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Automation & Standardization of Mass Spec Data
Industry Insight

Automation & Standardization of Mass Spec Data

Automation & Standardization of Mass Spec Data
Industry Insight

Automation & Standardization of Mass Spec Data


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Genedata announced a new version of their Expressionist software for mass spectrometry at the recent ASMS conference. Through automating and standardizing data analysis workflows, Expressionist helps MS users by enabling faster characterization of biopharmaceuticals at all stages of research and development.

We spoke to Jens Hoefkens, Head of the Expressionist Business Unit at Genedata AG to learn more about the company, their latest offering and some of the challenges they face.

AB: Can you tell me more about Genedata?

Jens Hoefkens (JH): Founded in 1997, Genedata is recognized as a leading provider of advanced software solutions for drug discovery and life science research. We’ve grown from a small team of experts to a major bioinformatics company serving most leading pharmaceutical, agrochemical, and biotechnology companies worldwide. Because of the strong market demand for data analytics solutions that improve research and development productivity, we’ve experienced steady growth over the years. We have more than 150 employees globally, based in our Basel headquarters and in Munich, Boston, San Francisco, and Tokyo. Our offerings include complete data management systems supporting end-to-end biologics research and development processes and data analysis platforms like e.g. Expressionist for Mass Spectrometry.

AB: You announced the latest version of Genedata Expressionist for Mass Spectrometry at ASMS, can you tell me more about the product and the new features?

JH: Genedata Expressionist is a comprehensive data processing and analysis software platform specifically designed for the characterization of biopharmaceuticals. The software was developed in collaboration with leading biopharma companies to automate and standardize the biotherapeutics characterization workflows. Genedata Expressionist specifically supports the analysis of intact mass measurements, protein sequence variants, PTMs, C- and N-terminals, glycopeptides, released glycans, and disulphide bonds. The workflows are independent of instrumentation and cover all processing and analysis steps from raw data to final reports. Bioanalytical scientists value the scalability of the system, which significantly increases their productivity and the overall throughput of their labs. 

The new version of Genedata Expressionist enhances the workflow for the analysis of intact mass measurements and peptide mapping experiments. More specifically, the workflow can now be fully automated, resulting in highly reproducible results. In addition, Expressionist advanced its algorithms for protein inference, a procedure to identify the proteins that were originally present in a sample based on the characterized peptides.

AB: Genedata Expressionist for Mass Spectrometry is available for characterizing biopharmaceuticals and metabolomic profiling, how do the challenges of these two areas compare?

JH: The two application areas are very different but share some challenges: Scientists use a number of different assays and utilize a battery of different instruments, often from different vendors. In addition, throughput demands continue to increase and experimental designs continue to become more complex. In that environment the ability of Expressionist for MS to provide a unified software platform which can handle this amount of data and from different sources is of highest priority. The workflows and algorithms in Expressionist for MS are specifically designed to handle these challenges and allow running complex workflows automatically in a standardized format.

AB: There have been significant advances in mass spectrometers over the past few years, how much of a challenge is it keeping up with these?

JH: Our team is used to rapid technology changes in the industry – we have seen many technologies come and go in the past 17 years. For us, technology advancements are an opportunity, rather than a threat, especially when they produce large and complex datasets. All our software platforms are designed to enable fast adaptation to technological progress. Most importantly, we work very closely with our customers, all leading companies in their field, to foresee industry trends and changes. Often, our customers come to us for advice before embracing a new platform to ensure that the data processing and analysis will be taken care of. In addition, one of our advantages is our large product portfolio covering various data workflows in different industries, such as pharma, biopharma, crop science, industrial biotech, etc. To give you an example, our MS software benefits from proven knowledge we’ve gained from building solutions to handle large data in next generation sequencing analysis, which produces terabytes and petabytes of data, many orders larger than MS data. 

AB: With the advancements in mass spectrometers there has been a huge increase in the amount data produced, how much of a problem is bottlenecking in data analysis?

JH: The amount of data undeniably constitutes a bottleneck for many institutions that process data manually. We usually say that if the data analysis takes as long as producing the data, we are the right partner. Mass spectrometry data analysis is a good example of this. The benefits of high-resolution MS instruments for the characterization of biotherapeutics are obvious, but their utilization throughout drug development, production, and quality control is still limited due to the complexity of the data output. We believe that adopting Genedata Expressionist, and thus standardizing and automating the high-resolution MS data analysis pipelines, will accelerate the endorsement of mass spectrometry and ultimately result in higher quality biotherapeutics products.

Further details on Genedata and their full range of products can be found at genedata.com 

Jens Hoefkens was speaking to Ashley Board, Managing Editor for Technology Networks. You can find Ashley on  and follow Technology Networks on Twitter.

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