Proteomics Markers and Non-Markers

Proteomics is the study of the complete set of proteins within a cell, including their expression, function, and regulation. In proteomics research, "labelled" and "label-free" are two main methods.

 

Labelled Proteomics

In this method, proteins or their fragments are chemically labelled, usually for quantification. For instance, through mass spectrometry, the relative abundance of proteins in different samples can be compared. Common labelling techniques include isotope labelling (such as silicate labelling and stable isotope labelling of amino acids), fluorescent labelling, etc.

 

1. Isotope Labelling

(1) Mass Spectrometry-Based Stable Isotope Labelling

It includes Isotope-Coded Affinity Tag (ICAT), Stable Isotope Labelling with Amino acids in Cell culture (SILAC), and isobaric Tags for Relative and Absolute Quantitation (iTRAQ). These methods distinguish proteins or peptides from different samples using markers containing different isotopes.

 

(2) Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) 

It's a biological method that labels proteins by using amino acids containing heavy isotopes in cell culture.

 

2. Chemical Labelling

(1) Fluorescent Labelling

Proteins are labelled with fluorescent dyes, making them easy to identify in mass spectrometry or other optical detection methods.

 

(2) Reactive Group Labelling

Specific chemical reactive groups react with specific amino acid residues of proteins to form covalent bonds.

 

3. Enzymatic Labelling

For example, proteins are modified by using specific enzymes (such as kinases), and this modification is then detected by specific methods.

 

Label-Free Proteomics

This method does not involve directly labelling proteins. It relies on comparing mass spectrometry data from different samples to analyse changes in protein expression. The advantage of label-free methods is that they do not require complex chemical treatment and can study proteins in a more natural state.

 

1. Advantages

(1) No chemical labelling is required, simplifying the sample processing process.

(2) It's more suitable for analysing large-scale samples or complex samples.

(3) It allows for the study of protein expression in its most natural state.

 

2. Applications

(1) It's widely used in the discovery of disease biomarkers, the study of protein networks, the exploration of drug action mechanisms, etc.

(2) It's particularly suitable for samples that are difficult to use labelling methods, such as clinical samples.

 

Labelled methods are usually more accurate in quantitative analysis, while label-free methods may be more convenient when dealing with large-scale samples or complex samples.