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Software Automates Deep Characterization of Biotherapeutic Proteins

Thermo Fisher Scientific
18 Jun 2014
Sarah Thomas
Associate Editor

Product news

As protein-based drugs become more important in treating major diseases, producers face the critical challenge of deeply characterizing these highly-complex molecules for efficacy and safety, as well as to meet quality requirements. Now there’s a new software tool designed to increase the speed, quality and confidence in comprehensive biotherapeutic protein characterization useful for drug development and production quality control.

Thermo Scientific PepFinder software is making its debut at the 62nd ASMS Conference on Mass Spectrometry and Allied Topics, booth 127, and at the company’s hospitality suite: Holiday, Baltimore Hilton.

PepFinder software is designed to streamline relative and absolute quantitation, and identification of proteins from biological samples using liquid chromatography-mass spectrometry.

Therapeutic proteins such as monoclonal antibodies, interferons, and insulin must be produced in biologically-active forms that have proper folding and have specific post-translational modificiations (PTM). Traditional analysis of these complex biological molecules is highly complex and time-consuming. PepFinder software uses multidimensional dynamic search capabilities to automatically integrate complex data into concise reports.

“This is a new paradigm for peptide mapping data analysis,” said Ken Miller, vice president, marketing mass spectrometry for Thermo Fisher Scientific. “Customers can expect to reduce analysis time from weeks to hours in some cases, while generating high-confidence, comprehensive characterization reports, including known and unknown modifications.”

“Using PepFinder, a complex protein was analyzed with great details (including PTMs), and with great ease and speed!” said Shiaw-Lin (Billy) Wu, Head of Analytical Sciences at BioAnalytix and Research Associate Professor at Northeastern University.

PepFinder software, based on Mass Analyzer software licensed from Amgen, is compatible with Thermo Scientific LC-MS instruments, including the industry-leading high resolution, accurate-mass Orbitrap-based systems. This software is designed for fast, high-quality PTM profiles and peptide identifications based on a novel prediction algorithm. The software displays sequence coverage maps, automates relative changes in site specific PTMs for rapid monitoring of modifications in a single sample or across sample comparison. The software is written to provide an automated workflow for glycopeptides ID, disulfide bond mapping and other common PTM’s, including oxidation, deamidation and phosphorylationThis can eliminate time consuming and error-prone manual PTM mapping.

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UHPLC and HPLCHigh performance liquid chromatography (HPLC) and ultra high performance liquid chromatography (UHPLC), also known as UPLC, are analytical techniques used to separate, identify and quantitate components of complex mixtures including biological samples such as proteins and lipids as well as chemical mixtures of pesticides, drugs and oils. Both techniques are liquid chromatographic methods but differ by operating pressures (HPLC < 6000 psi < UHPLC ). Components of HPLC and UHPLC systems include columns, detectors, pumps, autosamplers and column heaters. Explore a range of UHPLC and HPLC columns for your specific sample needs including reverse phase, normal phase, ion exchange, HILIC, ion exclusion and size exclusion columns. For more specialized HPLC, explore FPLC, countercurrent LC and simulated moving bed systems. Find the best UHPLC and HPLC equipment in our peer reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.LC-MSLC-MS (liquid chromatography-mass spectrometry) systems and equipment are used for separation and quantitative analysis of complex mixtures, combining liquid chromatography and mass spectrometry. Quantify proteins, contaminants, pesticides or screen for drug metabolites with a high level of sensitivity. LC-MS systems and equipment include reverse phase, normal phase and specialized columns integrated with various MS detectors such as time-of-flight (TOF), quadrupole, orbitrap or ion trap mass analyzers. LC-MS/MS instruments equipped with a qTOF or triple quadrupole analyzer give greater sensitivity and resolving power to your analysis. Find the best LC-MS equipment in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.Mass SpectrometryMass spectrometry (MS) is a powerful analytical technique used to identify and quantify molecules based on the mass-to-charge ratio of gas-phase ions. It provides detailed information about the structure, composition, and properties of compounds and is widely used across fields such as environmental monitoring, materials science, drug discovery and development, food and beverage testing, and wider chemical research. Key MS techniques include tandem mass spectrometry (MS/MS), liquid chromatography–mass spectrometry (LS-MS) and inductively coupled plasma (ICP-MS). Choosing from these wide range of techniques and technologies can be a daunting task, so keep up to date with scientific applications, performance expectations, and customer reviews here all in one place. Visit our product directory to receive quotes direct from the manufacturer. ProteomicsProteomics is the systemic bioinformatics study of proteins and amino acids, including their structure, size, function and identification. Tools used in proteomics include chromatography, blotting and gels, protein arrays, mass spectrometry and ELISA and associated analysis software. Analyzers and proteomic systems should be sensitive, high resolution, fast and may be automated for high-throughput.Drug DevelopmentDrug development refers to the process of bringing a new drug to market.Protein BiologyThe analysis of protein expression, identity and function is vital for many areas of life science research and drug discovery. Some of the most commonly used techniques in protein analysis include Western blotting, electrophoresis and mass spectrometry.BiotherapeuticsBiotherapeutics are proteins and other compounds (such as nucleic acids) produced by living organisms that have uses as therapeutics or in <i>in vivo</i> diagnostics. The most well-known example of a biotherapeutic product, and the first to be approved for therapeutic use, was recombinant human insulin.ASMSThe American Society for Mass Spectrometry (ASMS) is an organization dedicated to advancing the science and application of mass spectrometry. ASMS supports professionals through events, publications, and research initiatives, promoting innovation in areas like proteomics, metabolomics, and environmental analysis.

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Software Automates Deep Characterization of Biotherapeutic Proteins