Description
ALEX¹²³ (Analysis of Lipid EXperiments for processing FTMS, MS² and MS³ data) is software framework for analyzing high resolution shotgun and MALDI-based lipidomics data.

► The procedure for high confidence lipid identification using MALDI-based FTMS and ITMS² data is described in Ellis et al. Nat Methods. 2018. A link to a user guide and an example dataset is provided below.

► ALEX¹²³ software modules can also be downloaded at GitLab.

NOTICE that there are no warranties or representations as to the fitness of this equipment/software for any particular purpose and no responsibility or contingent liability, including indirect or consequential damages, for any use to which the user may put the equipment/software provided, or for any adverse circumstances arising therefrom.

Requirements
-The ALEX¹²³ software framework is operational on desktop and labtop computers running Microsoft™ Windows™ 7 or 10 (Professional 64-bit), and having at least a 2.7 GHz dual core processor with at least 8 GB RAM. The user should have administrator rights.
-Install Java (64-bit) to use Java-based ALEX¹²³ software modules.
-Install MSFileReader (64-bit) (”MSFileReader_x64_3.1 SP4.exe”) (Thermo Fisher Scientific) to use the Python-based ALEX¹²³ converter.
-Install Python 3.6.1 (64-bit) and comtypes to use the Python-based ALEX¹²³ converter. Click here for instructions.
-Install SAS® 9.2 with SAS® Enterprise Guide 5.1 to use scripts (file extension .epg) for automated high confidence lipid identification. More information is available here.
– Install Tableau® Desktop (version 10.2 or later) to use and modify data visualization templates (file extensions .twb). More information is available here.

Example dataset for high confidence lipid identification using MALDI-based FTMS and ITMS² data
This example dataset relates to our publication: Ellis et al. Nat Methods. 2018.
The example dataset includes all ALEX¹²³ software modules (executed using Java and Python), scripts for high confidence lipid identification (executed using SAS Enterprise Guide) and data visualization templates (navigated using Tableau Desktop).
Click here to download the user guide (.pdf).
Click here to download the example dataset (.zip, 93 MB). Note that mass spectrometry data files (.RAW) should be downloaded separately from the MetaboLight repository (MTBLS597).

Download individual components of the of ALEX¹²³
Note that all ALEX¹²³ software modules can be downloaded as part of the above-listed example dataset
Download the user guide for description of the ALEX¹²³ software modules, and instructions on how to use the ALEX¹²³ framework.
Click here to download user guide.

► ALEX¹²³ converter
This tool extracts and averages spectral data stored in proprietary .RAW files.
“Scan filters” are extracted from all .RAW files, and stored in specific folders as searchable .txt files.
For download and more information, click here.

► ALEX¹²³ target list generator
This software tool is used for making “target lists” for searching FTMS, MS² and MS³ data.
Click here to download.

► ALEX¹²³ isotope compiler
This tool adds ¹³C isotope information to “target lists” (.txt files).
Click here to download.

► ALEX¹²³ extractor
This software tool uses information in “target lists” to search for lipid species and fragment m/z values.
Click here to download.

► ALEX¹²³ unifier
This software tool concatenates results of multiple searches into a single output file.
Click here to download.

► ALEX¹²³ script for ¹³C deisotoping
This SAS Enterprise Guide-based script performs deisotoping of FTMS data.
It is recommended to download this script as part of the example dataset.
Click here to download.

► ALEX¹²³ script for high confidence lipid identification
This SAS Enterprise Guide-based script performs lipid identification using MALDI-based FTMS and ITMS² data.
It is recommended to download this script as part of the example dataset.
Click here to download.