Journal of Pathology Informatics Journal of Pathology Informatics
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Table of Contents    
J Pathol Inform 2013,  4:1

The successful implementation of a licensed data management interface between a Sunquest® laboratory information system and an AB SCIEX TM mass spectrometer

1 Director of Mass Spectrometry, Clinical Laboratories, Department of Laboratory Medicine, University of California, San Francisco, CA, USA
2 Chief of Laboratory Information Systems, Clinical Laboratories, Department of Laboratory Medicine, University of California, San Francisco, CA, USA

Date of Submission06-Oct-2012
Date of Acceptance05-Dec-2012
Date of Web Publication31-Jan-2013

Correspondence Address:
Enrique Terrazas
Chief of Laboratory Information Systems, Clinical Laboratories, Department of Laboratory Medicine, University of California, San Francisco, CA
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Source of Support: None, Conflict of Interest: None

DOI: 10.4103/2153-3539.106682

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Background: Interfacing complex laboratory equipment to laboratory information systems (LIS) has become a more commonly encountered problem in clinical laboratories, especially for instruments that do not have an interface provided by the vendor. Liquid chromatography-tandem mass spectrometry is a great example of such complex equipment, and has become a frequent addition to clinical laboratories. As the testing volume on such instruments can be significant, manual data entry will also be considerable and the potential for concomitant transcription errors arises. Due to this potential issue, our aim was to interface an AB SCIEX TM mass spectrometer to our Sunquest® LIS. Materials and Methods: We licensed software for the data management interface from the University of Pittsburgh, but extended this work as follows: The interface was designed so that it would accept a text file exported from the AB SCIEX TM × 5500 QTrap® mass spectrometer, pre-process the file (using newly written code) into the correct format and upload it into Sunquest® via file transfer protocol. Results: The licensed software handled the majority of the interface tasks with the exception of converting the output from the Analyst® software to the required Sunquest® import format. This required writing of a "pre-processor" by one of the authors which was easily integrated with the supplied software. Conclusions: We successfully implemented the data management interface licensed from the University of Pittsburgh. Given the coding that was required to write the pre-processor, and alterations to the source code that were performed when debugging the software, we would suggest that before a laboratory decides to implement such an interface, it would be necessary to have a competent computer programmer available.

Keywords: Data management interface, mass spectrometry, sunquest

How to cite this article:
French D, Terrazas E. The successful implementation of a licensed data management interface between a Sunquest® laboratory information system and an AB SCIEX TM mass spectrometer. J Pathol Inform 2013;4:1

How to cite this URL:
French D, Terrazas E. The successful implementation of a licensed data management interface between a Sunquest® laboratory information system and an AB SCIEX TM mass spectrometer. J Pathol Inform [serial online] 2013 [cited 2022 Jul 7];4:1. Available from:

   Introduction Top

The use of complex instruments has become commonplace in the clinical laboratory. [1],[2] An example of such complex equipment is a liquid chromatography-tandem mass spectrometry (LC-MS/MS) system, which, in recent years has become a frequent addition to clinical laboratories for a variety of applications including testing for drugs of abuse, therapeutic drug monitoring and steroid analysis. [3],[4],[5],[6] Such devices offer high potential sample throughput, [7],[8] but, as they are not currently accompanied by vendor-supplied interfaces to enable them to be connected to a laboratory information system (LIS), they also impose a potentially burdensome requirement for manual data transfer with the concomitant risk of transcription errors.

To the authors' knowledge, the only commercially available software to software interface that exists for the mass spectrometer in use here, is from Data Innovations LLC (South Burlington, Vermont, USA). [9] The advantage of using a commercially available product is that the company already has software developed for a number of different instruments and the laboratory does not require expertise in computer programing to implement such an interface. However, the disadvantages are the significant cost of such an interface and the decrease in control and ease of adaptability of such a product as far as the laboratory is concerned.

A group in the Department of Pathology at the University of Pittsburgh Medical Center developed a data management interface to help solve this problem [10] successfully interfacing a Waters 2795 LC-MS/MS to a Sunquest® LIS. We describe here the implementation of the same data management interface using the same LIS, but a different mass spectrometer that is in use in our laboratory and we extend their work by describing the pre-processor code that was required to convert the data output from the mass spectrometer into a format accepted by the LIS.

