Lipid search

Disclaimer

If you use the Lipid Search Module, please cite the MZmine 2 paper and the following article:

Korf, A., Jeck, V., Schmid, R., Helmer, P. O., & Hayen, H. (2019). Lipid Species Annotation at Double Bond Position Level with Custom Databases by Extension of the MZmine 2 Open-Source Software Package. Analytical chemistry, 91(8), 5098-5105.

MS/MS rules were derived from various sources listed below or from MS/MS experiments performed in the Hayen lab (University of Münster, Germany)

LipidBlast
Kind, T., Liu, K. H., Lee, D. Y., DeFelice, B., Meissen, J. K., & Fiehn, O. (2013). LipidBlast in silico tandem mass spectrometry database for lipid identification. Nature methods, 10(8), 755.
MoNA
https://mona.fiehnlab.ucdavis.edu/
LipidMatch
Koelmel, J. P. et al. (2017). LipidMatch: an automated workflow for rule-based lipid identification using untargeted high-resolution tandem mass spectrometry data. BMC bioinformatics, 18(1), 331.

Description

This module holds methods to search for lipids in peak lists. Potential lipids will be annotated according to there accurate mass on MS1 level. If MS/MS data is available an identification on fatty acid residue level is also possible.

Method parameters

Lipid classes
Selection of lipid classes to consider for annotation. Lipid classes are classified in three groups. From left to right: Lipid core class, lipid main class and lipid class. Simply check the classes to consider for annotation. More classes can be added as desired (contact "ansgar.korf@wwu.de" or write an issue at the MZmine homepage).
Minimum number of carbon in chains
Set the minimum number of carbon in chains
Maximum number of carbon in chains
Set the maximum number of carbon in chains
Minimum number of double bonds
Set the minimum number of double bonds in chain
Maximum number of double bonds
Set the maximum number of double bonds in chains
m/z tolerance MS1 level
Enter m/z tolerance for exact mass database matching on MS1 level
Ionization method
Type of ion used to calculate the ionized mass
Search for lipid class specific fragments in MS/MS spectra
Check if you want to search for lipid class specific fragments in MS/MS spectra. To see which lipid class has a MS/MS library check out the database table.
m/z tolerance MS2 level
Enter m/z tolerance for exact mass database matching on MS2 level
Noise level for MS/MS scans
Intensities less than this value are interpreted as noise
Search for lipid modification
If checked the user can add masses to all selected lipids. Click "Add" button on the right and enter "+" plus any sum formula, and/or "-" plus any sum formula. Example: "+O2-H". Numbers have to be entered AFTER the element. This feature allows the user to build any possible lipid, based on the already implemented lipids. This also allows the annotation of lipid derivatization products. Entered modifications can be exported and/or imported using the buttons on the right side.

Database table

By clicking the button "Show database" at the bottom of the window, the user can browse through a database table which holds a lot of information of the created lipid database. All lipids are displayed in two Kendrick mass plots (KMD CH2 left, KMD H right). Lipids that interfere in the selcted m/z window are marked yellow, isobaric lipids are marked red. The others are displayed green.

Results

Peaks will be annotated as potential lipids by setting its peak identity. Always check for multiple assignments and compare the status with the database table and Kendrick plots! The comment holds information on the utilized ionization method, mass accuracy and MS/MS annotation. An MS/MS annotation will be added if MS/MS data was acquired and fragmentation information is listed in the database. More MS/MS data will be added in the future. If you have data on lipid class specific fragmentation you can contact "ansgar.korf@wwu.de" or write an issue at the MZmine homepage. The information can then possibly be added.