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Birhanu AG. Mass spectrometry-based proteomics as an emerging tool in clinical laboratories. Clin Proteomics 2023; 20:32. [PMID: 37633929 PMCID: PMC10464495 DOI: 10.1186/s12014-023-09424-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 08/03/2023] [Indexed: 08/28/2023] Open
Abstract
Mass spectrometry (MS)-based proteomics have been increasingly implemented in various disciplines of laboratory medicine to identify and quantify biomolecules in a variety of biological specimens. MS-based proteomics is continuously expanding and widely applied in biomarker discovery for early detection, prognosis and markers for treatment response prediction and monitoring. Furthermore, making these advanced tests more accessible and affordable will have the greatest healthcare benefit.This review article highlights the new paradigms MS-based clinical proteomics has created in microbiology laboratories, cancer research and diagnosis of metabolic disorders. The technique is preferred over conventional methods in disease detection and therapy monitoring for its combined advantages in multiplexing capacity, remarkable analytical specificity and sensitivity and low turnaround time.Despite the achievements in the development and adoption of a number of MS-based clinical proteomics practices, more are expected to undergo transition from bench to bedside in the near future. The review provides insights from early trials and recent progresses (mainly covering literature from the NCBI database) in the application of proteomics in clinical laboratories.
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Pablo A, Laha TJ, Breit N, Hoffman NG, Hoofnagle AN, Baird GS, Mathias PC. A web application to support the coordination of reflexive, interpretative toxicology testing. J Pathol Inform 2023; 14:100303. [PMID: 36941960 PMCID: PMC10024164 DOI: 10.1016/j.jpi.2023.100303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/14/2023] [Accepted: 02/17/2023] [Indexed: 02/27/2023] Open
Abstract
Background Reflexive laboratory testing workflows can improve the assessment of patients receiving pain medications chronically, but complex workflows requiring pathologist input and interpretation may not be well-supported by traditional laboratory information systems. In this work, we describe the development of a web application that improves the efficiency of pathologists and laboratory staff in delivering actionable toxicology results. Method Before designing the application, we set out to understand the entire workflow including the laboratory workflow and pathologist review. Additionally, we gathered requirements and specifications from stakeholders. Finally, to assess the performance of the implementation of the application, we surveyed stakeholders and documented the approximate amount of time that is required in each step of the workflow. Results A web-based application was chosen for the ease of access for users. Relevant clinical data was routinely received and displayed in the application. The workflows in the laboratory and during the interpretation process served as the basis of the user interface. With the addition of auto-filing software, the return on investment was significant. The laboratory saved the equivalent of one full-time employee in time by automating file management and result entry. Discussion Implementation of a purpose-built application to support reflex and interpretation workflows in a clinical pathology practice has led to a significant improvement in laboratory efficiency. Custom- and purpose-built applications can help reduce staff burnout, reduce transcription errors, and allow staff to focus on more critical issues around quality.
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Key Words
- AMR, analytical measurement range
- AWS, Amazon Web Services
- CSV, Comma-separated values
- Custom web application
- GC-MS, gas chromatography-mass spectrometry
- LC-MS/MS, Liquid chromatography-tandem mass spectrometry
- LIS, laboratory information system
- Laboratory workflows
- MLS, medical laboratory scientist
- Mass spectrometry
- Python
- QC, Quality control
- Quality control
- RRT, Relative retention time
- S/N, Signal to noise ratio
- S3, Simple storage service
- TSV, tab-separated values
- UDT, urine drug testing
- UW Medicine, Department of Laboratory Medicine and Pathology at University of Washington Medicine
- XML, Extensible markup language
- mg, milligram
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Affiliation(s)
- Abed Pablo
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Thomas J. Laha
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Nathan Breit
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Noah G. Hoffman
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Andrew N. Hoofnagle
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Geoffrey S. Baird
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Patrick C. Mathias
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
- Department of Biomedical Informatics and Medical Education, University of Washington School of Medicine, Seattle, WA, USA
- Corresponding author at: University of Washington, 1959 NE Pacific St, Box 357110, Seattle, WA 98195-7110, USA
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Rappold BA. Review of the Use of Liquid Chromatography-Tandem Mass Spectrometry in Clinical Laboratories: Part II-Operations. Ann Lab Med 2022; 42:531-557. [PMID: 35470272 PMCID: PMC9057814 DOI: 10.3343/alm.2022.42.5.531] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/08/2022] [Accepted: 04/13/2022] [Indexed: 11/19/2022] Open
Abstract
Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is increasingly utilized in clinical laboratories because it has advantages in terms of specificity and sensitivity over other analytical technologies. These advantages come with additional responsibilities and challenges given that many assays and platforms are not provided to laboratories as a single kit or device. The skills, staff, and assays used in LC-MS/MS are internally developed by the laboratory, with relatively few exceptions. Hence, a laboratory that deploys LC-MS/MS assays must be conscientious of the practices and procedures adopted to overcome the challenges associated with the technology. This review discusses the post-development landscape of LC-MS/MS assays, including validation, quality assurance, operations, and troubleshooting. The content knowledge of LC-MS/MS users is quite broad and deep and spans multiple scientific fields, including biology, clinical chemistry, chromatography, engineering, and MS. However, there are no formal academic programs or specific literature to train laboratory staff on the fundamentals of LC-MS/MS beyond the reports on method development. Therefore, depending on their experience level, some readers may be familiar with aspects of the laboratory practices described herein, while others may be not. This review endeavors to assemble aspects of LC-MS/MS operations in the clinical laboratory to provide a framework for the thoughtful development and execution of LC-MS/MS applications.
