Proteome originates from the combination of protein and genome. It refers to the whole set of proteins expressed by a genome, including all proteins expressed by a cell or even a living creature. Proteomics  essentially refers to the study of the characteristics of proteins on a large scale, including the expression level of proteins, post-translational modifications, protein-protein interactions, so as to obtain an overall and comprehensive understanding of disease occurrence, cell metabolism and other processes at the protein level. The research content of proteomics includes itraq analysis  and TMT quantitative proteomics .

Itraq analysis  technique is a relative and absolute quantitative technique for in vitro labeling of the same heavy isotope. This technique can simultaneously label 8 polypeptide samples with isotopic reagents. After the labeled polypeptide samples are mixed in equal amounts, the first and second order mass spectrometry information of each peptide segment can be obtained by liquid chromatography separation and tandem mass spectrometry analysis. In the first order mass spectrometry, the same peptide from different samples showed the same mass to charge ratio. In the secondary mass spectrometry, the mass to charge ratio of the peptide fragment ions and the signal strength of the ions reported by the itraq analysis of 8 kinds of peptide fragments, including the sequence information of the peptide and the relative expression amount information of the peptide in different samples, can be identified by bioinformatics analysis of the tested protein and its expression differences in each sample.

Itraq analysis technology has been widely used in studies on the co-forcing mechanism of microbial resistance, the mechanism of animal and plant development and differentiation, and the molecular weight of protein . The itraq reagent is composed of three parts, including the reporting group, the balancing group and the peptide reactive group. Report groups have 8 kinds of molecular weight, balance group 8 kind of different molecular weight, it is also match with different report group, to make sure that the different sources of the same marked peptides in the level of mass spectrometry with the same mass-to-charge ratio, peptide can reactive groups and n-terminal peptides and lysine side chain amino occurring covalent connection make peptides on tag.

In the first order mass spectrometry, the same peptide segment in different samples labeled by any itraq reagent showed the same mass to charge ratio. In the second-order mass spectrometry, itraq reported ions were released by the break of chemical bonds, and 8 reported ion peaks were generated in the low-mass region of the mass spectrometry, whose intensity reflected the relative expression amount information of the peptide segment in different samples. In addition, the fragment ion peak mass-to-charge ratio in the second-order mass spectrometry reflected the sequence information of the peptide segment. These original mass spectrometry data can be retrieved from the database to obtain protein Quantification  and relative quantitative information of protein.

Early proteomic studies were devoted to the identification and understanding of the function of individual proteins or protein complexes. Ten years ago, we might have been able to analyze hundreds of proteins. Today, we can analyze thousands. At this level of analysis, we can study the global protein dynamics of cells, tissues, or organisms. This proteome research, along with the current hot fields of genomics, transcriptome and metabolomics, gives us a better understanding of overall biological processes and how they respond to different stimuli or change in disease states.

As a powerful tool in proteomics research, mass spectrometry has long been used only for qualitative research, protein identification and post-translational modification. Why can't we quantify it? Because the physicochemical properties of the hydrolyzed peptides varied greatly from run to run, the mass spectrometric responses varied. In addition, mass spectrometry can only analyze a portion of the sample peptides. As a result, quantitative proteomics methods have been developed to understand the overall protein dynamics of cells, tissues, or organisms.

TMT quantitative proteomics  is further divided into relative quantitative and absolute quantitative methods. Relative quantitative method is used to compare the protein or peptide abundance between samples, and the absolute quantitative target peptide can be achieved by adding synthetic peptide labeled with known concentration isotope in unlabeled samples.

Obviously, absolute quantification is more desirable than relative quantification because absolute values of peptides in different samples can also be used to compare relative protein changes. However, relative quantification is more commonly used because the absolute quantification of each target protein requires expensive reagents and takes a lot of time to develop and analyze. Among the relative quantitative methods, SILAC is the most commonly used one.

The SILAC method has many advantages. The efficiency of protein labeling was more than 90 % after 6-8 passage. The labeling was introduced before sample treatment, followed by protein separation, enzyme digestion and identification. The subsequent experiments had the same effect on the samples, so the quantitative error caused by sample treatment was very low. This is particularly useful in detecting very low levels of protein changes or post-translational modifications. In addition, SILAC is highly sensitive and requires a small sample size, usually only a few tens of micrograms of protein per sample.