Advantages and Disadvantages of De Novo Protein Sequencing

Traditional protein sequencing methods primarily rely on existing protein databases for matching and identification, but these methods have significant limitations for proteins and antibodies with unknown sequences. De novo protein sequencing, a database-independent technology, can directly decode unknown protein sequences, offering important scientific and practical value.

 

De novo protein sequencing primarily uses high-resolution mass spectrometry to analyze protein samples. First, the protein samples are digested into smaller peptides using enzymes such as trypsin, Lys-C, and Glu-C. These peptides are then ionized and measured for their mass-to-charge ratio (m/z) in the mass spectrometer. The ionized peptides are further fragmented, producing a series of fragment ions of different lengths. By analyzing the spectra of these fragment ions, algorithms and software tools reconstruct the amino acid sequence of the peptides. This process involves highly complex data processing and bioinformatics analysis.

 

Advantages

1. Database Independence

De novo protein sequencing does not rely on existing protein databases, making it capable of analyzing any unknown protein sequences. This is particularly significant for newly discovered proteins and specific biological samples, especially in researching novel antibodies and unknown biomarkers.

 

2. High-Precision Sequence Analysis

This method can accurately identify antibody complementarity-determining regions (CDRs) and other important domains, providing detailed sequence information. This is crucial for antibody engineering and immunological research.

 

3. Diverse Protein Modification Analysis

De novo sequencing can identify and analyze various protein modifications, including phosphorylation, acetylation, and glycosylation. This provides valuable data support for understanding protein function and regulatory mechanisms.

 

Disadvantages

1. Complex Data Analysis

De novo protein sequencing generates large and complex data sets that require high-performance computing and specialized software tools for data processing and analysis. This process is not only time-consuming but also demands a high level of technical expertise from analysts.

 

2. High-Quality Data Requirement

This method relies on high-quality mass spectrometry data, requiring rigorous sample preparation and mass spectrometry operation. Poor-quality mass spectrometry data can significantly affect the accuracy of sequence analysis.

 

3. High Cost

De novo protein sequencing requires high-end mass spectrometry instruments and extensive computational resources, leading to high overall costs. This may limit its widespread application in some laboratories.

 

MtoZ Biolabs provides integrate De Novo protein sequencing service.