Rapid Novor Technology Resources.

Rapid Novor has established mass spectrometry-based de novo protein sequencing as a commercially viable, highly sensitive, and precise bioanalytical method to advance research and development (R&D) pipelines within the life sciences. With access to top-of-the-line mass spectrometers and our patented chemistry and proprietary AI-powered algorithms, we provide comprehensive characterization and analyses of diverse proteins and their interactions.

Explore our wide array of resources to learn about our technologies and services and their applications toward R&D for biologics, biosimilars, IVD, and much more.

Learn How Proteomics-based Technologies are Leveraged in Characterizing Proteins and Biomolecular Interactions.

What is HDX-MS Epitope Mapping? – Article
Characterizing Biomolecular Interactions with Surface Plasmon Resonance – Article
Selecting Specific Monoclonal Antibodies by SPR – Alpaca Antibody Showdown – Webinar

For more information about our technology, please continue exploring our latest resources available below.

Webinar

Latest Advancements in Antibody Engineering – Bispecifics, Diagnostic Controls, and More

September 28

10 AM EDT / 8 AM MDT / 4PM CET

Latest Posts

Latest Advancements in Antibody Engineering – Bispecifics, Diagnostic Controls, and More

Confirming the Binding Site Between Cellular DNA Repair Proteins with HDX-MS

Antibody Discovery from a Chicken Polyclonal Mixture

Antibody Discovery Dead Ends and New Approaches

Single-Molecule Characterization of Subtype-Specific β1 Integrin Mechanics

CAR-iNKT Cells Targeting Clonal TCRVβ Chains as a Precise Strategy to Treat T Cell Lymphoma

Resources

Key Pain Points in Amino Acid Sequencing & How to Avoid Them

Amino acid sequencing is commonly performed using Edman degradation or mass spectrometry (MS). While mass spectrometry is favoured for its high throughput capabilities and ease of use, both techniques possess their own features and limitations. This article summarizes some of the key pain points inherent in the two methodologies when determining the amino acid sequence.

De Novo Protein Sequencing vs DNA Sequencing

DNA sequencing is the process of determining the precise order of four nucleotides bases—adenine (A), guanine (G), cytosine (C), and thymine (T)—that make up the DNA molecule. From Sanger sequencing to next-generation sequencing (NGS), DNA sequencing’s accessibility and ease of use make it one of the most widely used technologies in life sciences.

How to Determine Peptide Sequences

Amino acids (aa)—the building blocks of proteins—are simple molecules characterized by a variable R group flanked either side by an amino group and a carboxyl group. With around 20 different commonly found amino acids, each one can bond with another to produce chains that can be classified as peptides (typically below 50 aa) and proteins (sequences above 50 aa)—molecules ubiquitous to every known organism.

Why is Protein Sequencing Useful?

Protein sequencing is a method that typically utilizes mass spectrometry (MS) to determine the amino acid code of a protein1. Prior to the development of mass spectrometry, Edman degradation, a method involving the stepwise degradation of peptides to derive the order of amino acids, was the mainstream approach. Nowadays, mass spectrometry is favored due to its ease of use and high throughput capabilities, though Edman degradation is still employed for specific applications in which the technique is well suited.

What is Protein Sequencing by Mass Spectrometry?

Nowadays, DNA sequencing is so popular that it is easy to forget that the first sequenced biological material was protein – insulin, by Sanger. Sanger, and another researcher, Edman, separately pioneered protein sequencing.

Antibody Protein Sequence Analysis Using Mass Spectrometry

One of the most important pieces of information researchers need to know during early stage antibody drug research and development is the sequence information of the antibody protein. With the advancement of mass spectrometry instrumentation and technologies, it is helpful, and sometimes critical, to conduct sequence analysis using mass spectrometry experiments.

Isoleucine and Leucine

Because they share the same mass, isoleucine and leucine are known as isobaric amino acids. Conventional mass spectrometry-based proteomics cannot be easily used to distinguish between isoleucine and leucine.

Ushering the New Era in Anti-Drug Antibody Assays with Next Generation Protein Sequencing

Anti-drug antibody (ADA) assays are critical to assess the clinical efficacy and safety of a biological drug and rely on control reagents that mimic the ADA response to the biological drug being tested. These positive controls typically consist of animal-derived pooled polyclonal antibodies or human monoclonal antibody reference panels against the target protein drug.

DNA Sequencing vs Next Generation Protein Sequencing

The protein sequence is key to understanding the function of a protein target and is critical to therapeutic and diagnostic development. This is particularly important for antibodies whose code diversity and glycosylation impact both function, and stability.

Prevalence of Secondary Light Chains

Monoclonal antibodies (mAbs) are widely used in research, diagnosis, and pharmaceutical purposes. Lately, the relatively lower quality of research-purpose mAbs is a point of concern within the research community.

Increased De Novo Protein Sequencing Coverage with Optimal Protease Cocktail

In this study, we conducted a large-scale statistical analysis of protein sequencing data from samples digested with multiple proteases to understand the impact of using different combinations of proteases to improve the depth of sequence coverage in the application of de novo protein sequencing.

A Large-Scale Comparison of MS-based Antibody De Novo Protein Sequencing and Targeted DNA Sequencing

The DNA sequences of antibodies are highly diverse due to the V-(D)-J recombination and hypersomatic mutations. As such, relying on homology-based searches to sequence novel antibodies can introduce bias to sequences obtained from proteomics approaches.

In-Depth Characterization of Monoclonal Antibodies with a Single Experiment and Fully Automated Data Analysis

To develop robust mAb biologics, it is vital to fully characterize the protein, including its primary sequence, mutations, and important post-translational modifications

Next Generation Protein Sequencing in Veterinary Medicine and Industry

Since 2006, the One Health Initiative (OHI)’s goal has been to demonstrate the inextricable link between humans, animals, and the environment. Certainly, the current global pandemic is a great testament to the ties between climate change, humans, and animals that OHI has been working to highlight. The rise of other zoonotic diseases (e.g., Hendra, and Nipah viruses) not only directly affect humans through disease transmission but may also result in deep impacts to the food supply

Recombinant Antibodies: A New Generation Enabled by Protein Sequencing

Recombinant antibodies are artificially synthesized antibodies. Recombinant antibodies are generated from expression systems (e.g., E.coli, yeast, mammalian cell lines) via transfection with two separate plasmids encoding the amino acid sequences for the light and heavy chains, respectively. In order to recombinantly produce mAbs, the amino acid sequence of the light and heavy chains must be known. There are many ways to obtain the sequence of an antibody.

Sequencing and Recombinant Expression of Goat Antibodies from a Polyclonal Mixture

Circulating in blood is a multitude of biologically important antibodies. These pools of polyclonal antibodies (pAb) are invaluable sources for drug discovery against various diseases, and for the development of robust immunoreagents for diagnostics, and research.

First Immunoassay for Measuring Isoaspartate in Human Serum Albumin

The ongoing pandemic has reinforced the need for in vitro diagnostics to globally surveille emerging pathogens and provide better medical care. In particular, immunoassays are favoured due to their affordability, ease, and speed. Nevertheless, the combination of rapidly evolving pathogens, and more complex diseases resulting from increasing life expectancy worldwide require more sensitive and specific immunoassays in the nick of time. To increase sensitivity, immunoassay development can benefit from exploiting industry-leading technologies such as de novo protein sequencing.

Why Is Sequence Blindness Acceptable with Antibodies?

There have been cases where researchers have trusted a kit, and they see a positive reaction only to, unfortunately, realize that the kit was actually detecting another protein because the kit’s antibody lot changed. Such was the case for the University of Toronto’s Diamandis team who spent half a million dollars and nearly two years due to an unreliable antibody. A certificate proving that the protein sequence of an antibody remains unchanged would have easily avoided the aforementioned mishaps.

Identifying CDRs by Antibody Sequencing

The acronym “CDR” stands for complementarity determining region, a variable sequence of amino acids that folds into loops capable of binding to an antigenic amino acid sequence, also known as an epitope

Generation and Diversification of Recombinant Monoclonal Antibodies

Monoclonal antibodies are essential reagents and research tools. They are commonly generated and produced in hybridoma cells and are expected to be highly consistent. However, the instability and fragility of hybridoma cells can cause unwanted mutations, additional chains, and permanent loss of important antibodies. On the other hand, the lack of standardization validation for commercial antibodies often keeps researchers in the dark leading to the reproducibility crisis.

Introduction to De Novo Protein Sequencing

In this on-demand webinar, our scientific sales executive Jennifer, will briefly cover the fundamentals of protein sequencing, how researchers have benefited from implementing protein sequencing into their pipelines, and discuss how Rapid Novor is able to routinely and robustly achieve 100% accuracy and 100% coverage for both monoclonal and oligoclonal antibodies.

Leveraging Recombinant Patient Antibodies in Therapeutic Applications

Our team has perfected the art of monoclonal antibody sequencing and is now ready to demonstrate our ability to sequence mAbs from polyclonal mixtures. In this talk, Anthony will walk through our new polyclonal sequencing platform that uses both proteomics and genomics to sequence the most abundant antibodies found in polyclonal sera.

