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# ALEX123

## 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. (2018, under review). A link to a user guide and an example dataset is provided below.


## 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. (2018, under review)**
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).**