Metabolomics Freeware and workflow

1. http://www.metaboanalyst.ca for statiscal calculation, based on xcms, but user-friendly workflow and UI. ID based on exact mass only.
2. https://xcmsonline.scripps.edu/landing_page.php?pgcontent=mainPage XCMS online version. Need to sign in and upload files. Allows statistical treatment and match with METLIN database.
3. http://mona.fiehnlab.ucdavis.edu/downloads MoNA repository of MS/MS database for spectral similarity search. Downloadable .
4. http://prime.psc.riken.jp/Metabolomics_Software/MS-DIAL/ MS-DIAL allows peak matching for DIA experiment and MS/MS search for data-dependent workflow. Needs to convert data to abf format with https://www.reifycs.com/AbfConverter/.
5. https://msbi.ipb-halle.de/MetFrag/ MetFrag allows in silico fragmentation search
6. https://msbi.ipb-halle.de/MetFusion/ MetFusion allows in silico AND MS/MS search from selected database.

How to setup and run CompassXport

1. Download from Bruker site
2. Click on executable file to install
3. Setup data path (https://www.java.com/en/download/help/path.xml). CompassXport is in C:\Program Files (x86)\Bruker Daltonik\CompassXport
4. lauch Command prompt (https://www.lifewire.com/how-to-open-command-prompt-2618089)
5. At Command prompt, change directory to the directory that contains the data file. (https://www.makeuseof.com/tag/a-beginners-guide-to-the-windows-command-line/)
5a. d: switch to data folder in most Bruker computer
5b. cd \data\xxx\xx\xx.d change directory to data (just copy from windows File Explorer).
5c. compassxport -mode 2 -a analysis.baf