Quantitative Proteomics: Label-Free versus Label-Based Methods

Proteomics focuses on the complete set of proteins expressed by a genome, including their quantities, modifications, interactions, and functions, providing a deeper understanding of cell behavior, disease mechanisms, and potential therapeutic targets.

Quantitative proteomics takes this one step further, and involves the systematic identification and quantification of proteins within a sample, serving a crucial role in elucidating changes in protein expression levels that occur in response to disease, environmental stressors, or other biological stimuli.

Quantitative proteomics provides a means to compare protein levels across different conditions, identify protein-protein interactions, post-translational modifications, and also helps in discerning pathway dynamics, and has become a popular area of study within biomedical research, drug development, biomarker discovery, and systems biology.

Find out about the most important isotope labeling techniques

Understanding Label vs Label-Free Quantitative Proteomics

Both methods have their unique strengths and potential limitations, with the choice between the two often depending on the specific research, availability of resources, and the nature of the sample(s).

By understanding the mechanisms, advantages, drawbacks, and applications of both methods, it is possible to make informed decisions about which method to use, in order to improve the reliability and reproducibility of your proteomic data.

Graphic: Label-Free vs. Label-Based Quantitative Proteomics
Image: Proteomics Core Facility Cologne

Label-Free Quantitative Proteomics

Label-Free Quantitative Proteomics is a technique that enables the quantification of proteins in a given sample without the need for chemical labeling.

This methodology relies on measurements taken directly from the raw data obtained from the mass spectrometer, utilizing one of two techniques – intensity-based and spectral counting methods.

Intensity-based methods rely on the measurement of peak intensities in the mass spectrometer to calculate protein quantity. A raw abundance of each protein is generally determined by integrating the peak area of its corresponding peptides in the mass spectra.

On the other hand, spectral counting methods derive protein quantity based on the number of identified spectra that can be matched to a particular protein. Essentially, the assumption is that the more times a protein is detected (i.e., the more spectra corresponding to it), the higher its abundance in the sample.

Label-Based Quantitative Proteomics

Label-based quantitative proteomics involves the use of stable isotopic labels to tag proteins or peptides in a sample before mass spectrometry analysis.

The labels effectively “mark” the proteins from different samples, allowing for simultaneous measurement and direct comparison of protein abundance across samples in the same experiment. This approach enhances the accuracy and reproducibility of the quantification results.

There are several label-based techniques used in quantitative proteomics, each with their unique attributes.

The Pros and Cons of Label-Free Quantitative Proteomics

The primary advantage of label-free methods is their simplicity and cost-effectiveness.

This method does not require the use of expensive labeling reagents, and can handle a larger number of samples compared to label-based methods. Moreover, these techniques are less complex, making them more accessible to labs without extensive proteomics expertise.

However, label-free methods also have certain limitations.

These methods typically require more replicates to achieve the statistical power comparable to label-based methods. They are also highly dependent on the quality of the sample preparation and the consistency of the mass spectrometry analysis, making them potentially more prone to variability.

Pros and Cons of Label-Based Quantitative Proteomics

Label-based methods offer several advantages.

The following three methods provide accurate and precise quantification of proteins because the isotopic labels serve as internal standards.

SILAC (Stable Isotope Labeling by Amino acids in Cell culture)

This technique involves growing cells in media containing heavy isotopes of essential amino acids. These isotopes are incorporated into proteins as they are synthesized, allowing for a clear distinction between proteins from different samples. SILAC is particularly advantageous in studies of cell culture models.

iTRAQ (Isobaric Tags for Relative and Absolute Quantitation)

This method uses isobaric tags that can bind to peptides, labeling them for comparison. Each tag consists of a reporter group, a balance group, and a peptide-reactive group. The advantage of iTRAQ is its capacity to compare multiple samples in one experiment, improving throughput.

TMT (Tandem Mass Tags)

Similar to iTRAQ, TMT uses isobaric tags to label peptides. However, the structure of the TMT tags is slightly different, allowing for an expanded multiplexing capability, i.e., the ability to compare a greater number of samples in a single experiment.

These methods also allow for multiplexing, facilitating the comparison of multiple samples in one experiment. This approach reduces both the instrument time required and the experimental variability, as samples can be combined and analyzed simultaneously.

However, label-based methods also have their limitations. They require additional steps for labeling, increasing the complexity of the sample preparation. The cost of isotopic labels can also be significant, especially for large-scale studies. While SILAC is specifically for cell culture, a modified technique – SILAM – extends the applicability of this isotopic labeling technique to whole animals, including mice, fish, flies and worms.

Label vs Label-Free: Which Method is Best?

label free vs label based quantification

If high precision, accuracy, and reproducibility are the primary concerns, and the study involves a limited number of samples, label-based methods are most suitable. If your study involves cell culture models, using a technique like SILAC is best to use.

Reproducibility is also typically better with label-based methods due to the ability to compare multiple samples simultaneously in one experiment, reducing variations associated with separate experimental runs.

While label-free techniques can handle larger sample sizes, the drawback with using a label-free approach is the need to run each sample separately, which not only increases time, but can also cause challenges with reproducibility and precision.

They tend to require more replicates to achieve comparable statistical power and can be more susceptible to variations in sample preparation and analysis, and lower-abundance proteins can also be harder to detect.

Choosing Your Approach With Silantes

Choosing between label-free and label-based methods should be guided by the specific research objectives, available resources, and nature of the samples.

Researchers aiming for high accuracy and precision, dealing with a smaller number of samples, or working with cell culture models may prefer label-based methods. Either way, it is crucial for you as the researcher to familiarize yourself with both methodologies to make an informed decision that best serves the research needs.

If you are looking for guidance and assistance with your research approach and methodology our team at Silantes is more than happy to help. As experts in the field of quantitative proteomics, we are more than happy to guide you through your experimentation and analysis to ensure you get the best possible results for your research.


What is label-free proteomics?

Label-free proteomics is a method used in the field of proteomics to identify and quantify proteins without the need for chemical labels or tags. This approach relies on the direct analysis of the sample.

What is used to label proteins?

One of the most common methods is by using isotopic labels. These could be stable isotopes, as used in Stable Isotope Labeling with Amino acids in Cell culture (SILAC), or they could be isobaric labels, as used in techniques like Isobaric Tags for Relative and Absolute Quantitation (iTRAQ) and Tandem Mass Tags (TMT).

Which technique is best for quantitative proteomics?

The “best” technique for proteomics largely depends on the specific requirements of the experiment. Label-free methods, for instance, are cost-effective and suitable for large-scale analyses. On the other hand, label-based methods, like SILAC, iTRAQ, or TMT, can provide high precision and accuracy, whilst accelerating the speed of your research – especially when comparing multiple samples simultaneously.

What are the different types of label-free proteomics?

Label-free quantification can be split into two distinct methods – spectral counting and intensity-based. Spectral counting quantifies proteins based on the number of identified spectra for each protein, reflecting its abundance. Intensity-based methods quantify proteins based on the peak intensities of the respective peptide ions in the mass spectra.

What are the disadvantages of label-free proteomics?

Label-free proteomics has some disadvantages, including variability between runs, difficulty in detecting low-abundance proteins, a requirement for high reproducibility in sample preparation, separation, and data acquisition. Also, comprehensive data analysis can be complex and require advanced bioinformatics tools.

What is the principle of label-free proteomics?

label-free proteomics revolves around determining protein abundance without the use of stable isotope labeling. Protein abundance is inferred from the intensity of the respective peptide ions in the mass spectra or the number of identified spectra per protein.