README.md 1.97 KB
Newer Older
Christer Ejsing's avatar
Christer Ejsing committed
1
2
# ALEX123

Christer Ejsing's avatar
README    
Christer Ejsing committed
3
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.
Christer Ejsing's avatar
Christer Ejsing committed
4
5
6
7
8
9

+ 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

Christer Ejsing's avatar
Christer Ejsing committed
10
+ 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.
Christer Ejsing's avatar
Christer Ejsing committed
11
+ Install Java (64-bit) to use Java-based ALEX123 software modules.
Christer Ejsing's avatar
README    
Christer Ejsing committed
12
+ Install MSFileReader (64-bit) (”MSFileReader_x64_3.1 SP4.exe”) (Thermo Fisher Scientific) to use the Python-based ALEX123 converter.
Christer Ejsing's avatar
Christer Ejsing committed
13
+ Install Python 3.6.1 (64-bit) and comtypes to use the Python-based ALEX123 converter. **Click here for instructions.**
Christer Ejsing's avatar
Christer Ejsing committed
14
+ 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.**
Christer Ejsing's avatar
README    
Christer Ejsing committed
15
+ Install Tableau® Desktop (version 10.2 or later) to use and modify data visualization templates (file extensions .twb). **More information is available here.**
Christer Ejsing's avatar
Christer Ejsing committed
16
17
18
19


## Example dataset for high confidence lipid identification using MALDI-based FTMS and ITMS2 data

Christer Ejsing's avatar
README    
Christer Ejsing committed
20
21
22
23
24
25
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).**  

Christer Ejsing's avatar
Christer Ejsing committed
26