Applications of De Novo Protein Sequencing in Proteomics
Proteomics seeks to systematically characterize the composition, modifications, and functions of proteins in biological systems. However, traditional approaches depend on pre-existing genomic databases, limiting their ability to analyze unknown proteins, complex modifications, and non-model organisms. De novo protein sequencing circumvents these constraints by directly determining the primary amino acid sequence of proteins, establishing itself as a transformative tool in proteomics. This review highlights its core applications and explores how it facilitates advancements in life sciences.
Novel Protein Discovery: Exploring Uncharacterized Protein Space
1. Characterization of Unknown Pathogen Proteins
In emerging infectious disease research, viral proteins often lack genomic references. De novo protein sequencing enables direct sequencing of key pathogen proteins from clinical samples, providing molecular insights for vaccine and drug target development.
2. Investigation of Microorganisms in Extreme Environments
For microbial species in deep-sea, polar, and other extreme environments, de novo sequencing addresses challenges posed by the absence of genomic data, enabling the discovery of functional enzymes (e.g., thermophilic proteases) with industrial and pharmaceutical applications.
Comprehensive Characterization of Post-Translational Modifications (PTMs)
1. Open Modification Profiling
Without requiring prior knowledge of modification types, de novo sequencing detects PTMs by identifying mass shifts (e.g., phosphorylation and glycosylation). This capability has been instrumental in identifying novel disease-associated modifications and elucidating their regulatory roles.
2. Analysis of Coexisting Modifications
De novo sequencing allows simultaneous characterization of multiple modifications on a single peptide (e.g., ubiquitination and acetylation), facilitating mechanistic studies of complex pathological processes such as cancer and neurodegenerative diseases.
Advancing Research on Non-Model Organisms
1. Host-Pathogen Interactions
In infectious disease models, de novo sequencing differentiates between host- and pathogen-derived proteins, enabling precise identification of immune evasion factors.
2. Paleoproteomics
For highly degraded ancient biological specimens, this technology reconstructs key protein sequences, providing molecular evidence for evolutionary and extinction studies.
Accelerating Precision Medicine and Biopharmaceutical Development
1. Antibody Drug Development
(1) CDR Sequencing: Enables direct sequencing of complementarity-determining regions, bypassing gene cloning bottlenecks and significantly reducing R&D timelines.
(2) Quality Control of Biopharmaceuticals: Ensures recombinant protein consistency by detecting sequence variations such as missense mutations and truncations.
2. Discovery of Disease Biomarkers
De novo sequencing enables the identification of low-abundance proteins in biofluids, providing novel targets for early disease diagnosis.
De novo protein sequencing is reshaping proteomics by transitioning from database-dependent validation to data-driven discovery. Continued advancements in mass spectrometry, single-molecule sequencing, and AI-driven analysis will further enhance its sensitivity and throughput, enabling a more comprehensive understanding of protein structure and function.
MtoZ Biolabs, an integrated chromatography and mass spectrometry (MS) services provider.
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