MtoZ Biolabs utilizes a high-resolution tandem mass spectrometry platform, has launched the de novo sequencing service to perform de novo analysis of the amino acid order of proteins and obtain sequence information. The service is widely used in unknown protein sequence confirmation, sequence variant identification, and protein-level biomarker research, providing a reliable data foundation for advanced structural and functional studies.

Overview

De novo sequencing is a sequencing method that infers the amino acid order of proteins from MS/MS fragmentation spectra without relying on existing databases. The principle is based on controlled collision-induced peptide dissociation, generating stable b/y ion series, and deducing residue arrangement through precise mass differences between adjacent fragment ions to reconstruct unknown sequences. Its significance lies in the direct identification of peptide-level sequence composition and variant information, helping promote unknown protein sequence characterization and the progress of protein functional studies.

De Novo Sequencing Service at MtoZ Biolabs

MtoZ Biolabs through high-resolution mass spectrometry and de novo sequence reconstruction, offers core sequence interpretation services to its clients.

• Amino acid sequence analysis of proteins

• Sequence reconstruction of unknown proteins

• Confirmation of key modification states

• Identification of sequence mismatches or truncations

• Profiling of common modification spectra

Our analyses provide robust insights into full-length sequences and key modifications, enabling researchers to advance protein structure and functional studies.

Workflow of De Novo Sequencing Service

1. Sample Pre-Processing

Solubilize and clarify protein samples, and perform concentration or desalting when required, ensuring stable conditions for instrument loading.

2. Peptide Generation and Chromatographic Separation

Digest proteins using proteolytic cleavage and obtain controlled, stable chromatographic elution peak shapes.

3. MS/MS Acquisition

Continuously record fragment ion signals under defined collision energy to support sequence deduction.

4. Spectral Calibration and Data Processing

Perform mass calibration, noise reduction, and correction of measured mass-difference between adjacent fragment ions.

5. Data Interpretation and Reporting

Deduce amino acid order, reconstruct peptide sequences, and identify variants or truncations for final reporting.

Figure 1. The Workflow of De Novo Sequencing.

Why Choose MtoZ Biolabs?

• High Sequence Coverage: Deep mass-difference readout of fragment ions enables robust reconstruction of full-length protein sequences.
• Precise Residue Calling: High-resolution MS platforms ensure accurate interpretation of fragment ion mass spacing.
• Database-Free Discovery: Unknown sequences and variants are resolved without requiring prior database assumptions.
• Standardized Workflow: Unified calibration delivers high cross-sample and cross-batch comparability.
• End-to-End Delivery: Sample assessment to final reporting is fully integrated to accelerate structural and functional research.

Applications of De Novo Sequencing Service

1. Engineering Construct Validation

Used for residue-order interpretation of recombinant or fusion protein sequences, supporting confirmation of engineering sequence convergence.

2. Biomarker Discovery

Applied to extraction of candidate sequence patterns from clinical or biofluid proteomes, supporting establishment of sequence-feature lists.

3. Signaling Peptide Screening

Used for residue-order readback of key peptide fragments in signaling pathways, aiding functional molecule prioritization.

4. Molecular Fingerprint Characterization

Used for amino-acid-order interpretation of unknown functional molecules, supporting generation of sequence-fingerprint features.

5. Environmental Response Molecule Research

Used for sequence interpretation of responsive molecules from temperature, stress, or ecological models, supporting sequence-trend analysis.

Deliverables

• Comprehensive Experimental Details
• Materials, Instruments, and Methods
• Protein Sequence Analysis Results
• Related Spectral Data
• Bioinformatics Analysis
• Raw Data Files

FAQ

Q1: What types of samples are suitable?

A1: Suitable for soluble, clear, and high-purity protein samples. Multiple protein sources are accepted, including plasma, serum, cell lysates, tissue lysates, and proteins purified through immunoaffinity or chromatographic systems. Submissions should avoid high-salt buffers, strongly viscous solutions, or highly complex, interference-rich matrices.

Q2: What is the service general workflow?

A2:

Q3: What data formats will be delivered?

A3: MtoZ Biolabs provides multiple types of standardized output, including:

• Mass spectrometry raw data files (instrument-compatible formats)

• Protein sequence lists (table formats supported)

• Mass spectrometry fragmentation spectra (image formats supported)

• Annotation of residual modifications (documents or tables supported)

• A comprehensive characterization report containing experimental materials, instrument parameters, and sequencing conclusions (PDF)

If special analytical requirements exist, data formats can be customized according to project specifications.

Q4: How should I prepare proteins before submission?

A4: To ensure optimal identification results, it is recommended to prepare samples in the following aspects:

• Purity Control: Protein solutions should be free of precipitation or turbidity, with minimized residual salts, glycerol, and surfactants, and reduced contaminating proteins or chemical interference.
• Storage Specifications: Short-term at 4℃, long-term at -80℃, avoiding repeated freeze-thaw cycles.
• Transportation Guidelines: Leak-proof sealing and cold-chain shipping using ice packs or dry ice, preventing particulate introduction.
• Additional Information: Provide sample origin, estimated concentration, solvent or buffer composition, known or expected modification states, and theoretical sequence or structural expectations to support mass calibration and sequence interpretation optimization.

For more information, please refer to Sample Submission Guidelines for Proteomics, Sample Submission Guidelines for Metabolomics.

Start Your Project with MtoZ Biolabs    

Contact us to discuss your experimental design or request a quote. Whether you are exploring unknown patterns in protein sequences or conducting functional molecular characterization research, MtoZ Biolabs can provide you with high-confidence sequence analysis support.