De novo sequencing service enables the direct determination of protein and antibody primary structures without relying on existing sequence databases. As a core analytical strategy in structural proteomics, de novo sequencing reconstructs amino acid sequences from tandem mass spectrometry (MS/MS) data by interpreting ion fragmentation patterns, rather than matching spectra to known entries. This makes it particularly valuable for analyzing novel proteins, therapeutic antibodies, and non-model organisms, where database-dependent methods are insufficient.
The technology relies on high-resolution mass spectrometry platforms—such as Orbitrap Fusion Lumos and Q Exactive—to acquire detailed MS/MS spectra. Combined with advanced algorithms including PEAKS, Novor, and pNovo, de novo sequencing allows accurate sequence assembly, mutation localization, and post-translational modification (PTM) identification. Bottom-up, top-down, and hybrid workflows can be employed depending on the nature and complexity of the target protein, offering flexibility for various research applications.
MtoZ Biolabs provides a comprehensive de novo sequencing service based on this robust analytical framework. Our solution integrates optimized sample processing, high-sensitivity MS acquisition, and a multi-algorithm bioinformatics pipeline, delivering high-confidence, publication-ready sequence data. The service supports applications in antibody discovery, biosimilar evaluation, vaccine target identification, and synthetic biology. With minimal sample requirements, fast turnaround, and exceptional data quality, MtoZ Biolabs empowers clients to achieve precise sequence characterization and drive innovation in protein research and development.
Foundations and Strategies of De Novo Sequencing
De novo sequencing service encompasses a suite of experimental and computational strategies designed to determine the amino acid sequences of proteins and peptides without referencing any existing database. This innovation emerged from the need to characterize unknown proteins, antibody variants, and biologics lacking database representation. The foundation of this field was established in the 1990s, when visionary mass spectrometrists and bioinformaticians developed algorithms capable of interpreting MS/MS data beyond the constraints of traditional database matching.
The evolution of de novo sequencing has paralleled advances in mass spectrometry instrumentation. High-resolution platforms such as Orbitrap Fusion Lumos and Q Exactive have dramatically improved sensitivity, accuracy, and confidence in peptide fragmentation analysis. Concurrently, algorithmic advancements—from dynamic programming approaches to AI-assisted spectrum interpretation—have made sequence assembly more precise and reliable.
Today, de novo sequencing includes three methodological strategies:
1. Bottom-Up Sequencing
Proteins are enzymatically digested into peptides, which are analyzed via tandem MS. Computational algorithms reconstruct the peptide sequences and assemble them into full-length protein sequences.
2. Top-Down Sequencing
Intact proteins are directly fragmented inside the mass spectrometer, enabling sequence data collection without enzymatic digestion.
3. Hybrid Workflows
These integrate bottom-up and top-down approaches to optimize sequence accuracy, particularly for complex proteins or those with extensive post-translational modifications.
Applications of De Novo Protein Sequencing
De novo protein sequencing has a profound impact across a range of scientific disciplines and industry sectors, and its main applications include:
1. Non-Model Organism Research
It enables comprehensive characterization of the proteome in species lacking complete reference databases, thereby supporting evolutionary studies and biodiversity assessments.
2. Antibody and Therapeutic Protein Characterization
As the biopharmaceutical industry expands, the ability to directly sequence monoclonal antibodies, including the detection of subtle mutations within complementarity-determining regions (CDRs) or post-translational modifications (PTMs), is essential for drug development, biosimilar evaluation, and intellectual property protection.
3. Vaccine Target Discovery
It rapidly identifies and characterizes viral or bacterial antigens, facilitating rational vaccine design, particularly in response to emerging or rapidly evolving pathogens.
4. Synthetic Biology and Protein Engineering
For custom-designed proteins and metabolic modules, rigorous sequence verification is critical. De novo protein sequencing ensures that engineered constructs conform to design specifications and deliver intended biological functions.
5. Diagnostics and Personalized Medicine
In clinical proteomics and biomarker discovery, protein isoforms or disease-specific variants that are missing from current databases are often discovered, and this technology fills this critical knowledge gap, thereby facilitating the development of new diagnostic strategies.
Through these diverse applications, MtoZ Biolabs' de novo sequencing service accelerates research timelines and delivers clients comprehensive, publication-quality data.
MtoZ Biolabs' De Novo Sequencing Service Workflow
Our service employs a streamlined, rigorously controlled workflow from sample submission to final report delivery:
1. Sample Submission and Quality Control
Clients submit purified protein or antibody samples, adhering to detailed submission guidelines to ensure optimal outcomes. All samples undergo thorough assessment for concentration, integrity, and purity using SDS-PAGE and additional quality control measures.
2. Advanced Mass Spectrometry Data Acquisition
Samples are enzymatically digested, typically with trypsin, and the resulting peptides are analyzed using Orbitrap Fusion Lumos or Q Exactive mass spectrometry systems. This process yields high-resolution, high-sensitivity MS/MS data.
3. Multi-Algorithmic Sequence Assembly
Raw data are subjected to multi-stage computational analysis, utilizing industry-leading software tools such as PEAKS, Novor, pNovo, alongside proprietary algorithms. Running these tools in parallel maximizes the accuracy and confidence of sequence reconstruction, including identification of PTMs and sequence variants.
4. Bioinformatics Validation and Expert Review
Preliminary sequences undergo rigorous quality control, including computational scoring and manual curation by experienced experts, ensuring both biological plausibility and technical robustness.
