MSACL 2018 US Abstract

Topic: Data Science

A Survey of Clinical Laboratories to Determine Needs for Clinical Mass Spectrometry Data Exchange

Patrick Mathias (Presenter)
University of Washington

Bio: Patrick Mathias completed a MD degree and a PhD in Bioengineering from the University of Illinois, with a focus on nanophotonics and label-free biosensors. He completed residency training in Clinical Pathology as well as a Clinical Informatics fellowship at the University of Washington. He is currently the Associate Director of the Informatics division in the Department of Laboratory Medicine at the University of Washington. His clinical and research interests lie in improving electronic health record systems to improve ordering and interpretation of laboratory tests, developing infrastructure for novel analytical technologies in the clinical laboratory, and applying analytics to improve laboratory operations and clinical care at a population level.

Authorship: Patrick C. Mathias (1), Joshua A. Hayden (2), Judith A. Stone (3), Daniel T. Holmes (4), Randall K. Julian (5), Tony M. DaSilva (6)
(1) University of Washington, (2) Weill Cornell Medicine, (3) University of California at San Diego, (4) University of British Columbia, (5) Indigo BioAutomation, (6) Kaiser Permanente Regional Laboratories, Northern California

Short Abstract

Mass spectrometry is a valuable platform for many clinical laboratories, but setting up data exchange between these instruments and laboratory information systems can be challenging. Instrument vendors utilize proprietary file formats and there is no standardization of data for clinical purposes. The Mass Spectrometry Data Interface Standardization (MSDIS) working group is assessing these challenges and distributed a survey to clinical laboratories to understand their data exchange needs. A variety of laboratory settings were represented and most laboratories had successfully interfaced their instruments. Data mapping and the need for verification rules were cited as important requirements among the surveyed laboratories.

Long Abstract


Modern clinical laboratories depend on the electronic exchange of data from high-throughput analyzers to laboratory information systems (LISs) to facilitate efficient, error-free resulting and high quality patient care. The increasing adoption of mass spectrometry by clinical laboratories promises to improve the accuracy of results across a number of analytes. However, these instruments have not historically been developed for the clinical laboratory, so laboratories without specialized IT resources resort to manual transcription of results into their LISs. Those who are successful interfacing may spend considerable time and effort between instrument vendor staff, laboratory staff, and IT staff developing a custom solution. The Mass Spectrometry Data Interface Standardization (MSDIS) working group assembled to better understand the challenges in interfacing mass spectrometers and develop solutions that are applicable for all laboratories. To gain a better understanding of the current state across multiple clinical laboratories performing mass spectrometry, the working group distributed a survey to understand their functional requirements for performing clinical testing.


An online survey was distributed to participants of an MSACL online discussion about the challenges of interfacing instruments as well as more broadly through a clinical chemistry community message board. The survey gathered broad data bout clinical laboratory setting, number of tests performed, and information systems utilized. General questions about mass spectrometry testing covered testing volumes, types of testing, staffing, and instrument vendors. For laboratories who successfully set up electronic data exchange, details about the type of interface, functionality, and needs were assessed


Fourteen sites responded to the survey, of which 50% were based in academic medical center or health system settings. Test volumes (counted by number of orders) for the entire clinical laboratory ranged from 10,000 to 20 million per year. Sites used diverse information systems in the clinical laboratory, with the most common systems being Data Innovations (42.9%), Cerner (35.7%), Sunquest (35.7%), and Epic (28.6%). A majority of responding laboratories (78.6%) have performed mass spectrometry for at least 5 years. The number of clinical mass spectrometers in these labs ranged from 1 to 15, and they performed testing from 40 to 10,000 samples per week. More than half of the laboratories performed the following types of testing: vitamins, endocrine, toxicology, and therapeutic drug monitoring. Sciex and Waters were the most common instrument vendors, with 50% of laboratories reporting they had at least one instrument from each of these vendors. Eleven of the fourteen sites reported successfully interfacing at least one of their instruments, and nine of the eleven reported using a flat file transfer mechanism to exchange data from instrument to LIS. Five sites reported a mechanism to transfer sample list between LIS/middleware/liquid handler and instrument and four sites implemented verification rules. Eight of eleven interfaced sites (72.7%) cited the mapping of data fields from instrument to LIS as the most significant challenge in their interfacing project. The most common desired functionality that was not already available was either the use of flags and rules or increased flexibility for verification rules.

Conclusions & Discussion

Among a sample of clinical laboratories with experience interfacing mass spectrometers or interest in doing so, there were diverse practice settings and information systems represented. A majority of surveyed laboratories had greater than 5 years of experience performing mass spectrometry and successfully developed data exchange mechanisms to move data between instrument and LIS. A majority of interfaced laboratories struggled with the mapping of data between instrument and LIS. There was a strong desire to utilize result verification rules among sites who had not already set up such a system. These data indicate that MSDIS efforts should focus on standardizing the mapping of data from mass spectrometers, including relevant metadata needed for verification rules.

References & Acknowledgements:

The working group would like to acknowledge the efforts of all the laboratories who responded to our survey. In addition we would like to acknowledge the helpful input from Fred Strathmann in the initial stages of this work.

Financial Disclosure

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IP Royalty: no

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