Research Insurance with De Novo Protein Sequencing

If you could have guaranteed stability, certainty, and reproducibility for your research, would you be interested? Imagine this, if you’re 2 years into your project and your freezer died along with all of your important cell lines, what would you do? This is just one of the situations covered in this webinar, along with many other solutions researchers have begun to implement to safeguard their efforts. Whether you’re looking to proceed with stability and certainty or you’re looking for an immediate solution for your current reproducibility challenges, protein sequencing may be the answer.

Antibody Sequencing as a Tool to Improve Reproducibility in the Life Sciences

At PepTalk 2021, we discussed the importance of antibody standardization and explained why it’s crucial for the longevity of your research. You can listen to the full on-demand video here.

Leveraging Polyclonal Antibody Sequencing to Get High Affinity Binders Against Tough Targets

When it comes to polyclonal antibodies, how they are discovered can be just as important as how they are reproduced. In our talk originally presented at Antibody Engineering & Therapeutics Digital 2021, we highlighted the latest technology that’s capable of capturing the most abundant and high-affinity monoclonal antibodies directly from a poly mixture.

Leveraging pAbs for Therapeutic Development

Over the past several years Rapid Novor has been developing the world’s best antibody protein sequencing platform, sequencing over 2700 monoclonal antibodies and proteins. In 2020, they unveiled their most advanced technology to date - REpAb® polyclonal antibody sequencing. The platform combines the world’s best protein sequencing technology and NGS to comprehensively mine the antigen-specific antibody repertoire present in rabbit and human patient samples. By leveraging the platform, teams can build robust antibody assays and therapeutic leads derived from patients’ blood.

Polyclonal Antibody Sequencing with Only Proteomics

Over the past 5 years Rapid Novor has perfected monoclonal antibody sequencing, and is now sequencing mAbs from polyclonal mixtures using REpAb®. After successfully launching their proteogenomics based sequencing technology to deconvolute the immune response, the team has further evolved the technology and has derived the most abundant mAb sequences directly from rabbit blood using only proteomics. The talk will surround the development, progress and use cases for REpAb®.

Overcoming Irreproducibility in Life Science Research

Our team, along with four other industry panelists, discuss ways to safeguard their research through recombinant antibodies, cell culturing procedures, antibody protein sequences, and reference identifiers.

DNA vs Next Generation Protein Sequencing – a Deep Dive

This webinar offers insight into how DNA and protein sequencing compare to each other.

Antibody Characterization by Mass Spectrometry

In this on-demand webinar, we discuss why it is important to characterize antibodies based on their physical properties not just by what they bind, and how you can easily do the former via mass spectrometry-based protein sequencing.

Non-Fungible Antibodies

Other than a paucity in widespread use, such efforts still do not address the main issue: the uniqueness of antibodies. Unlike currency, antibodies are non-fungible. To manufacture a replica of a specific antibody, we must first know its sequence. Sometimes, scientists may obtain the sequence through nucleotide sequencing means.

Recombinant Therapeutic pAbs are Now Possible

Polyclonal antibodies are popular research reagents for their high sensitivity and robust cross-platform performance. But few companies consider them viable for therapeutic applications as they are almost impossible to characterize. Additionally, they suffer from a lack of reproducibility and limited supply. Monoclonal antibodies (mAbs) can be reliably characterized and produced for therapeutic applications, but are more costly to discover and develop. Rapid Novor’s REpAb technology can overcome these limitations by capturing the sequences of the most abundant IgG in a pAb and enabling indefinite antibody production. Here we report the first successful conversion of a goat polyclonal antibody into a cocktail of recombinant mAbs using only the pAb protein sample.

Polyclonal Antibody Sequencing in Therapeutics Development Pipelines

Over the past several years Rapid Novor has been developing the world's best antibody protein sequencing platform, with over 2700 monoclonal antibodies and proteins sequenced. In 2020, they unveiled their most advanced technology to date- REpAb® polyclonal antibody sequencing. The platform combines the world's best protein sequencing technology and NGS to comprehensively mine the antigen specific antibody repertoire present in rabbit and human patient samples. By leveraging the platform, teams can build robust antibody assays and therapeutic leads derived from patient's blood.

Species-Agnostic Antibody Sequencing & Discovery in Veterinary Medicine R&D

Research Challenges in Veterinary Medicine Since 2006, the One Health Initiative (OHI)’s goal has been to demonstrate the inextricable link between humans, animals, and the environment.

