction of scans in which a certain peak has to be present.
 The filter is applied for both MS and MS/MS according to the given import setting for each scan type.
@@ Line 58: / Line 55: @@
 Moreover, the frequency-filter itself leads to a consistent intensity report for each acquisition file and in the aligned masterscan. In this perspective, one has to expect a reduction in a number of lipid identifications without losing abundant lipids.
-All settings together can be stored in the file given at the top of the panel. 'lpdxImportSettings.ini' is the standard file in which a small collection of configuration are already stored. Select the configuration 'FAS_LTQ_100000MS1' under 'Select a Configuration'. These are the appropriate settings for the selected spectra.
+Click the 'Browse' button and upload the lpdxImportSettings_mice_lung.ini file. Then select the appropriate configuration from the dropdown.
 Now hit 'Start Import' on the bottom of the panel and the import will start.

@@ Line 51: / Line 51: @@
 For every import, machine-specific settings have to be set.
-The '''LipidXplore 1.2.8''' offers new import settings which are the MSFilter and MSMSFilter.
+'''LipidXplorer 1.2.8''' offers new import settings which are the MSFilter and MSMSFilter.
 The MSFilter and MSMSFilter take a value between  0 and 1 that can be chosen to represent the fraction of scans in which a certain peak has to be present.
 The filter is applied for both MS and MS/MS according to the given import setting for each scan type.

@@ Line 56: / Line 56: @@
 For each precursor ion, all associated MS/MS scans are collected according to the selection window. The counting of MS/MS scans and the association of the precursor are done automatically.
 Accordingly, the number of MS/MS scan can vary for each precursor ion in the shotgun acquisition, as might occur when using a DDA strategy.
-Moreover, the frequency-filter itself leads to a consistent intensity report for each acquisition file and in the aligned Masterscan. In this perspective, one has to expect a reduction in a number of lipid identifications without losing abundant lipids.
+Moreover, the frequency-filter itself leads to a consistent intensity report for each acquisition file and in the aligned masterscan. In this perspective, one has to expect a reduction in a number of lipid identifications without losing abundant lipids.
 All settings together can be stored in the file given at the top of the panel. 'lpdxImportSettings.ini' is the standard file in which a small collection of configuration are already stored. Select the configuration 'FAS_LTQ_100000MS1' under 'Select a Configuration'. These are the appropriate settings for the selected spectra.

@@ Line 54: / Line 54: @@
 The MSFilter and MSMSFilter take a value between  0 and 1 that can be chosen to represent the fraction of scans in which a certain peak has to be present.
 The filter is applied for both MS and MS/MS according to the given import setting for each scan type.
-For each precursor ion, all associated MS/MS scans are collected according to the selection window. The counting of MS/MS scans and association of precursor is done automatically.
+For each precursor ion, all associated MS/MS scans are collected according to the selection window. The counting of MS/MS scans and the association of the precursor are done automatically.
 Accordingly, the number of MS/MS scan can vary for each precursor ion in the shotgun acquisition, as might occur when using a DDA strategy.
 Moreover, the frequency-filter itself leads to a consistent intensity report for each acquisition file and in the aligned Masterscan. In this perspective, one has to expect a reduction in a number of lipid identifications without losing abundant lipids.

@@ Line 51: / Line 51: @@
 For every import, machine-specific settings have to be set.
-The '''LipidXplore 1.2.8''' offers new import settings which are the MSFilter and MSMSFilter
+The '''LipidXplore 1.2.8''' offers new import settings which are the MSFilter and MSMSFilter.
-The MSFilter and MSMSFilter take a value between  0 and 1 can be chosen representing the fraction of scans in which a certain peak has to be present.
+The MSFilter and MSMSFilter take a value between  0 and 1 that can be chosen to represent the fraction of scans in which a certain peak has to be present.
 The filter is applied for both MS and MS/MS according to the given import setting for each scan type.
-For each precursor ion all associated MS/MS scans are collected according to the selection window. Counting of MS/MS scans and association of precursor is done automatically.
+For each precursor ion, all associated MS/MS scans are collected according to the selection window. The counting of MS/MS scans and association of precursor is done automatically.
 Accordingly, the number of MS/MS scan can vary for each precursor ion in the shotgun acquisition, as might occur when using a DDA strategy.
 Moreover, the frequency-filter itself leads to a consistent intensity report for each acquisition file and in the aligned Masterscan. In this perspective, one has to expect a reduction in a number of lipid identifications without losing abundant lipids.
-All settings together can be stored in the file given at the top of the panel. 'lpdxImportSettings.ini' is the standard file in which a small collection of configuration are already stored. Select the configuration 'FAS_LTQ_100000MS1' under 'Select a Configuration'. This are the appropriate settings for the selected spectra.
+All settings together can be stored in the file given at the top of the panel. 'lpdxImportSettings.ini' is the standard file in which a small collection of configuration are already stored. Select the configuration 'FAS_LTQ_100000MS1' under 'Select a Configuration'. These are the appropriate settings for the selected spectra.
 Now hit 'Start Import' on the bottom of the panel and the import will start.

@@ Line 46: / Line 46: @@
 ===Specify the import settings===
-[[Image:lx128.png|400px|right|LipidXplorer Import]]
+[[Image:lx128_import.png|400px|right|LipidXplorer Import]]
 Go to the panel ''Import Settings''.

@@ Line 21: / Line 21: @@
 ====The LipidXplorer graphical user interface====
 LipidXplorer comes with a comfortable graphical user interface. It is divided into 4 parts:
-[[Image:lx128_header.png|380px|right|LipidXplorer modules]]
+[[Image:lx128_header.png|400px|right|LipidXplorer modules]]
 # Import Source
 # Import Settings