   Materials and Methods Top

Liquid chromatography-tandem mass spectrometry system

The targeted analytical mass spectrometer was the AB SCIEX TM × 5500 QTrap® (AB SCIEX TM , Foster City, CA) coupled to a Shimadzu Prominence UFLC (Ultra-Fast Liquid Chromatography, Shimadzu Scientific Instruments, Pleasanton, CA) LC system. The standalone computer running the LC-MS/MS was a Dell Optiplex 960 that uses the Microsoft Windows 7 operating system (Microsoft Corporation, Redmond, WA). The Analyst® 1.5.1 application (AB SCIEX TM , Foster City, CA) acquires data from the mass spectrometer and generates a results table upon the user's request. A text file (txt) of the results table can then be exported from Analyst® by the user and saved in the appropriate folder.

Data management software

The data management software was licensed from the University of Pittsburgh (Automated File Transfer for MIM Batch Style Interfaces; ID01516). [10] The data management software and the other support modules are written in AutoHotKey (AHK), a free open-source scripting language for automating activities on a computer operating under the Windows operating system. [11] Both the compiled executable programs and the source text files are included with the data management software. The software program was installed solely on the computer running the LC-MS/MS system.

Laboratory information system

The LIS utilized was Sunquest® (Sunquest Information Systems Inc., Tuscon, AZ). Standard parameters such as analyzer and assay identification codes as well as quality control (QC) definitions for the LC-MS/MS assay were defined by adding them to the Sunquest® maintenance, using the straightforward and well-documented methods provided by the vendor.

   Results and Discussion Top

Data required to transfer results to Sunquest®

Four discrete data are required to successfully transmit an individual patient result from the LC-MS/MS output text file to Sunquest® : The unique patient container identification number (CID - a barcode affixed to the patient sample container that is scanned by a barcode reader, electronically entering the CID into the LC-MS/MS software); the Sunquest® test code for the assay being performed (in this case test code PTES for pediatric total testosterone); the assay result for each patient and the QC data (the total testosterone concentrations obtained from running 3 QC materials with each batch of patient samples with mean concentrations of 9, 168 and 535 ng/dL respectively in this case).

Data management software

The data management software consists of libraries of code that are called from a primary compiled program that handles the various aspects of export file management and transfer to the LIS via file transfer protocol (FTP). [12] The documentation included with the licensed data management software was comprehensive; however, minor discrepancies were discovered between the documented installation file locations and the actual locations specified in the software source code (included with the software). Accurate placement of the library and resource files in appropriate directories and subdirectories was required for the compiled program to find them. Although the author was not familiar with AHK at the time of installation, its similarities to other scripting languages permitted casual review to catch these discrepancies.

File pre-processing

The documentation supplied with the data management software clearly describes the process of integrating a pre-processor, which is required if the data output format from the LC-MS/MS software does not match the input format of the LIS, but is not supplied with the data management software. In this case, pre-processing of the text file exported from the Analyst® software was required in order for Sunquest® to accept the data and Perl was chosen by the authors for writing the pre-processor. Perl is a popular and well-established open-source scripting language used in many contexts, including biomedicine, [13] is freely available for multiple platforms and can be installed on Windows platform (as well as others) via ActivePerl installer. [14] Perl stands for "Practical Extraction and Report Language" and is highly suitable for parsing text, making it an ideal language to use for a pre-processor in the context of the Analyst® -Sunquest® interface. A particularly helpful feature of Perl utilized extensively in the pre-processor is its implementation of "regular expressions," which facilitates searching for particular patterns in a given text string and optionally replacing them with another string. Although the data management software includes a log file, we found that additional logging was helpful during the debugging process, and thus we added additional logging to the Pittsburgh software source files, which were then recompiled. With this in mind, the pre-processor includes a separate log with output to verify that the various steps in the program occur each time it is run. A flow chart documenting the steps in the process is shown in [Figure 1]. The source code for the pre-processor is shown in [Figure 2], and an explanation of each line of the code can be found in [Table 1].
Figure 1: The workflow process from the Analyst® software to the pre-processor, the data management software and finally to the transfer by file transfer protocol to the laboratory information system

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Figure 2: Source code written in Perl to pre - process the text file output from the liquid chromatography - tandem mass spectrometry system to a format suitable for transfer to Sunquest® via file transfer protocol

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Table 1: Key to the purpose of each line of the source code that was used to pre-process the data output file from the liquid chromatography-tandem mass spectrometry system

