Unlocking Antibody Potential
The success of monoclonal antibody (mAb) drugs has paved the way for next-generation antibody-based treatments, including bispecific and multispecific antibodies, antibody-drug conjugates (ADCs), and even polyclonal therapies. However, as antibody-based therapeutics develop and evolve, so does the need for comprehensive bioanalytical methods to meet regulatory requirements.
DeepAB is a collection of powerful antibody sequencing and characterisation services designed to support the development of antibody-derived biologics. From precise de novo sequence identification to in-depth profiling of PTMs, glycans and drug conjugation sites, our services provide the critical insights needed to optimise function, stability, and manufacturability. This platform includes:
Key Service Advantages
- Comprehensive Characterisation – Multi-level mass spectrometry workflows provide full-spectrum antibody analysis.
- AI-Powered Insights – Proprietary in-house software integrates world-leading deep learning algorithms for enhanced data interpretation.
- Advanced Sequence Resolution – Clear differentiation of isobaric residues, including 3-Tier Leu/Ile distinction and deep-learning-based retention time prediction.
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Monoclonal de novo Sequencing and Characterisation
Service Description:
Our standard procedure integrates top-down and bottom-up MS techniques to construct and validate full protein sequences with high accuracy.
We process in-solution samples and use five different enzymes for digestion to ensure complete sequence coverage. Liquid chromatography coupled with mass spectrometry (LC-MS) generates raw peptide spectral data, which is then de novo sequenced and assembled into full protein sequences using our advanced software. Every project includes manual verification and sequence analysis to ensure accuracy. The final sequence is validated by comparing the theoretical mass to the deconvoluted intact mass. Additionally, comprehensive glycan profiling and post-translational modification (PTM) analysis are included, providing deeper insights into the structure and function of the antibody.
- A full report containing
- The Experimental Procedure
- Complete Sequence With Coverage View
- Spectra Supporting the CDR regions
- Intact Mass Validation within ±2 DA
- Each Amino Acid Supported by 20 unique peptides
- Ile/Leu Differentiation
- Project files and raw data provided upon request
- Scientist Support to Review Results
- 100 μg of antibodies in solution
- >80% purity
- Species type
- Buffer information
- Samples must be free of detergents and polymers (Triton X-100, Tween-20, PEG, etc.)
Polyclonal de novo Sequencing and Characterisation
Service Description:
We use optimised LC methods to efficiently resolve and separate simple antibody mixtures from a complex sample. Each LC fraction is divided into 3 portions and used for intact, bottom-up, and top-down data acquisition. This data is combined within our PolySeq.AI software for the correct assembly of multiple antibody sequence constructs. Intact mass measurements enable the correct pairing of the heavy and light chains. Additionally, this service can be combined with B-Cell sequencing for cross-matching and validation. Combining both offers insight into the genomic basis of the immune system as well as the functional survivors present. Manual verification and sequence analysis are always included, and a comprehensive report is delivered upon project completion. Glycan profiling and a targeted search for post-translational modifications can be included as an optional add-on to this service.
- A full report containing
- Complete sequences of at least the 4 most abundant antibodies per sample fraction with peptide coverage view
- Intact mass measurements with heavy and light chain pairings
- Top-down peptide mapping and fragment ion annotation
- 3-tiered I/L differentiation and supporting statistics
- High-quality peptide spectra spanning variable regions
- Scientist Support to Review Results
- 1 mg of antibodies in solution
- >95% purity
- Species type
- Buffer information
- Samples must be free of detergents and polymers (Triton X-100, Tween-20, PEG, etc.)
Antibody Drug Conjugate (ADC) Characterisation
Service Description:
Bioanalytical methods are a critical part of antibody-drug conjugate (ADC) development for pharmacology considerations such as optimal dosing strategies and drug potency, safety, and efficacy. During early phases of research and development, this involves identifying the site(s) within the antibody where the linker and payload are conjugated, calculating drug-to-antibody ratios, and characterising the different ADC proteoforms within a sample. To address this, we optimised a complete workflow that includes sample preparation, instrumentation, and data analysis. Importantly, we integrate intact, top-down, and bottom-up mass spectrometry data for in-depth characterisation of ADC products.
The information from the 3 levels of mass spec can be integrated into our ProteoformX software, allowing precise localisation of the drug conjugate at the exact subunit of the antibody.
- A full report containing
- Intact mass analysis and DAR calculation
- Peptide mapping with MS/MS spectra confirming conjugation sites
- Top-down sequence coverage with conjugation site identification
- Antibody Sequence with I/L differentiation, MS2 spectra covering variable region (If sequence is unknown)
- 50 μg of antibodies in solution
- >95% purity
- Antibody sequence if known
- Buffer information
- Structure and mass of conjugate
- Binding Residue
- Samples must be free of detergents and polymers (Triton X-100, Tween-20, PEG, etc.)
Characterisation and CQA Assessment of Bispecific Antibodies
Service Description:
Bispecific antibodies harness the unique ability to bind 2 different antigens at the same time. Acting as a bridge, these T-Cell Engagers (TCEs) directly connect immune and diseased cells. A major aspect of developing TCEs is ensuring the correct product has been made and assessing critical quality control attributes.
We have developed a service to fully characterise bispecific antibodies through combining mass spectrometry data from multiple levels in our software ProteoformX. The combination of this data provides in-depth information on the molecule's structure, mapping critical quality attributes across intact, subunit, and peptide levels.
1. Intact Mass Analysis
First, an intact analysis will be completed to assess the overall purity and match major peaks to the expected mass of the bispecific antibody. Any mis-paired products can be identified, as shown below.
2. Top-Down
Next, we perform top-down proteomics analysis to extract detailed information at the individual subunit level of the antibody. Product stability can be assessed by identifying full-length and truncated antibody subunits. As well, the relative abundance of subunit proteoforms (i.e., modified vs. unmodified subunit) is provided.
3. Bottom-Up combined with Top-Down
Bottom-up data is next integrated with the top-down to allow for additional sequence validation, accurate PTM localisation, and glycan profiling. Bottom-up peptides from multiple enzymatic digests are mapped to antibody subunits and finally associated with each proteoform subunit.
Full report includes:
- Intact mass analysis with peak annotation for:
- Intact antibody matching to expected mass
- Antibody pairing analysis
- Detection of impurities or host cell proteins
- Reduced/deglycosylated heavy and light chain mass
- Top-down analysis:
- Identification of all antibody subunits, detection of truncations
- Localisation of PTMs and glycans
- Bottom-up analysis:
- Sequence validation and variant detection, PTM/glycan localisation
- 200 μg of antibodies in solution
- >80% purity
- Expected antibody sequence
- Buffer information
- Samples must be free of detergents and polymers (Triton X-100, Tween-20, PEG, etc.)
Antibody services, done right.
From one-off sequencing to routine quality checks to large-scale ongoing projects, we've got you covered.
Your research is important to us. We want to help you get the results you're looking for. Contact us to schedule a free consultation to discuss your project. We will help you determine the optimal experimental setup for a fast turnaround time and the best price.
References & Resources
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