Absolute Quantification or Relative Quantification

Sebas , April 21 2020
Good morning all,
I am a beginner and I am trying to understand what can be done with lipidomics not targeted on absolute quantification and relative quantification.
I want to study the difference in lipids between sample A and sample B.
I weigh the dry weight of each plant sample (20 mg dry matter).
I carry out the extraction of lipids under the same conditions (MTBE).
I don't set an internal standard.I inject in LC-MSMS (full scan mode in ddMS2 mode).
I process the data with MsDial.
I keep that lipids annotated.
When I process the data:
- can I do the relative quantification (area of a peak, PC 32: 1) * 100) / (Area of the sum of the annotated peaks) and compare the sample A and B?
- can I do the absolute quantification (area of a peak, PC 32: 1) / starting weight (mg / DM) and compare the sample A and B?
thank you
Have a good day
Michal Holčapek
I would strongly discourage to use any type of mass spectrometry
based quantitation without the use of suitable internal standard (IS), because
the use of IS should be an integral part of any MS quantitation including
lipidomics. The minimum requirement is the use of at least 1 IS per
lipid class to be quantified. More detailed recommendations can be found here:


The second important issue is a manual inspection of your data
in addition to software annotation, which is urgently needed to remove false
identification and supervise your data. The use of data without supervision
cannot be recommended. More details here: