Vendor Column: Centralizing Data Management and Processing for Mass Spectrometry

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  • Published: Jan 6, 2014
  • Author: Chris Stumpf
  • Channels: Laboratory Informatics / Chemometrics & Informatics
thumbnail image: Vendor Column: Centralizing Data Management and Processing for Mass Spectrometry

I recently led a workshop on mass spectrometry and laboratory informatics where one delegate described the situation like this, “I am responsible for about a dozen open access LC/MS systems. Each LC/MS system is controlled by an isolated workstation sitting right next to the LC/MS. My question is, “How can I view, process and work with the data from my office which is two floors above these laboratories? Oh, and by the way, I need to easily transfer the LC/MS data into the organization’s electronic laboratory notebook.”

This delegate’s comment illustrates the growing needs of lab managers for ready access to data and the changing demands on IT department by laboratories. In this column, I will discuss these data management challenges as well as a solution that could address them.

I would contend that optimal mass spectrometry data management is achieved by leveraging a networked software solution that can not only control the instrument but also automatically transfer data into a centralized data repository that is stored in a secured data center. Chromatographers may recognize the prescribed solution as similar to the Empower Chromatography Data System (CDS). Such a solution for mass spectrometry would provide the following:

  • A centralized data repository (powered by a relational database) for storing and retrieving LC/MS data
  • Ability to process LC/MS data from a remote computer that connects into the server
  • Improved data processing capabilities via powerful centralized servers
  • Easily transferring or linking data from centralized server into an ELN
  • The option to use data traceability or 21 CFR Part 11 technical controls depending on whether you’re in research, quality, or a non-regulated industry.
  • Tailored LC/MS data processing for applications such as mass confirmation, complex sample analysis, peptide mapping, structural elucidation, etc.
  • Ability to standardize projects and methods by storing acquisition, processing, and reporting methods on a centralized server (so that everybody performs workflows in a consistent manner)

Although some leading CDS solutions can control quadrupole based LC/MS systems, the industry (e.g., pharmaceutical, chemical materials, food & environmental, clinical) is beginning to demand a CDS like solution for more advanced mass spectrometers, such as those capable of high-resolution, high mass accuracy, and ion mobility. Until now the challenge with managing data from high performance mass spectrometers has been the size of the data files generated; however, improvements in software, networking, and relational database technology (i.e., the technology used for organizing and finding data) has essentially removed these obstacles.

That’s all well and good, but how then do you respond to someone who says, “Sounds like you’ve got the technological problems solved for a CDS-like solution for mass spectrometry, but my IT department will never go for it.” Delegates at workshops I’ve led have told me that compatibility with antivirus software and installation of a mass spectrometry based data solution would be too complicated for their lean IT staff to handle. It’s a point well taken but if we draw historical parallels to the adoption of CDS solutions from 20 years ago, IT departments were resistant to them at first too. Then it was, “We have a policy of not installing laboratory software in the corporate IT data center.” However, after years of CDS focused education and collaboration, IT departments routinely operate and manage them. While occasionally there are antivirus or network compatibility problems with any software, (e.g., email, document management systems, LIMS, ELN, CDS, etc.) the issues are quickly addressed by both the IT department and the vendor providing the software. Finally, although it’s true that many IT departments run lean, software providers may be able to help with adoption as they are better equipped to offer professional services to install, integrate, and qualify software.

Now that I’ve addressed the challenges in adopting a CDS like solution for mass spectrometry, what are some of the benefits? Without question, enhancing productivity is a common theme. For example:

  • With data automatically transferred from instrument to a centralized relational database, the need for manual data back-ups are a thing of the past.
  • Once data is on the server, all data processing can be performed at the server. There is no need to move gigabytes of data from computer to computer in order to process data (as is currently done with isolated workstations attached to LC/MS systems).
  • Centralized data management facilitates scientific collaboration by enabling the sharing of results, methods and conditions for LC/MS separations, as well as data processing methods.
  • Centralized data management also allows for the linking of mass spectrometry results with ELN entries.

As mass spectrometry’s adoption continues to expand outside the sphere of the specialist practitioner, new users more familiar with the way today’s chromatography software works are demanding easier reporting of results, automated data management, streamlined data analysis workflows and interfacing with other informatics solutions. And mass spectrometry vendors are listening and are updating their software offerings to provide capabilities similar to what chromatographers have enjoyed with CDS solutions. So if you’re thinking about bringing LC/MS into your laboratory, make sure you ask about the capabilities discussed in this article. As with the attendees of my workshops, I think you’ll be pleasantly surprised by the possibilities.


The views represented in this article are solely those of the author and do not necessarily represent those of John Wiley and Sons, Ltd.

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