Label-free versus Labelled - How to Choose Your Quantitation Method


question Questions
  • What are benefits and drawbacks of different quantitation methods?
  • How to choose which quantitation method bests suits my need?
objectives Objectives
  • Choose your quantitation method.
requirements Requirements

time Time estimation: 15 minutes


A basic question while planning any quantitative proteomic experiment is the choice between label-free versus labelled quantitation. Here, we would like to address and discuss benefits and drawbacks of each method. Finally, we will offer a guideline to arrive at a decision on which labeling method to use. We will not discuss various labelling methods here in detail, but focus on our basicquestion on the choice of quantitation method.

A basic overview of various quantitation techniques is shown below (original artwork by Marc Vaudel):

Overview quantitation techniques


In this tutorial, we will deal with:

  1. Benefits and Drawbacks of Labelled Quantitation
    1. Benefits and Drawbacks: Overview Table
    2. Benefits and Drawbacks: Detailed Explanation
  2. Guideline: How to Choose Your Technique

Benefits and Drawbacks of Labelled Quantitation

Label-free methods for quantitation are popular in the proteomics community and may be the most straight-forward laboratory technique in the field. However, labelled approaches have some benefits, which make them the method-of-choice for some scientific questions or experimental designs.

We summarized the Pros and Cons in the table below:

Benefits and Drawbacks: Overview Table

category label-free labelled
machine time more less
wet lab complexity & time little medium
comparability of samples difficult easy
data analysis complex complex
study design flexible fixed

The superior technique in each line is marked in bold.

Benefits and Drawbacks: Detailed Explanation

question Questions

  1. What is the difference between metabolic and chemical labelling?
  2. What is the “Super-SILAC” approach?

solution Solution

  1. In metabolic labelling (e.g. “SILAC”), samples like cells or whole animals are labelled in vivo by providing amino acids containing stable isotope before starting the experiment. In chemical labelling, samples are labelled in vitro after extracting the proteins.
  2. The “Super-SILAC” approach features mixing of easy obtainable control samples that are related to the sample of interest. An example is to use a mixture of several breast cancer cell lines to compare to breast cancer patient samples. The control sample usually is labelled with heavy isotopes, while the sample of interest is unlabelled. The “Super-SILAC” approach thus combines benefits of labelled and label-free experiments.

Guideline: How to Choose Your Technique

Considering the points mentioned above, the following guideline may help you in finding the right method for your scientific question:

  1. Study design & Comparability of samples: If you cannot predict the availability of samples in beforehand, flexibility is highly important. Therefore, it is advised to use a label-free approach for animal or clinical samples.
  2. Wet lab complexity & Data analysis: Your experience matters! If you see only weak advantages of one approach, stick to the technique you are already used to. It will save time and reduce the likelihood of errors, both in the wet lab and in silico.
  3. Machine time: If you have only limited access to the mass spectrometer, choose a labelling approach.
  4. Wet lab complexity & time: If you have limited lab resources (e.g. time, man-power, chemicals), choose a label-free approach.

keypoints Key points

  • Label-free and labelled methods are not better or worse *per se*.
  • Different scientific question call for different quantitation methods.
  • Be wise in choosing the right method before starting your LC-MS/MS runs.

Useful literature

Further information, including links to documentation and original publications, regarding the tools, analysis techniques and the interpretation of results described in this tutorial can be found here.

congratulations Congratulations on successfully completing this tutorial!