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Affiliation(s)
- Brian A. Rappold
- Laboratory Corporation of America Holdings, Research Triangle Park, NC, USA
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A Second-generation Opioid LC-MS/MS Assay Improves Laboratory Workflow and Capacity. J Chromatogr B Analyt Technol Biomed Life Sci 2022; 1210:123438. [DOI: 10.1016/j.jchromb.2022.123438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 08/04/2022] [Accepted: 08/25/2022] [Indexed: 11/24/2022]
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Pablo A, Hoofnagle AN, Mathias PC. Listening to your mass spectrometer: An open-source toolkit to visualize mass spectrometer data. J Mass Spectrom Adv Clin Lab 2022; 23:44-49. [PMID: 35028636 PMCID: PMC8739458 DOI: 10.1016/j.jmsacl.2021.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 12/08/2021] [Accepted: 12/08/2021] [Indexed: 10/28/2022] Open
Abstract
Introduction We have developed a set of tools built with open-source software that includes both a database and a visualization component to collect LC-MS/MS data and monitor quality control parameters. Description of tool To display LC-MS/MS data we built a parsing tool using Python and standard libraries to parse the XML files after each clinical run. The tool parses the necessary information to store a database comprised of three distinct tables. Another component to this toolkit is an interactive data visualization tool that uses the data from the database. There are 5 different visualizations that present the data based on interchangeable parameters. Evaluation of tool Using histogram visualization, we assessed how quality control parameters that feed our quality control algorithm, SMACK, which assists to improve the efficiency of data review and results, performed against the collective data. Using the newly identified QC parameter values from the toolkit, we compared the output of the SMACK algorithm; the number of QC flags changed in that there was a 1.7% (31/1944 observations) increase in flags and a 7.1% (138/1944 observations) decrease in presumed false positive flags, increasing the overall performance of SMACK which helped staff focus their time on reviewing more concerning QC failures. Discussion We have developed a customizable web-based dashboard for instrument performance monitoring for our opiate confirmation LC-MS/MS assay using data collected with each batch. The web-based platform allows users to monitor instrument performance and can encompass other instruments throughout the laboratory. This information can help the laboratory take proactive measures to maintain instruments, ultimately reducing the amount down time needed for maintenance.
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Affiliation(s)
- Abed Pablo
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA.,Department of Laboratory Medicine and Pathology, 1959 NE Pacific St, University of Washington, Seattle, WA 98195-7110, USA
| | - Andrew N Hoofnagle
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA.,Department of Laboratory Medicine and Pathology, 1959 NE Pacific St, University of Washington, Seattle, WA 98195-7110, USA
| | - Patrick C Mathias
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA.,Department of Laboratory Medicine and Pathology, 1959 NE Pacific St, University of Washington, Seattle, WA 98195-7110, USA
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Thomas SN, French D, Jannetto PJ, Rappold BA, Clarke WA. Liquid chromatography–tandem mass spectrometry for clinical diagnostics. NATURE REVIEWS. METHODS PRIMERS 2022; 2:96. [PMCID: PMC9735147 DOI: 10.1038/s43586-022-00175-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 10/07/2022] [Indexed: 12/13/2022]
Abstract
Mass spectrometry is a powerful analytical tool used for the analysis of a wide range of substances and matrices; it is increasingly utilized for clinical applications in laboratory medicine. This Primer includes an overview of basic mass spectrometry concepts, focusing primarily on tandem mass spectrometry. We discuss experimental considerations and quality management, and provide an overview of some key applications in the clinic. Lastly, the Primer discusses significant challenges for implementation of mass spectrometry in clinical laboratories and provides an outlook of where there are emerging clinical applications for this technology. Tandem mass spectrometry is increasingly utilized for clinical applications in laboratory medicine. In this Primer, Thomas et al. discuss experimental considerations and quality management for implementing clinical tandem mass spectrometry in the clinic with an overview of some key applications.
