A. Proteome Profiling
Proteome profiling can identify the maximum amount of protein species from a complex sample extract, such as tissue, plasma, and body fluid. Based on mass spectrometry (MS) technology, it can supply a satisfactory sample size to serve as a foundation for future quantitative studies or modification studies of target proteins.
B. Protein Identification
Mass spectrum based protein identification aims to identify the maximum amount of protein from gel samples or those with a low to moderate protein complexity. By combining the gel based separation system and mass spectrometry (MS) technology, Gel band identification is broadly used to identify proteins in samples with low protein complexity, such as IP samples, proteins with a specific molecular weight, etc. Gel spot identification is used to identify the proteins in a 2DE gel spot containing a single or several proteins.
C.Post-Translational Modification Proteomics——phosphoproteome identification
Protein post-translational modification (PTM) increases the functional diversity of the proteome either by the covalent addition of chemical moieties or functional groups, or by the proteolytic cleavage of regulatory subunits or the degradation of protein complexes. Many large-scale post-translational modification studies have recently been performed on various organisms, and phosphorylation, acetylation, methylation, and glycosylation are among the most intensively studied PTM proteomes.
Protein phosphorylation is an ubiquitous post-translational modification, essential to many physiological and biological processes and cellular events. Phosphoproteomic analysis provides identification of phosphorylated proteins and peptides, providing key data for understanding their biological functions. This proteomic method has greatly enhanced our understanding of cellular phosphoproteins and their dynamic regulatory mechanisms in diverse organisms. Profiling of phosphoproteins in relation to different cellular events has enabled us to establish phosphor-relay networks in different cellular signaling.
Phosphoproteomics is a protein analytical process and high-throughput technology, by which a temporal and spatial dynamic phosphoproteome of organisms can be profiled through sample preparation, phosphopeptide enrichment, LC-MS/MS analysis, and bioinformatics analysis.
D. Quantitative proteomics
Quantitative proteomics is a powerful method of discovering proteins that are expressed differently across time, disease state, or other conditions. Quantitative proteomics can be applied in many research areas, such as developmental biology, disease mechanisms, drug target discovery, biomarker screening, disease-resistant breeding, and in the study of pathogens, functional microbes, etc.
E. Targeted Proteomics Analysis
Targeted proteomics, based on multiple reaction monitoring, is able to selectively detect and quantify special function-related proteins in a large sample with the aim of inferring their molecular function. Multiple reaction monitoring (MRM) is a highly sensitive and selective method for quantifying target proteins, and currently draws the attention of many researchers worldwide, as it provides a robust and accurate measurement of protein profiles.
The MRM technique solves the problem of time consuming immunological methods and has greatly reduced the verification and validation time in the research into protein biomarkers. Compared to the antibody technique, which measures a protein using an antibody, the MRM technique enables researchers to study tens and hundreds of targeted proteins at one time. In light of these advantages, MRM technique has been widely used to verify disease related biomarkers, the detection of low-abundance proteins in highly complex mixtures, and the study of protein post-translational and chemical modification.