December 2022

The Hunt for Novel Therapeutics Through Antibody Engineering

2022-12-02T11:22:32-05:00December 2nd, 2022|Articles|

Written by Genya Gorshtein, MSc November 1, 2022 Contents Introduction Approaches for Engineering Antibody Therapeutics Driving Antibody Engineering with Next Generation Protein Sequencing and Proteomics Introduction Antibody engineering encompasses various development, production strategies, and modification techniques to improve the biological properties of monoclonal antibodies (mAbs) as therapeutic [...]

Cell Specific Protein Degradation with Antibody Conjugated PROTACs

2022-12-02T10:23:52-05:00December 2nd, 2022|Articles|

Written by Genya Gorshtein, MSc November 25, 2022 Contents Introduction General PROTAC Structure and Function Antibody-Conjugated PROTACs Developing AbPROTACs with De Novo Antibody Sequencing and Proteomics Introduction Small-molecule drug development is aimed at inhibiting disease-promoting protein function through occupancy-driven protein inhibition. A major caveat of this therapeutic [...]

October 2022

Characterizing Biomolecular Interactions with Surface Plasmon Resonance

2022-10-21T10:16:43-04:00October 21st, 2022|Articles|

Written by Vanessa Yoon Calvelo, PhD September 15, 2022 Contents Analyzing Biomolecular Interactions SPR Applications for Biomolecular Interactions SPR – A golden standard for biomolecular interaction analysis Analyzing Biomolecular Interactions Biological processes are driven by molecules that interact through specific molecular contacts, often to form a stable [...]

September 2022

Antibody Drug Conjugates as Anti-Cancer Therapeutics

2022-11-17T13:44:08-05:00September 19th, 2022|Articles|

Written by Genya Gorshtein, MSc September 14, 2022 Contents Introduction ADCs as Novel Anti-Cancer Chemotherapeutics Key Components of ADCs Future Generation of ADCs De Novo Protein Sequencing Applications in ADC Development Introduction An antibody-drug conjugate (ADC) is a monoclonal antibody (mAb) with a covalently attached cytotoxic payload [...]

August 2022

What Generates Antibody Diversity?

2022-11-28T11:08:39-05:00August 31st, 2022|Articles|

Written by Genya Gorshtein, MSc August 31, 2022 Contents Introduction Antibody Loci and V(D)J Recombination Somatic Hypermutation Class Switch Recombination De Novo Proteomic Sequencing of Antibodies Introduction Without the presence of an antigen, the human immune system can generate more than 1012 different antibodies and as many [...]

What are Polyclonal Antibodies?

2022-11-17T13:24:32-05:00August 18th, 2022|Articles|

Written by Genya Gorshtein, MSc August 18, 2022 Contents Introduction How are Polyclonal Antibodies Produced? Applications of Polyclonal Antibodies Challenges of Polyclonal Antibodies De Novo Polyclonal Antibody Sequencing Introduction Polyclonal antibodies (pAbs) are a heterogeneous mix of antibodies derived from B cells in the adaptive immune system. [...]

Surface Plasmon Resonance Spectroscopy

2022-08-17T19:50:31-04:00August 16th, 2022|Articles|

Written by Vanessa Yoon Calvelo, PhD August 11, 2022 Contents What is Surface Plasmon Resonance Spectroscopy? How Does SPR Work? SPR Experimental Workflow SPR Sensorgram SPR Advantages Antibody-Antigen Binding Analysis with SPR SPR Antibody-Antigen Interaction Analysis at Rapid Novor What is Surface Plasmon Resonance Spectroscopy? Surface plasmon [...]

Structure and Function of Antibodies

2022-08-24T17:37:21-04:00August 10th, 2022|Articles|

Written by Genya Gorshtein, MSc August 10, 2022 Contents General Structure of Antibodies Fab and Fc Fragments Hinge Region CDR and FR Regions Antibody Structure Analysis Services General Structure of Antibodies Antibodies or immunoglobulins (Ig) maintain a common quaternary structure consisting of two identical heavy chains (HCs) and two [...]

Moving Towards Biosimilar Drugs

2022-11-17T13:38:05-05:00August 4th, 2022|Articles|

Written by Vanessa Yoon Calvelo, PhD August 3, 2022 Contents What are Biosimilar Drugs? Why are Biosimilars Being Developed? Biosimilars are not the Equivalent of Generics Biosimilar Development Biosimilar Monoclonal Antibodies De Novo Protein Sequencing Solutions in Biosimilar Development What are Biosimilar Drugs? Biosimilar drugs, also known [...]

