MSACL 2018 US Abstract

Topic: Data Science

Interfacing MS Instrumentation in a Clinical Chemistry Routine Laboratory: Squeezing Standards vs Real Life Constraints

Pierre-Alain Binz (Presenter)
CHUV Lausanne University Hospital

Authorship: Pierre-Alain Binz
Clinical Chemistry Laboratory, Lausanne University Hospital, Switzerland

Short Abstract

Automation is a key feature in today’s laboratory medicine practice. Many industrial robotic and automated analyzers are interfaced with Laboratory Informatics Systems (LIS) and electronic patient record systems (EPR) using standard protocols and formats such as HL7 and ASTM. This also implies the use of middleware, data backup and archive architecture. Reaching this level of interoperability with current mass spectrometry equipment is not straightforward. Although specific data exchange formats exist in addition to the generic industrial ones (HUPO-PSI mzML and mzTAB for instance), the task is challenging due to heterogeneity of instrumentation, of vendors constraints, of data types and of result reporting format requirements. We will discuss how we have integrated our MS instruments into our clinical routine, from sample reception to results reporting.

Long Abstract


Automation is a key element in today’s laboratory medicine practice. This implies the integration of a number of steps in a classical patient sample handling workflow. Those might include informatics-driven biochemical test ordering, sample transport, sample treatment, sample aliquoting, distribution to analytical platforms, performing of the analytical tests, transfer of results to Laboratory information systems (LIS), automated technical validation, transmission of results to medical doctors, billing, archiving, etc. In order to achieve the necessary level of integration, there is a need to control the interfaces, i.e. the communication between software and hardware. Routine analytical chains implement established IT protocols and normative standards, such as HL7 and ASTM, to transport data and results from instruments to LIS. Mass spectrometry is a technology that is not yet as much integrated into routine laboratories as for instance immunoassay and photometric automated systems. Nevertheless, options exist that allow MS instrumentation to communicate with LIS and other elements of a complete workflow. In the proteomics field, data standards such as the HUPO-PSI mzML, mzIdentML and mzTAB have been developed as generic information and data exchange formats, designed to transport MS-based datasets and are supported by a number of MS vendors.


We will discuss how we are interfacing our MS instrumentation (GC-MS, LC-MS, LC-MS/MS from different vandors) in the routine production infrastructure, which is operated under ISO15189:2012 regulations. Other elements of the puzzle include electronic prescription, sample preparation robotics, institutional LIS, electronic patient record system and storage systems. Raw data, processed data and results are treated separately.


The implementation of the integration of MS systems is heterogeneous; depends on the type of instrument, vendor, complexity of the analyte panel and of the sample preparation. Constitutive IT elements of the implemented workflows include sql-queries, perl scripts incorporated in the institutional LIS, generation and exchange of xml files, various parsing codes. We will show a couple of example implementations.

Conclusions & Discussion

The integration of MS instrumentation in a routine clinical chemistry laboratory is currently far from being a plug and play approach. Existing industrial standards are not always applicable. Standards dedicated to MS exist and are improving. They demonstrate a good potential for replacement of hand-made solutions, providing that they are becoming supported by the major players, i.e. the instrument and software vendors.

References & Acknowledgements:

Financial Disclosure

Board Memberno

IP Royalty: no

Planning to mention or discuss specific products or technology of the company(ies) listed above: