Here is a good starter workflow for first time user of MZMine. Kindly prepared by Dr. Joshua Kellogg!

1. Welcome to MZmine
• MZmine is an open-source metabolomics processing software.
• Download from http://mzmine.github.io/download.html
• Requirements
• Java SE runtime (JRE) up to date - remember to select the 64-bit version if your OS is 64-
bit! Verify your Java version here
• (Optional) Install R. R is required for certain modules (e.g. baseline correction and heat
maps).

2. Basic MZmine Workflow
1. Load raw data
2. Mass detection
3. Chromatogram builder
4. Chromatogram deconvolution
5. Deisotoper
6. Aligner
7. Gap-filling
8. Export

3. MZMine Workflow Overview
Build chromatogram
from successive scan
events
‘Deconvolute’
chromatograms into
data points

4. Import RAW Data
Load each individual data file
Can support:
• mzML (mzML versions 1.0 and 1.1)
• mzXML (mzXML versions 2.0 to 3.1)
• mzData (mzData versions 1.04 and 1.05)
• NetCDF (no MSn support)
• Thermo RAW
• Waters RAW

5. Mass Detection & Chromatogram Builder

6. Centroid mass detection
Give it a name you will recognize
Click to set noise level
Click to see preview of scans

7. Check TIC for several files
Establish a baseline/threshold value

8. Chromatogram Builder
Choose mass list to create chrom
Minimum time required for peak
to appear to be built into a
chromatogram
Minimum peak height required
for peak to be built into a
chromatogram
Difference in m/z that will trigger
a new chromatographic peak
Give it a name you’ll recognize

9. Chromatogram Peak
Table

10. Chromatogram Deconvolution

11. Chromatogram Deconvolution
Choose chromatograms you want
deconvoluted
Give a recognizable suffix Different algorithms for
deconvolution
Set minimum peak height (usually
mass cut off from earlier
Set baseline level (usually 1% of
minimum peak, give or take)
Range of time to look for peaks
(set to whole chromatogram
window)

12. Chromatogram Deconvolution
Table
Your peak table is now longer with all the
deconvoluted peaks
Some peaks look
suspiciously similar!

13. De-isotoping
Give these a suffix
Set m/z tolerance and RT
tolerance

14. De-isotoping
Table
The 13C peak has
disappeared

15. Join Aligner
Set m/z tolerance and RT
tolerance
Set aligning weight for m/z and RT

16. Join Aligner
Table

17. Plot Module

18. Plot Module

19. Gap Filling
Give the new peak list a suffix
Choose maximum peak deformation that
will count as a gap-filled peak
Set m/z tolerance and RT
tolerance

20. Gap-Filling
Table

21. Export Data
Choose a folder and give the final file a
name
Select which elements you want to export
(m/z, RT, #detected peaks, etc.)
This must be selected for export to work
Select other information from each data
file you want exported (peak height, peak
area, asymmetry, etc.)
If you have used the ID feature and want
the peak IDs exported, click here

22. Ta Da!
• The data is now in an Excel file ready to be read and manipulated
further (statistical analysis, etc.)
• This covers only the bare basics of how to import and process MS
data in MZmine… there is certainly many other features available
depending on needs.