Fully Harnessing the Power of Immunotherapy through Protein Sequencing

Of interest to human and veterinary drug development scientists, biologics and biosimilars development scientists, scientists performing pre-clinical assay development, immunotherapy researchers, oncolytic therapy development scientists, gene therapy development scientists, gene therapy, and oncolytic therapy researchers, CAR-T, and CAR-NK development scientists

Broadly Neutralizing Antibody Cocktails Targeting Nipah Virus and Hendra Virus Fusion Glycoproteins

Hendra virus (HeV) and Nipah virus (NiV) are types of Henipaviruses (HNVs) that originated in bats and can infect the human respiratory system with detrimental consequences. As enveloped, single-stranded RNA viruses, HeV and NiV use attachment (G) and fusion (F) glycoproteins on the envelope membrane to enter host cells. So far, there are no approved therapeutics or vaccines to combat the viruses in humans.

Leveraging the Power of Next Generation Protein Sequencing to Shape Tomorrow’s In Vitro Diagnostics

Non-invasive, sensitive, accurate, and easy-to-manufacture IVDs will be critical to detect and monitor diseases where misfolded proteins play a significant role such as neurological illnesses like Alzheimer’s, cancers like multiple myeloma, among others.

Enriching Engineered T Cells with Antibody Sequencing & Modulation

Known, high-performing and well used antibodies against useful targets on CAR-T cells can be examined for mechanism of action using proteomics and mass spectrometry. Knowledge of the antibody sequences via Next Generation Protein Sequencing (NGPS) can be useful for humanizing or otherwise engineering constructs. Rapid Epitope mapping by HDX can be useful for both epitope and paratope engineering strategies.

What is HDX-MS Epitope Mapping?

The origin of hydrogen-deuterium exchange (HDX) dates back to the 1950s, when protein scientist Linderstrøm-Lang created a method involving protein deuteration to distinguish amide hydrogens participating in secondary structures. Today, scientists frequently rely on HDX data to investigate protein structure, conformational dynamics, and protein-ligand interaction.

What is Polyclonal Antibody Sequencing?

The most straightforward solution would be to determine sequences of the dominating antibody forms in a polyclonal mixture to enable recombinant antibody generation and ensure reproducibility. This was recently made possible by the development of polyclonal antibody sequencing technology, which will be reviewed in this article.

Characterization and Modulation of Anti-αβTCR Antibodies and Their Respective Binding Sites at the βTCR Chain to Enrich Engineered T Cells

αβTCR-engineered T cells have been applied in clinical trials, specifically directed against cancer/testis antigens. Though the clinical outcomes are promising, only a small proportion of patients benefit from these novel treatments. Lower response rates are partially attributed to a heterogeneous mixture of non-engineered and poorly engineered T cells that remain in the administered therapeutic product. For successful translation of these novel treatments into the clinic, engineering efforts should be reinforced with effective methods for engineered T cell purification and engineered T cell elimination post infusion into patients.

Chimeric Antigen Receptors and T cells – CAR-T

Written by: Vanessa Yoon Calvelo, PhD Published: June 13, 2022 Contents What is CAR-T Cell Therapy? CAR Structure and Function CAR-T Cell [...]

Next Generation Vaccine Development with Proteomics

As nearly all individuals have pre-existing immunity to influenza viruses, influenza-specific memory B cells will likely be recalled upon COBRA HA vaccination. By comparing the antibody response towards specific wild-type influenza strains and COBRA antigens, we can begin to understand the potential for COBRA-based vaccines to be used in the clinic.

Adeno-Associated Virus Vectors for Gene Therapy Delivery

Written by: Vanessa Yoon Calvelo, PhD Published: July 11, 2022 Contents What is Gene Therapy? What are Adeno-Associated Viruses? Engineering of [...]

Protein Characterization by HDX-MS

Characterization of proteins and protein complexes is a major keystone of structural biology. As our understanding of cellular processes continues to evolve from simple pathways to complicated networks, our need for advanced analytical methods is quite apparent. Mass spectrometry (MS)-based structural approaches can be used to study protein conformational changes and dynamics, protein motion/flexibility, ligand-protein binding, and protein-protein interfaces.

Moving Towards Biosimilar Drugs

Written by: Vanessa Yoon Calvelo, PhD Published: August 3, 2022 Contents What are Biosimilar Drugs? Why are Biosimilars Being Developed? Biosimilars [...]

Surface Plasmon Resonance Spectroscopy

Written by: Vanessa Yoon Calvelo, PhD Updated: January 19, 2023 (Published: August 11, 2022) Contents What is Surface Plasmon Resonance Spectroscopy? [...]