5. Custom Reporting and Data Delivery
Clients receive a comprehensive report that details all experimental conditions, sequence assignments, annotated spectra, and mutation/PTM mapping, as well as complete raw data files.
Computational Analysis in MtoZ Biolabs' De Novo Sequencing Service
The effectiveness of any de novo protein sequencing service fundamentally depends on the synergy between rigorous experimental procedures and powerful computational analysis. MtoZ Biolabs' analysis framework incorporates multiple algorithmic paradigms to address different sequencing challenges:
1. Data-Driven Methods
These reconstruct peptide and protein sequences solely from spectral data, ideal for novel or engineered proteins with no existing references.
2. Template-Driven Methods
When partial reference sequences are available—such as conserved motifs or homologous proteins—template-driven reconstruction improves alignment and sequence assembly confidence.
3. Multi-Algorithm Pipelines
Our analytical platform integrates multiple sequence assignment tools (PEAKS, Novor, pNovo) in parallel, enabling cross-validation. Proprietary machine learning models further enhance result reliability, particularly in detecting PTMs and subtle mutations.
MtoZ Biolabs' de novo sequencing service leverages the Orbitrap Fusion Lumos mass spectrometer for exceptional resolution and accuracy, combined with an advanced, multi-algorithm bioinformatics platform. This enables deep sequence coverage and robust detection of mutations and PTMs, even in low-abundance or highly modified proteins.
What Could Be Included in the Report?
MtoZ Biolabs' de novo sequencing service delivers reports that set a new industry standard, including:
1. Comprehensive Experimental Details
Thorough documentation of sample preparation, enzymatic digestion, and mass spectrometry acquisition parameters.
2. Materials, Instruments, and Methods
Full disclosure of all instruments, reagents, and analytical workflows used in the project.
3. Total Ion Chromatogram and Quality Control Assessment (project-dependent)
Advanced visualization and quantitative metrics to verify data quality and ensure reproducibility.
4. Data Analysis, Preprocessing, and Estimation (project-dependent)
Stepwise description of all computational processes, including software versions, parameter settings, and data preprocessing methods.
5. Bioinformatics Analysis
Tables and figures presenting reconstructed sequences, mutation and post-translational modification (PTM) sites, corresponding confidence scores, as well as functional and domain annotation with expert commentary on biological relevance.
6. Raw Data Files
Complete access to original mass spectrometry spectra and intermediate results, supporting regulatory submissions, publications, and patent applications.
Each report is fully customized to the unique requirements of every project, ensuring relevance for regulatory filings, intellectual property documentation, peer-reviewed publication, or internal research.
Why Choose MtoZ Biolabs' De Novo Sequencing Service?
MtoZ Biolabs stands out in the global de novo sequencing service market with:
1. Advanced Analytical Platform
Utilizing state-of-the-art mass spectrometry systems, including Orbitrap Fusion Lumos and Q Exactive, we deliver reliable, rapid, and highly accurate de novo sequencing service, even for the most challenging protein and antibody samples.
2. One-Time-Charge
Pricing model is straightforward and fully transparent, with no hidden fees or unexpected costs. Clients benefit from a single, all-inclusive charge, ensuring complete budget clarity and peace of mind.
3. High Data Quality
Through stringent quality control and deep data coverage, we achieve comprehensive protein and antibody sequencing results. Proprietary AI-powered bioinformatics platform integrates multiple industry-leading algorithms, maximizing data reliability and enhancing scientific insights, ultimately providing clients with highly detailed and actionable reports.
4. Exceptional Result Confidence
Achieve up to 95% accuracy in N-terminal amino acid identification, along with robust detection of mutations and post-translational modifications (PTMs). All results undergo rigorous validation and expert review.
5. Minimal Sample Requirements
Highly efficient protocols minimize sample consumption, preserving valuable or rare materials and ensuring suitability for a wide range of research applications.
6. Rapid Turnaround and Reproducibility
Benefit from fast and predictable project delivery timelines, with consistently reproducible results, empowering researchers to meet critical deadlines with confidence.
Empower Your Research with MtoZ Biolabs' De Novo Sequencing Service
MtoZ Biolabs, an integrated chromatography and mass spectrometry (MS) services provider, provides advanced proteomics, metabolomics, and biopharmaceutical analysis services to researchers in biochemistry, biotechnology, and biopharmaceutical fields. Our ultimate aim is to provide more rapid, high-throughput, and cost-effective analysis, with exceptional data quality and minimal sample consumption.
Our advanced de novo sequencing service leverages state-of-the-art instrumentation and proprietary bioinformatics technologies to deliver highly accurate, database-independent protein and antibody sequencing. This enables researchers to gain comprehensive proteomics insights, driving breakthroughs in therapeutic protein development, biosimilar validation, synthetic biology, and the discovery of novel proteins. Whether your objectives are to accelerate drug discovery, ensure the validation of biosimilars, design next-generation biologics, or explore previously uncharacterized proteomes, MtoZ Biolabs provides customized solutions that deliver the depth, reliability, and actionable data essential for scientific advancement.
Interested in discovering how MtoZ Biolabs' de novo sequencing service can transform your research and accelerate innovation?
Contact our expert scientific team today to unlock new possibilities for your scientific endeavors:
Name: Terry
Company: MtoZ Biolabs
Email: marketing@mtoz-biolabs.com
Phone: +1-857-362-9535
Address: 155 Federal Street, Suite 700, Boston, MA 02110, USA
Country: United States
Website: https://www.mtoz-biolabs.com/
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