Advantages and Challenges of Mass Spectrometry in Protein Structure Analysis

Mass spectrometry is a high-end technology used to quantify proteins, determine protein sequences, and verify modifications. The basic principle is to use an electromagnetic field to separate ions, and then determine the structure or nature of the molecule by measuring the Houssdorff effect (or mass/charge ratio) of the ions.

 

Application and Advantages of Mass Spectrometry in Proteomics

1. High Quantitative Accuracy

Mass spectrometry shows a high degree of quantitative accuracy in proteomics research. It can not only accurately determine the molecular weight of proteins, but also quantify the abundance of proteins, providing empirical basis for dynamic changes of proteins in the organism, comparisons across tissues, and across species.

 

2. Comprehensive Modification Identification

It has also shown significant advantages for studying post-transcriptional modifications (PTMs) of proteins. Whether it is commonly seen modifications such as phosphorylation, ubiquitination, and acetylation, or less common modifications such as glycosylation and hydrophobic groups, they can all be comprehensively and accurately identified through mass spectrometry.

 

Challenges of Mass Spectrometry in Protein Structure Analysis

1. Dependent on Proteolytic Enzymes

A key step in mass spectrometry analysis is to use enzymes to cut proteins into peptides. However, in practice, the cutting efficiency of the enzyme will be affected by various factors, such as the size, structure, and modification of the protein. This makes "missing in the base map" an inherent problem.

 

2. Time-Consuming and Energy-Consuming

Although mass spectrometry instruments have made rapid progress, the data processing process still requires a lot of time and manpower. Especially for large-scale sample libraries, data processing time often becomes the bottleneck of the experiment.

 

As a high-end and high-precision analytical technology, mass spectrometry has played a significant role in proteomics research. Although there are some challenges, with the rapid changes in instruments, databases, and analytical methods, it is believed that mass spectrometry analysis will bring a broader field to proteomics.