Clinical Biochemistry – Links for LIMS being used with an Agilent LC-MS/MS Mass Spectrometer in the Regional Hospital Galway

An integration solution for Vitamin D testing for an Agilent 6460 LC MS-MS instrument connected to the Roche PSM Middleware system and the CSC (iSOFT) APEX LIS/LIMS system.

The clinical biochemistry laboratory of the Regional Hospital in Galway, Ireland have been running routine Vitamin D screening using an Agilent LC-MS/MS based method for its patients since 2011. In fact the number of assays requested have increased substantially each year.

For a video describing the laboratory and it’s work, introduced by it’s Principal Clinical Biochemist Liam Blake, please click here.

While the method and instrument are robust and fast run times have been possible, setting up the instrument and entering the Vitamin D2 and Vitamin D3 results into the APEX LIS/LIMS system once the assay is completed was a time consuming and error prone task. Consequently the laboratory looked for possible solutions to make this process completely electronic. In 2012 the laboratory were introduced to CSols and the two organizations have worked together to create a working solution which works in the local IT setting.

APEX Interface
It is of course possible to link instruments and analysers directly to the APEX LIS/LIMS system. However in order to make the connection it is usual to purchase a connection licence and appropriate services effort from CSC. When requested CSC did not have any experience of working with the Agilent instrument, consequently there was no ‘off the shelf’ software driver, so this direct route was discounted as being too expensive an option. However like many laboratories Galway run a large pathology facility with a full compliment of Roche Clinical chemistry analysers on a track. These analysers were already linked to APEX using the Roche PSM Middleware system. As this was already being used to process millions of results annually, CSols evaluated this option as an interfacing route. After some investigation with Roche and experimentation with different PSM and Links for LIMS ‘driver’ software, CSols were able to create a viable combination of ‘drivers’ and this was installed initially in April 2012.

Data exchange issues
During the initial testing of the link, the Galway team picked up a number of interesting issues which they needed to address for routine operation of their method. These included the following :

Time stamp
The PSM system needs a date/time value sending for each of the results, and by default the Agilent MassHunter software saves a US formatted date into the instrument raw and processed results files. As this is a function of the instrument configuration it was not possible to reconfigure this easily. Consequently CSols adjusted the Links for LIMS PSM driver to perform date/time conversion.

Less than results e.g. <6.0
PSM was not able to process any result proceeded by a less than ‘<‘ or greater than ‘>’ sign. These are used by the Links for LIMS Report results program to indicate results which are above or below the method detection limits (LLOD, ULOD). It was agreed instead to add a conditional calculation to the Links for LIMS method to override any < results with 0 (zero).

Signal:Noise ratio
During the initial method validation the laboratory determined that if the instrument produced a signal:noise <8 then the result should be discarded and reported as zero. Again Links for LIMS was configured to perform this calculation on all samples.

IQC results
Finally as PSM was being used for all Internal and External quality control checks, the laboratory wanted to also transfer all IQC and EQC results upon run completion. A combination of Links for LIMS filter settings and changes to the Links for LIMS PSM driver were implemented to pass both unknown and IQC sample results to PSM at the end of each batch run.

The CSols Links for LIMS interface link is a viable and robust option for interfacing LC-MS/MS instruments, in particular those with a PC based instrument workstation. The system now been running trouble-free since 2012, processing an increasing large number of results per year.

Further information

Links for LIMS is not limited to running the applications that are described above and can be used for many other LC-MS/MS applications, with other vendor instruments and with a range of different LIMS systems. For a copy of an article describing the solution above, for further information about another instrument application or for a demonstration please ask via our enquiry page or call or email us at:

CSols Ltd. The Heath, Runcorn, Cheshire, WA7 4QX, UK Tel:   +44 (0) 1928 513535  Fax: +44 (0) 7006 061106 Web:

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