MSACL 2026 Abstract

A Unified Web-Based Automation Tool for Conversion of Mass Spectrometry Result Files to LIS-Compatible Format

Amir Karin (1,2), Meng Wang (1,2)
(1) Vancouver General Hospital, Vancouver, Canada, (2) University of British Columbia, Vancouver, Canada

Amir Karin, PhD, FCACB (Presenter) Vancouver General Hospital

Relevant Financial Disclosures (within past 24 months, reported on Apr 17, 2026) No relevant financial relationship(s) to disclose.

INTRODUCTION:
Many clinical laboratories use LC-MS/MS instruments from different vendors, each producing results in distinct report formats. Automating the filing of these results typically requires configuring vendor-specific communication drivers on a common middleware (1) or installing custom software on individual instrument computers (2). The latter is more flexible, but can be brittle when vendor software updates or local machine configurations change. We developed a web application that translates output files from our different instruments into a single standardized text format, ready for download by the Laboratory Information System (LIS).

METHODS:
The web app was written in the R programming language (3) using the Shiny package (4), with a modular architecture. The technologist launches the web app on our organization's private cloud, selects the specimen type and uploads the instrument .txt or .xlsx reports. The app validates the file, detects the instrument platform and applies the appropriate parsing function. Patient identifiers, analyte names, and quantitative results are extracted and mapped to a common schema via configuration tables. The app validates file format, detects possible duplicates, and verifies that all analyte names match expected LIS codes. The final output is transmitted to the LIS middleware (Data Innovations). The app is accessible from any pre-authorized workstation, avoiding the need for any local installation. Performance was evaluated using intact and error-injected versions of previous result files.

RESULTS:
The app successfully transforms result files from our Waters and Agilent LC-MS/MS platforms into text files for the middleware. Error simulation confirmed that built-in validation caught unrecognized analytes, duplicate specimens, malformed identifiers and invalid results at the point of processing. Adding a new analyte requires only a new row in a configuration file without code changes. Presently, the application supports 14 tests across two instrument platforms.

DISCUSSION:
This app demonstrates a generalizable approach based on open-source software to improve LC-MS/MS result filing workflows in laboratories operating heterogeneous instrument platforms. The modular design allows for easy expansion to future analytes with no code change. Introducing new instruments would require only a new parser function. Private cloud deployment ensures all workstations access the same app and configuration, avoiding discrepancies from locally maintained tools or scripts.

REFERENCES
1. Scott GD, Schrandt C, Ho CC, Chung MC, Zhou D, Shi RZ. Interfacing Complex Laboratory Instruments during a Change to Epic Beaker. J Pathol Inform. 2018;9:24.
2. Blank GE, Virji MA. Development and implementation of an electronic interface for complex clinical laboratory instruments without a vendor-provided data transfer interface. Journal of Pathology Informatics. 2011;2:14.
3. R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria, 2024. https://www.R-project.org/.
4. Chang W, Cheng J, Allaire J, et al. shiny: Web Application Framework for R. R package, 2025. R package version 1.11.1, https://CRAN.R-project.org/package=shiny/.