De Novo Protein Sequencing Analysis Service
De novo protein sequencing analysis service is an analytical method that determines the primary structure of proteins—namely, their amino acid sequence—directly through mass spectrometry, without the need for any pre-existing reference sequence. Unlike conventional protein identification approaches that depend on database matching, de novo protein sequencing is particularly well-suited for scenarios involving novel proteins, unknown post-translational modifications, antibody variable regions, or non-model organisms. It has become an indispensable technology in modern proteomics and biopharmaceutical research. This service enables researchers to acquire sequence information in the absence of any reference, thereby supporting downstream applications such as functional analysis, structural modeling, antibody development, and biomarker discovery. De novo protein sequencing analysis service is widely employed across diverse fields, including basic research, drug development, and vaccine design, and serves as a powerful tool for advancing bioinformatics innovation and achieving precise molecular characterization. Increasingly, this service is being integrated with other omics technologies to facilitate multidimensional protein analysis. For instance, comparative studies with ribosome profiling (Ribo-seq) data can reveal discrepancies between translation products and expressed proteins; integration with analyses of modifications such as phosphorylation and glycosylation provides comprehensive insights into protein functional states. In structural biology, de novo sequencing offers accurate sequence information to support atomic-level resolution studies using cryo-electron microscopy or X-ray crystallography. Its strategic value is particularly evident when studying proteins with unknown structures or sequences that cannot be resolved by traditional techniques.
At the core of the de novo protein sequencing analysis service is high-resolution mass spectrometry. Using instruments such as Orbitrap or TOF-MS, enzymatically digested peptide fragments of target proteins are analyzed via tandem mass spectrometry (MS/MS), generating fragmentation spectra that are computationally interpreted to determine amino acid sequences. In contrast to database-driven methods, de novo sequencing reconstructs peptide sequences based solely on the mass differences of fragment ions, with no reliance on pre-existing protein databases. This approach is crucial for proteins of unknown origin, limited database representation, or those that contain numerous mutations and post-translational modifications. In contexts such as polyclonal antibody analysis, proteomics of traditional medicine, and studies of natural toxins, de novo sequencing remains the only dependable approach for obtaining accurate sequence data.
A major advantage of de novo protein sequencing analysis service lies in its robust ability to resolve unknown or uncharacterized sequences. Standard database search methods are limited to identifying known proteins or those closely related to known sequences. Their accuracy declines significantly when the target protein contains mutations, novel modifications, or originates from species absent in reference databases. In contrast, de novo sequencing circumvents these limitations by leveraging high-quality fragmentation spectra and optimized algorithms to reconstruct sequences, enabling the identification of novel proteins, variant peptides, non-standard amino acid residues, and structural isomers. This capability is especially critical in antibody research, including the reconstruction of monoclonal antibodies, screening of bispecific antibodies, and localization of mutation sites. The technology can directly determine the variable regions of light and heavy chains, thereby facilitating antibody expression validation and structural refinement.
MtoZ Biolabs has extensive expertise in mass spectrometry and proteomics, offering high-quality, customized de novo protein sequencing analysis services tailored to a wide range of research needs. These services are applicable to antibody sequence determination, novel protein identification, characterization of post-translational modifications, and other specialized proteomic analyses.
MtoZ Biolabs, an integrated chromatography and mass spectrometry (MS) services provider.
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