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Affiliation(s)
- Stefani N. Thomas
- grid.17635.360000000419368657Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN USA
| | - Deborah French
- grid.266102.10000 0001 2297 6811Laboratory Medicine, University of California San Francisco, San Francisco, CA USA
| | - Paul J. Jannetto
- grid.66875.3a0000 0004 0459 167XDepartment of Pathology & Laboratory Medicine, Mayo Clinic, Rochester, MN USA
| | - Brian A. Rappold
- grid.419316.80000 0004 0550 1859Research and Development, Labcorp, Burlington, NC USA
| | - William A. Clarke
- grid.21107.350000 0001 2171 9311Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD USA
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Vogeser M, Stone JA. A suggested standard for validation of LC-MS/MS based analytical series in diagnostic laboratories. CLINICAL MASS SPECTROMETRY (DEL MAR, CALIF.) 2020; 16:25-32. [PMID: 34820517 PMCID: PMC8600988 DOI: 10.1016/j.clinms.2020.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 02/03/2020] [Accepted: 02/25/2020] [Indexed: 11/25/2022]
Abstract
•Policies applied to confirm LC-MS/MS-based results differ between laboratories.•We suggest a systematic approach for validation of individual diagnostic series.•An individual series validation plan can be established with a checklist.
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Affiliation(s)
- Michael Vogeser
- Hospital of the University of Munich (LMU), Institute of Laboratory Medicine, Munich, Germany
| | - Judith A. Stone
- University of California, San Francisco Medical Center, Laboratory Medicine, Parnassus Chemistry, San Francisco, CA, USA
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Fung AWS, Sugumar V, Ren AH, Kulasingam V. Emerging role of clinical mass spectrometry in pathology. J Clin Pathol 2019; 73:61-69. [PMID: 31690564 DOI: 10.1136/jclinpath-2019-206269] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 10/14/2019] [Indexed: 12/20/2022]
Abstract
Mass spectrometry-based assays have been increasingly implemented in various disciplines in clinical diagnostic laboratories for their combined advantages in multiplexing capacity and high analytical specificity and sensitivity. It is now routinely used in areas including reference methods development, therapeutic drug monitoring, toxicology, endocrinology, paediatrics, immunology and microbiology to identify and quantify biomolecules in a variety of biological specimens. As new ionisation methods, instrumentation and techniques are continuously being improved and developed, novel mass spectrometry-based clinical applications will emerge for areas such as proteomics, metabolomics, haematology and anatomical pathology. This review will summarise the general principles of mass spectrometry and specifically highlight current and future clinical applications in anatomical pathology.
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Affiliation(s)
- Angela W S Fung
- Department of Pathology and Laboratory Medicine, St Paul's Hospital, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Vijithan Sugumar
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Annie He Ren
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Vathany Kulasingam
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada .,Clinical Biochemistry, University Health Network, Toronto, Ontario, Canada
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Automation of chromatographic peak review and order to result data transfer in a clinical mass spectrometry laboratory. Clin Chim Acta 2019; 498:84-89. [DOI: 10.1016/j.cca.2019.08.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 07/22/2019] [Accepted: 08/12/2019] [Indexed: 11/18/2022]
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Zhang YV, Rockwood A. Impact of automation on mass spectrometry. Clin Chim Acta 2015; 450:298-303. [DOI: 10.1016/j.cca.2015.08.027] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Revised: 08/13/2015] [Accepted: 08/30/2015] [Indexed: 12/18/2022]
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Mathias PC, Hayden JA, Laha TJ, Hoofnagle AN. Evaluation of matrix effects using a spike recovery approach in a dilute-and-inject liquid chromatography–tandem mass spectrometry opioid monitoring assay. Clin Chim Acta 2014; 437:38-42. [DOI: 10.1016/j.cca.2014.06.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 06/09/2014] [Accepted: 06/23/2014] [Indexed: 11/15/2022]
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