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Testing and implementation

During the validation of the PTES assay, the interface was tested by exporting the text file containing calibrator, QC and patient assay results into a specific folder; in this case the "report output folder" on the computer running the mass spectrometer. The log files on the same computer were then checked. The correct order of events is as follows: The text file containing the results will disappear from the "report output folder;" when the pre-processing has been completed, a text file will then be found in the "converted folder;" this file disappears from the "converted folder" and will then be found in the "sent folder;" the original text file exported from the LC-MS/MS system will then be placed in the "archived folder." In order to determine if the interface was performing as expected, when the pre-processed file was found in the "sent folder," the Sunquest® LIS was accessed (after a delay to allow Sunquest® to perform its periodic scan of the stipulated upload location for the data) to determine if the QC results and patient assay results had indeed been transferred via FTP, and that the calibrator results were essentially ignored by the pre-processor. As this process was working successfully, it was implemented once the PTES assay was placed into clinical use. To date, there have been no software problems or failures. The interface has eliminated the need for manual data entry and any associated manual transcription errors.

   Conclusions Top

We successfully implemented a licensed data management interface between Sunquest® and an AB SCIEX TM mass spectrometer that may allow the laboratory more control and adaptability than a commercially available software to software interface. Currently, this interface has only been used to transmit results from one test to individual patients, but the authors are confident in the adaptability of this interface in order to be able to handle more complex results, such as pharmacokinetic analysis consisting of a number of samples from the same patient over a given time period, each with a different concentration. Although the licensed software from the University of Pittsburgh was extremely useful in facilitating an interface between the LC-MS/MS system and the LIS, local expertise in programming was necessary to perfect the data transfer process.

   Acknowledgments Top

We acknowledge Dr. R.P. Channing Rogers and Kirk Sujishi for helpful discussions, Larry Rohe, Ryan Stache, Paul DeYoung and David Adams for technical assistance.

   References Top

1.Kricka LJ, Savory J. A guide to the history of clinical chemistry. Clin Chem 2011;57:1118-26.  Back to cited text no. 1
2.Dabkowski B. Chemistry analyzers for mid and highvolume laboratories, June ed. CAP Today 2012:3258.  Back to cited text no. 2
3.Fitzgerald RL, Griffin TL, Yun YM, Godfrey RA, West R, Pesce AJ, et al. Dilute and shoot: Analysis of drugs of abuse using selected reaction monitoring for quantification and full scan product ion spectra for identification. J Anal Toxicol 2012;36:106-11.  Back to cited text no. 3
4.Bunch DR, Heideloff C, Ritchie JC, Wang S. A fast and simple assay for busulfan in serum or plasma by liquid chromatography-tandem mass spectrometry using turbulent flow online extraction technology. J Chromatogr B Analyt Technol Biomed Life Sci 2010;878:3255-8.  Back to cited text no. 4
5.Van Der Gugten JG, Dubland J, Liu HF, Wang A, Joseph C, Holmes DT. Determination of serum aldosterone by liquid chromatography and tandem mass spectrometry: A liquid-liquid extraction method for the ABSCIEX API-5000 mass spectrometry system. J Clin Pathol 2012;65:457-62.  Back to cited text no. 5
6.van Deventer HE, Mendu DR, Remaley AT, Soldin SJ. Inverse log-linear relationship between thyroid-stimulating hormone and free thyroxine measured by direct analog immunoassay and tandem mass spectrometry. Clin Chem 2011;57:122-7.  Back to cited text no. 6
7.Grant RP. High throughput automated LC-MS/MS analysis of endogenous small molecule biomarkers. Clin Lab Med 2011;31:429-41.  Back to cited text no. 7
8.Vogeser M, Kirchhoff F. Progress in automation of LC-MS in laboratory medicine. Clin Biochem 2011;44:4-13.  Back to cited text no. 8
9.Available from: Solution_0.pdf. [Last accessed on 2012 Nov 26].  Back to cited text no. 9
10.Blank GE, Virji MA. Development and implementation of an electronic interface for complex clinical laboratory instruments without a vendor-provided data transfer interface. J Pathol Inform 2011;2:14.  Back to cited text no. 10
[PUBMED]  Medknow Journal  
11.Documentation and software download available from: [Last accessed 2012 Jul 29].  Back to cited text no. 11
12.IETF RFC for FTP, 1985. Available from: [Last accessed on 2012 Sep 18].  Back to cited text no. 12
13.Berman J, editor. Preface. Perl Programming for Medicine and Biology. Sudbury, MA, USA: Jones and Bartlett Publishers, Inc.; 2007. p. 10.  Back to cited text no. 13
14.Documentation and software download available from: [Last accessed 2012 Jul 29].  Back to cited text no. 14


  [Figure 1], [Figure 2]

  [Table 1]

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