Technology & Data Science for Enhanced Patient Care



The MSACL Organization

Interfacing Standardization

Mass Spec Data Interface Standardization (MSDIS)

This is a Working Group striving to improve inefficiencies in the application of clinical mass spectrometry.

The Mass Spectrometry Data Interface Standardization (MSDIS) working group arose out of recognition that clinical laboratories have struggled and/or spent significant resources to fit these specialized instruments into traditional clinical laboratory information systems (LISs).


  • Despite performing similar measurements, MS vendors use different native file formats with little consistency in data structure or vocabulary across vendors
  • Because of the varied export formats, data structures, and vocabulary, each lab interfacing an MS instrument must “reinvent the wheel” and expend resources performing data mapping
  • If laboratories cannot interface their instruments, they rely on manual data entry with the associated transcription errors and time wasted on non-value-added work
  • Challenges interfacing MS instruments present a barrier to wider adoption of this technology into the clinical laboratory

Our working group aims to lower the barriers to adoption of clinical MS by proposing a data standard that will make the process of interfacing MS instruments easy and predictable across platforms. Accomplishing this goal will entail:

  1. Assessing the needs of clinical laboratories from a variety of healthcare settings to ensure broad understanding of the current problems with data flow to and from MS instruments
  2. Integrating input from important stakeholders such as instrument vendors, liquid handler vendors, and information systems vendors to ensure that we can achieve consensus around functional and technical requirements for transporting data
  3. Ensuring a proposed data standard is mutually agreeable to instrument and information system vendors yet could improve upon current practices for data transfer and use of MS data.
  4. Exploring standardization for export of LC-MSMS metadata. Metadata is an under utilized resource with tremendous potential to enhance quality assurance practices and between instrument correlation. But standardizing metadata export is a necessary first step before tools can be developed for end users.

How to Participate

We are seeking input from a wide range of stakeholders to ensure that our recommendations can be utilized by all laboratories and vendors. Please contact us via email at pcm10 AT uw DOT edu.