Study: Increased De Novo Protein Sequencing Coverage with Optimal Protease Cocktail

Overview Introduction Sample preparation for complete LC-MS/MS sequencing of a pure protein sample differs substantially from the preparation used for protein identification in complex samples. To sequence a protein de novo, the experimental design should aim to identify each amino acid (a.a.) multiple times within different peptides, instead of relying on only a few peptides per protein for complex protein mixtures. Efforts to increase protein sequence coverage typically rely on using multiple proteases to digest the protein. In this study, we conducted a large-scale statistical analysis of protein sequencing data from samples digested with multiple proteases to understand the impact [...]

August 8th, 2019|

Study: De Novo Protein Sequencing Vs. DNA Sequencing

A Large-Scale Comparison of MS-based Antibody De Novo Protein Sequencing and Targeted DNA Sequencing Introduction The DNA sequences of antibodies are highly diverse due to the V-(D)-J recombination and hypersomatic mutations. As such, a new antibody of interest is unlikely to appear in any existing sequence database. Consequently, the database search approach commonly used in proteomics does not work for antibodies. De novo sequencing of antibody proteins directly from MS data is an improvement over the conventional database approach. However current published de novo sequencing methods are based on data from few, selected antibodies that may not be representative of samples. Here, [...]

June 7th, 2019|

Study: Prevalence of Secondary Light Chains

Introduction Monoclonal antibodies (mAbs) are widely used in research, diagnosis, and pharmaceutical purposes. Lately, the relatively lower quality of the research-purpose mAbs is a point of concern within the research community¹,². The problems include the lack of validation and low reproducibility. As most of the validation is done by immunoassay, the extent of protein contamination, including undesired antibody forms, remains unknown. Mass spectrometry based protein sequencing technology enables the discovery and characterization of undesired antibody forms in mAb reagents. In this study, we examine the existence of a second light chain in addition to the expected primary light chain. To [...]

February 5th, 2019|

Novor Paper Published @ JASMS

The paper, Novor: Real-Time Peptide de Novo Sequencing Software, is published. It is open access and can be downloaded here. At Rapid Novor, we believe technologies only get better when more people can access them. Thus, we provide Novor software Free of charge for academic research. Compared with the state-of-the-art, Novor significantly improved the de novo sequencing accuracy and is more than an order of magnitude faster. At a speed of 300 spectra per second on a laptop computer, Novor exceeds any mass spectrometer’s throughput. De novo sequencing now only requires a fraction of database search time and, therefore, becomes [...]

July 6th, 2015|