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# ALEX123

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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.
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+ The procedure for high confidence lipid identification using MALDI-based FTMS and ITMS2 data, described in **Ellis et al. (2018, under review)**, can be downloaded from the library "**Example dataset 1**".  
+ **Note** that *all* ALEX123 software modules are downloaded as part of the Example dataset.
+ The Example dataset also includes a user guide (.pdf).
  
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+ Individual ALEX123 software modules can be downloaded separately from the library: "ALEX123 software modules".
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**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.
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## Requirements

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+ 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.
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+ Install Java (64-bit) to use Java-based ALEX123 software modules (https://java.com/en/download/manual.jsp).
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+ Install MSFileReader (64-bit) (”MSFileReader_x64_3.1 SP4.exe”) (Thermo Fisher Scientific) to use the Python-based ALEX123 converter (https://thermo.flexnetoperations.com/control/thmo/login?).
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ALEX123    
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+ Install Python 3.6.1 (64-bit) and comtypes to use the Python-based ALEX123 converter.
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+ Install SAS 9.2 with SAS Enterprise Guide 5.1 (or later versions) to use scripts for automated high confidence lipid identification (file extension .epg) (https://www.sas.com/en_us/software/enterprise-guide.html).
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+ Install Tableau Desktop (version 10.2 or later) to use and modify data visualization templates (file extensions .twb) (http://www.tableausoftware.com/products/desktop).

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## References
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+ Ellis SR, Paine MRL, Eijkel GB, Pauling JK, Husen P, Jervelund M, Hermansson M, Ejsing CS, Heeren RMA. Automated, Parallel Mass Spectrometry Imaging and Structural Identification of Lipids (2018, under review).
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+ Pauling JK, Hermansson M, Hartler J, Christiansen K, Gallego SF, Peng B, Ahrends R, Ejsing CS. Proposal for a common nomenclature for fragment ions in mass spectra of lipids. [PLoS One. 2017 12(11):e0188394](https://doi.org/10.1371/journal.pone.0188394). 
+ Husen P, Tarasov K, Katafiasz M, Sokol E, Vogt J, Baumgart J, Nitsch R, Ekroos K, Ejsing CS. Analysis of lipid experiments (ALEX): a software framework for analysis of high-resolution shotgun lipidomics data. [PLoS One. 2013 8(11):e79736](https://doi.org/10.1371/journal.pone.0079736).
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## License

<a rel="license" href="http://creativecommons.org/licenses/by-nc-sa/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by-nc-sa/4.0/88x31.png" /></a><br />This work is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by-nc-sa/4.0/">Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License</a>.
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