Characterizing Fragile Protein Complexes

Webinar Highlights You will learn: Introduction to the structure and function of the tuberous sclerosis protein complex (pTSC) A novel strategy [...]

Characterizing Biomolecular Interactions with Surface Plasmon Resonance

Biological processes are driven by molecules that interact through specific molecular contacts, often to form a stable complex. These interactions are typically defined by the principles of thermodynamics as well as biomolecular structure and recognition. At the simplest level is the interaction between a target molecule with a specific binding site and a probing molecule that binds to that site, resulting in the bound complex.

Structural Characterization of Endogenous Tuberous Sclerosis Protein Complex Revealed Potential Polymeric Assembly

To date, near-complete cryo-electron microscopy (cryo-EM) density maps of pTSC were obtained by either employing chemical cross-linking or graphene oxide-coated grids during sample preparation; however, this may not reflect the true native state of pTSC.

Resistance to Autosomal Dominant Alzheimer’s Disease in an APOE3 Christchurch Homozygote

De novo protein sequencing provided the research team with insurance by securing the complete amino acid sequence of a therapeutic mAb candidate for ADAD. This mass spectrometry-based protein sequencing technique can be used to obtain the sequence information of any antibody or protein for biomarker discovery, characterization, and validation. Access to this structural information only broadens our understanding of disease pathogenesis and fosters the development of innovative therapeutic or preventative treatments.

Towards Antigen-Specific Tregs for Type 1 Diabetes: Construction and Functional Assessment of Pancreatic Endocrine Marker, HPi2-Based Chimeric Antigen Receptor

Antibodies with established, specific targets can be sequenced and utilized to engineer the hinge region and antigen-binding domains with antibody fragments and derivatives. With the sequence information in hand, further steps to optimizing a viable therapeutic approach can be more accessible.

Selecting Specific Monoclonal Antibodies by SPR – Alpaca Antibody Showdown

In this SPR webinar, you will learn: How SPR works and its unique advantages for kinetic analysis of [...]

Technologies for Antibody Discovery and Generation

The great debate on the use of in vivo versus in vitro sources and strategies for antibody discovery and generation continues to thrive among antibody research groups. On one side of the debate is the argument for non-animal-derived antibodies due to the technical advancements of current in vitro technologies, and the moral obligation to reduce animal usage. On the other side of the debate is the counterargument for animal-derived antibodies due to their better performance in affinity, specificity, and reduced immunogenicity risk.

Nanobody Lead Optimization with Epitope Mapping and Binning

In this webinar, you will learn: How Rapid Novor’s de novo polyclonal sequencing platform REpAb® can accelerate any nanobody development pipeline How [...]

Exploring the Sheep (Ovis aries) Immunoglobulin Repertoire by Next Generation Sequencing

By conducting an in-depth analysis of non-antigen immunized sheep Ig repertoires via NGS, this data provides further insight into the adaptive immunity of sheep and lays a foundation for future work on immunogenetics and ovine antibody drug development.

The Shortcut to Reliable Diagnostic, Control, and Assay Antibodies

In this webinar, you will learn: IVD and immunoassays, supply chain risk management considerations How monoclonal and polyclonal antibody sequencing works, requirements [...]

Evaluation and Selection of a Lead Diabody for Interferon-γ PET Imaging

De novo protein sequencing can support the development of antibody-based reagents, including Dbs and other antibody fragments. Working with the exact amino acid sequence of the mAb can help facilitate the in silico design and conjugation design processes, ensuring accuracy in the final engineered format.

Rational Antibody Design and Engineering with Next Generation Protein Sequencing

In this webinar, you will learn: A strategy for generating recombinant mAbs and antibody derivatives directed towards antigens involved in mitotic cell [...]

Single-Molecule Characterization of Subtype-Specific β1 Integrin Mechanics

To develop robust mAb biologics, it is vital to fully characterize the protein, including its primary sequence, mutations, and important post-translational modifications

CAR-iNKT Cells Targeting Clonal TCRVβ Chains as a Precise Strategy to Treat T Cell Lymphoma

With 22 functional T cell receptor (TCR)Vβ subunit families making up the normal T cell repertoire, signals from these cell surface receptors often determine the fate of normal cells. However, mutations in TCR signaling proteins are frequently associated with peripheral T cell lymphomas (TCLs), including adult T cell leukemia/lymphoma (ATL), which indicates a driving role for TCRs in TCL oncogenesis. As TCL and ATL are clonal in nature, tumour cells typically express a single TCRVβ subunit with no bias in the usage of TCRVβ subunit families. Consequently, targeting the specific TCRVβ subunit presents a promising therapeutic approach that is highly selective and tumour-specific.