ALEX software

Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.

The software and data processing workflow is described in the paper Husen, Tarasov et al. PLoS One 2013

As of September 2017 a new version of the ALEX converter is available, capable of processing very large (GB) .RAW files.

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.

This version of ALEX was originally designed for operation in Windows XP.
Two options exist for operation in Windows 7 or 10:
-use virtual Windows XP Mode, or
-install ALEX directly in Windows 7 or 10 (notes).

It is recommended to use a computer with a 64-bit processor and more than 8 GB RAM.

Install MSFileReader library (Thermo Scientific) (version 3.1 SP4).
Install Python 2.7.10 (Make sure that Python is installed at C:\ and that PIP (Preferred Installer Program) is installed).
NumPy and PySide must also be installed. These components are installed together with the ALEX extractor (see below).
The Python modules comtypes and SciPy must also be installed.

User manual for ALEX software
Download: User manual (2013 – for operation in Windows XP).

ALEX extractor
It is recommended to install this program first.
This program extracts peak intensities from spectra at target values specified in a target list.
The installer includes the required Python 2.7, PySide and NumPy.
Download: ALEX extractor

ALEX converter (new version as of September 2017)
This tool extracts and averages spectral data in .RAW files.
All “scan filters” are extracted from all .RAW files and stored in specific folders as .txt files.
For download and more information, click here.

ALEX target list generator
The program is installed in C:\Program Files\ALEX\Target List Generator.
Download: ALEX target list generator

ALEX unifier
A new version of the ALEX unifier is available as of September 2017.
This version of the ALEX unifier should be executable with both Python 3.6 and 2.7.
The ALEX unifier concatenates multiple .CSV files generated by the ALEX extractor into a single file and adds a variable termed “rangeID” to log the origin of the data. It also produces an Orange-friendly .tab file of the combined data.
Download: ALEX unifier.

ALEX lipid database for ALEX target list generator
Place the database file in the same folder as the ALEX target list generator.
Download: ALEX lipid database (version 11) for ALEX target list generator

ALEX lipid database source files
This database format is used by the ALEX lipid calculator (below) and is the source for generating the database file used by the ALEX target list generator (above). The included Python program generates the database file “lipids.sqlite” from txt files. Just double click to run.
Download: ALEX lipid database source files

ALEX lipid calculator
The program is installed in C:\Program Files\
The program uses txt files from the “ALEX lipid database source files” stored in the folder “lipids”.
Download: ALEX lipid calculator
See also the online version of ALEX lipid calculator

Example dataset
This sample dataset is for testing local installations of the ALEX software and the auxiliary workflow powered by Orange and Tableau Software.
Download: Example dataset

Additional tools
Orange 2.7
Tool used for data processing.

Tableau Software
Tool used for data visualization.