July 2022

Protein Characterization by HDX-MS

2022-10-27T11:20:06-04:00July 26th, 2022|Articles|

Written by Vanessa Yoon Calvelo, PhD July 21, 2022 Contents Mass spectrometry-based approaches for structural analysis of proteins HDX-MS Applications for ‘Difficult’ Proteins HDX-MS – A powerful analytical technique for protein characterization Mass spectrometry-based approaches for structural analysis of proteins Characterization of proteins and protein complexes is [...]

June 2022

Why do Post-Translational Modifications Matter?

2022-08-09T16:40:29-04:00June 14th, 2022|Articles|

Written by Vanessa Yoon Calvelo, PhD June 2, 2022 Contents What are post-translational modifications (PTMs)? Impact of PTMs Types of PTMs PTMs increase microheterogeneity of antibodies Characterization of PTMs by next generation protein sequencing What are Post-Translational Modifications? Post-translational modifications (PTMs) are processing events typically driven by [...]

Protein Structure and How to Study it

2022-06-10T10:22:08-04:00June 10th, 2022|Articles|

Written by Yuning Wang, PhD June 3, 2022 Contents Background Four levels of protein structure How are protein structures studied? Background Structural information provides a great deal of understanding of how a protein works, which can allow us to elucidate molecular mechanisms underlying human diseases. Rapidly developing [...]

What is Polyclonal Antibody Sequencing?

2022-11-24T16:16:27-05:00June 1st, 2022|Articles|

Written by Yuning Wang, PhD May 31, 2022 Contents Background What is Polyclonal Antibody Sequencing? Applications of Polyclonal Antibody Sequencing Advantages of Polyclonal Antibody Sequencing World’s First: De Novo Polyclonal Antibody Sequencing at Rapid Novor Background The native immune system produces polyclonal antibodies (pAb) by different B-cell [...]

May 2022

What is HDX-MS Epitope Mapping?

2022-06-28T15:04:22-04:00May 15th, 2022|Articles|

Written by Yuning Wang, PhD May 13, 2022 Contents What is HDX-MS? HDX-MS Workflow Applications of HDX-MS HDX-MS Advantages HDX-MS Epitope Mapping of Antibodies HDX-MS Epitope Mapping at Rapid Novor What is HDX-MS? The origin of hydrogen-deuterium exchange (HDX) dates back to the 1950s, when protein scientist [...]

April 2022

Identifying CDRs by Antibody Sequencing

2022-11-17T13:59:26-05:00April 1st, 2022|Articles|

Written by Yuning Wang, PhD March 15, 2022 Contents What are CDRs? Antibody CDRs De Novo Protein Sequencing as a Tool for Identifying CDRs Sequences Applying De Novo Protein Sequencing to Identify CDRs Sequences Annotation Schemes for Identifying CDRs by Sequence Rapid Novor can Help with Identifying CDRs by Sequence [...]

February 2022

Camelid Antibodies and Nanobodies

2022-11-17T14:09:21-05:00February 4th, 2022|Articles|

Written by Yuning Wang, PhD January 21, 2022 Contents Discovery of Camelid Antibodies What are Camelid Antibodies? Structure of Camelid Antibodies and Nanobodies Applications of Nanobodies How are Nanobodies Developed? References Discovery of Camelid Antibodies Three decades ago, the discovery1 of a peculiar [...]

January 2022

October 2021

What is Peptide Mapping?

2022-11-17T16:15:11-05:00October 28th, 2021|Articles|

Peptide mapping is a widely used analytical technique to verify the primary structure (amino acid sequence) and characterize the chemical modifications of a protein. It analyzes peptides generated from the digestion of an isolated protein, or a protein mixture

September 2021

Structure of an Amino Acid

2022-11-17T16:02:45-05:00September 14th, 2021|Articles|

Amino acids are small organic molecules that make up peptides and proteins. All living organisms share the same set of amino acids. Amino acids come together in different orders (sequences) to form proteins. As such, each type of protein has a different three-dimensional structure and biological activity.

Why is Protein Sequencing Useful?

2022-08-17T18:25:33-04:00September 3rd, 2021|Articles|

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.

