It is able to quickly respond to an antigen by generating antibodies specifically bound to it. The immune system works in a fascinating way. Antibodies are a special type of proteins generated by our immune system to protect ourselves against foreign agents. Sequencing antibody proteins is one of the best applications for the NGPS technology. The goal of the technology is to accurately determine the primary sequence of the protein in the given sample. Next-Generation Protein Sequencing or NGPS is the technology to derive the full protein sequences directly from protein samples using mass spectrometry. Our research interestsĪs a core facility within the NIBSC our aim is to optimise the sequencing process for applications in the development of biological standards and applied biological research.Insights from industry Mingjie Xie CEO Rapid NovorĪn interview with Mingjie Xie, conducted by James Ives, MPsych Please give an overview of next generation protein sequencing (NGPS) and how it can be used to decipher antibody proteins. It is the combination of both, high quality wet-lab NGS service and cutting edge, statistically robust bioinformatics working in unison that gives our collaborating groups in NIBSC the highest level of scientific support. These analyses are run on our high-performance computing cluster that combines the best of on-site and cloud resources. The core facility is committed to maintaining a comprehensive and up- to-date catalogue of software, backed by peer-reviewed journal articles. We use over 100 pieces of software and close to 500 different software libraries to provide the best and most appropriate analyses. Presentation – Providing custom publication standard graphics to present analysis results.The work we provide includes identification of SNPs, differentially expressed gene analysis, de novo assembly of genomes and metagenomics. Analysis – Finding significance in biological data using existing bioinformatics tools as well as developing custom solutions.Experimental design – Providing advice on factors such as biological and technical replicates as well as depth of sequencing coverage to ensure that results obtained are statistically meaningful. Although sequencing bioinformatics is our primary computational role, we also work with data generated by nuclear magnetic resonance spectroscopy, mass spectroscopy, light microscopy and electron microscopy experiments on our high-performance computing cluster. Utilising best practice techniques, the latest analyses and bespoke statistically robust methods, we apply computational methods to answer a large range of biological questions. Applications – Eukaryotic whole genome, exome, transcriptomics, metagenomics, high-throughput, highly multiplexed samplesīesides generating NGS, we provide rigorous bioinformatic analyses individually tailored to each project.Turnover time for large projects (human genome) in less than 30 hours.Applications – Viral/bacterial genome, targeted re-sequencing.Turnover time for small projects as fast as 9 hours run time.RNAseq - transcriptomics, mRNA, small RNA.DNAseq - whole genome, amplicons, de novo assembly, targeted re-sequencing.We undertake all NGS projects within the institute. We collaborate with groups in every scientific division across the NIBSC, with projects ranging from validation of SNPs in individual genes to viral/bacterial whole genome sequencing to transcriptomics. Our team of sequencing scientists and bioinformaticians provide end-to-end support in all stages of sequencing experiments: from experimental design through to final analysis. The NGS/Bioinformatics core facility was established in 2016 to cater for growing demands in NGS analyses at the NIBSC. The combined power of NGS and bioinformatics is vital for diagnostics, medical treatment and epidemiological research. Using mathematical and statistical methods implemented by a wide range of programmatic languages, bioinformatics tools organise, analyse and interpret biological information at the molecular, cellular and genomic level. Correspondingly, the field of bioinformatics is central to the interpretation and application of this biological data. Since the advent of modern sequencing techniques, identification of nucleic acid sequences has become a ubiquitous and essential tool across all areas of biological science. Next Generation Sequencing (NGS) technologies offer high-throughput, rapid and accurate methods of determining the precise order of nucleotides within DNA/RNA molecules.
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