LipidXplorer Advanced Interface

LipidXplorer Logo

LipidXplorer is a software that supports a variety of untargeted shotgun lipidomics experiments and experiments from LC/MS lipidomics. It is designed to support bottom-up and top-down shotgun lipidomics experiments performed on all types of tandem mass spectrometers. Lipid identification does not rely on a database resource of reference or simulated mass spectra.

This application provides a form-based, web-based graphical user interface to run LipidXplorer

The advanced interface allows you to upload your own LipidXplorer ini file as a template for the run settings.

Usage
  1. Click "Browse" next to "Custom LipidXplorer Ini File" to select a custom LipidXplorer ini file from your local computer
  2. After selecting a file, click "Upload" to transfer the file to our server
  3. The page will reload and shows the name of the uploaded Ini file
  4. Select the Ini file section that you want to use
  5. Click on "Apply as defaults" to load the selected ini file section
  6. The page will reload and shows an updated LipidXplorer configuration form
  7. Click "Browse" next to "LipidXplorer.zip" to select a zip file archive from your local computer that contains your input files (mzML or mzXML)
  8. Adjust the data type according to the files in the zip archive
  9. Check and adjust any settings
  10. Click "Run" to start processing of your data with LipidXplorer
  11. You will be redirected to the progress monitoring page
  12. You will be redirected to the results page, once processing has finished or failed
  13. The results page allows you to download your results as a zip archive and to access the processing log file
File LipidXplorer Version Description Created by Organism / Tissue
DIA-Sample (mzML) 1.2.8 A larger DIA sample for LipidXplorer Jacobo Miranda Ackerman Unknown
DIA-Sample (mzXML) 1.2.8 A small DIA sample for LipidXplorer Jacobo Miranda Ackerman Unknown
Human Serum Benchmark (mzML) 1.2.8 MTBE extracts of commercially available human serum. Dominik Schwudke Homo sapiens serum.
Human Serum Benchmark (mzXML) 1.2.8 MTBE extracts of commercially available human serum. Dominik Schwudke Homo sapiens serum.
Ini File Settings

Upload your LipidXplorer ini file:

Selected settings will be used as defaults in the form.
This file will be used to read default settings from. Please ensure to select the right ini file section below.
Select the ini file section to load settings from as defaults for the submission form. Submission form settings override settings from the ini file.
LipidXplorer

Upload your LipidXplorer archive for execution:

Zip archive containing your *.mzML or *.mzXML files and your custom *.mfql files
Select the file type of your MS runs.
Specify the half-width of the precursor isolation window
Select a timerange from within which the spectra should be imported (start seconds, end seconds).
Settings for MS1 data processing.
Comma-separated list of m/z values to use for linear recalibration of the spectra (use '.' as decimal separator).
Select a m/z range from within the spectra should be imported.
Set the resolution of the acquired spectra according to mass spec settings. This resolution refers to the smallest mass in the spectra. The change of resolution for greater masses is handled with the 'resolution gradient' below, at FWHM
Set the accuracy of the acquired masses according to mass spec settings.
Set a threshold to import only masses above a certain intensity.
Give a gradient of how the resolution changes the greater the m/z value is, in res/(m/z)
Select a minimum percentage of which a peak should is present in all samples.
MS1 Frequency Filter, MS1 m/z must occur this often in repeated measurements to be retained. Relative value.
MS1 m/z offset correction, All MS1 m/z values will be shifted by this value. Value in Da.
Settings for MS/MS data processing.
Comma-separated list of m/z values to use for linear recalibration of the MS/MS spectra (use '.' as decimal separator).
Select a m/z range from within the spectra should be imported.
Set the resolution of the acquired spectra according to mass spec settings. This resolution refers to the smallest mass in the spectra. The change of resolution for greater masses is handled with the 'resolution gradient' below, at FWHM
Set the accuracy of the acquired masses according to mass spec settings.
Set a threshold to import only masses above a certain intensity.
Give a gradient of how the resolution changes the greater the m/z value is, in res/(m/z)
Select a minimum percentage of which a peak should is present in all samples.
MS2 Frequency Filter, MS2 m/z must occur this often in repeated measurements to be retained. Relative value.
Precursor Offset Correction (PMO) Specifies a shift for the precursor masses, positive or negative. Precursor offset shifts can occur on LTQ Orbitrap. Value in Da.
LipidXplorer related publications
  1. LipidXplorer: a software for consensual cross-platform lipidomics. Herzog R, Schuhmann K, Schwudke D, Sampaio JL, Bornstein SR, Schroeder M, Shevchenko A. PLoS One. 2012;7(1):e29851. doi: 10.1371/journal.pone.0029851. Epub 2012 Jan 17.