August 2021

What are Monoclonal Antibodies?

2022-08-17T16:55:40-04:00August 25th, 2021|Articles|

Monoclonal antibodies (mAbs) are homogenous antibodies that bind to a single epitope on an antigen. Kohler and Milstein generated the first mAbs when they developed hybridoma technology in the 1970s. Because of the specificity, homogeneity and unlimited availability, mAbs are valuable reagents used in a variety of important applications including treatment and diagnosis of diseases

How to Determine Peptide Sequences

2022-04-25T18:38:14-04:00August 17th, 2021|Articles|

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.

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

2022-04-25T18:28:10-04:00August 13th, 2021|Articles|

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

2022-08-17T18:18:59-04:00August 1st, 2021|Articles|

Written by Yuning Wang, PhD August 1, 2021 What is 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 [...]

July 2021

Why Verifying the Protein Sequence Is Crucial for Antibody Validation

2022-04-25T19:13:45-04:00July 23rd, 2021|Articles|

Written by María Gerpe, PhD July 23, 2021 Why the Amino Acid Sequence Matters As proteins are assembled, they fold into different structural orders: from primary to quaternary. The exact sequence of the primary structure (the amino acid sequence) will dictate how a protein will fold and therefore function. The importance of [...]

What is the De Novo Amino Acid Sequencing Method?

2022-04-25T20:09:41-04:00July 19th, 2021|Articles|

Proteins are composed of peptide chains, which in turn are made up of a string or linear sequence of amino acids (Figure 1A). Every amino acid has a basic structure containing an amino (-NH2) group and a carboxylic (-COOH) group (Figure 1B). To form a peptide, amino acids link to each other via a peptide bond, which involves the reaction between the carboxylic group of one amino acid and the amine group of another amino acid (Figure 1B). As such, the primary structure of a protein is typically recorded starting at the amino-terminal (N) end and continuing to the carboxyl-terminal (C) end. The primary protein structure may be directly sequenced from a sample of the protein itself or inferred from the DNA sequence.

What is Protein Mass Spectrometry?

2022-04-25T15:22:40-04:00July 18th, 2021|Articles|

Protein mass spectrometry refers to the use of mass spectrometry in the study and characterization of proteins, including their quantification, profiling, interaction mapping, and identification of their post-translational modifications (1,2). Protein mass spectrometry may also be referred to as mass spectrometry-based proteomics. Mass spectrometry-based proteomics consist of three approaches: top-down, middle-down, and bottom-up proteomics

How Do You Obtain the Sequence of an Antibody?

2022-11-15T15:14:17-05:00July 10th, 2021|Articles|

Antibody sequences are critical for antibody engineering and protein characterization in therapeutic development. For antibody reagent users, knowing the sequences allows them to perform sequence analysis/alignment to identify binding and cross-reactivity so they can conduct rational experiment design.

Isoleucine and Leucine

2022-03-23T10:16:31-04:00July 7th, 2021|Articles|

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.

What is Amino Acid Sequencing?

2022-04-25T18:09:02-04:00July 5th, 2021|Articles|

Amino acid sequencing is the process of identifying the arrangement of amino acids in proteins and peptides. Numerous distinct amino acids have been discovered in nature but all proteins in the human body are comprised of just twenty different types.

June 2021

Types of Antibodies

2021-11-18T11:31:31-05:00June 25th, 2021|Articles|

Written by María Gerpe, PhD June 25, 2021 Introduction Antibodies or immunoglobulins (Ig) are Y-shaped glycoproteins produced by the adaptive immune system in response to antigens - substances or molecules the immune system deems as foreign. Antibodies bind to an antigen and either directly neutralize it, or activate other parts of [...]

August 2019

February 2017

Antibody Protein Sequence Analysis Using Mass Spectrometry

2022-04-25T18:11:31-04:00February 3rd, 2017|Articles|

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.

June 2016

Moving Towards Recombinant Monoclonal Antibodies

2021-12-14T18:06:16-05:00June 30th, 2016|Articles|

Recombinant Monoclonal Antibodies (rAbs) are highly reproducible, customizable and pure alternatives to the traditional antibodies produced by hybridomas. Get the antibody protein sequence, either by DNA sequencing or the de novo protein sequencing technology, you can rest assured that you can have the exact antibody made recombinantly anytime in the future.