Evaluation of thermal desorption-electrospray ionization mass spectrometry for characterization of Mycobacterium tuberculosis: Comparison with MIRU-VNTR and whole-genome sequencing

Tsung-Ying Yang^{1

2

3}, Hung Su⁴, Shu-Huei Jain⁵, Hsien-Ho Lin⁶, Chieh-Yin Wu⁶, Chao-Ju Chen^{5

7}, Jentaie Shiea^{4

8

9}, Po-Liang Lu^{10

11

12

13}

Affiliations

¹ Department of Medical Laboratory and Regenerative Medicine, MacKay Medical University, New Taipei City, Taiwan.
² Research Institute for Science and Engineering, Waseda University, Japan.
³ Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan.
⁴ Department of Chemistry, National Sun Yat-Sen University, Kaohsiung, Taiwan.
⁵ Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.
⁶ Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan.
⁷ College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.
⁸ Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung, Taiwan.
⁹ Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.
¹⁰ Center for Liquid Biopsy and Cohort Research, Kaohsiung Medical University, Kaohsiung, Taiwan.
¹¹ Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.
¹² School of Post-Baccalaureate Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.
¹³ Department of Biological Science and Technology, College of Biological Science and Technology, National Yang Ming Chiao Tung University, Taiwan.

PMID: 41280735
PMCID: PMC12637081
DOI: 10.1016/j.jmsacl.2025.10.005

Evaluation of thermal desorption-electrospray ionization mass spectrometry for characterization of Mycobacterium tuberculosis: Comparison with MIRU-VNTR and whole-genome sequencing

Tsung-Ying Yang et al. J Mass Spectrom Adv Clin Lab. 2025.

. 2025 Oct 26:38:50-57.

doi: 10.1016/j.jmsacl.2025.10.005. eCollection 2025 Dec.

Authors

Tsung-Ying Yang^{1

2

3}, Hung Su⁴, Shu-Huei Jain⁵, Hsien-Ho Lin⁶, Chieh-Yin Wu⁶, Chao-Ju Chen^{5

7}, Jentaie Shiea^{4

8

9}, Po-Liang Lu^{10

11

12

13}

Affiliations

¹ Department of Medical Laboratory and Regenerative Medicine, MacKay Medical University, New Taipei City, Taiwan.
² Research Institute for Science and Engineering, Waseda University, Japan.
³ Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan.
⁴ Department of Chemistry, National Sun Yat-Sen University, Kaohsiung, Taiwan.
⁵ Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.
⁶ Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan.
⁷ College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.
⁸ Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung, Taiwan.
⁹ Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.
¹⁰ Center for Liquid Biopsy and Cohort Research, Kaohsiung Medical University, Kaohsiung, Taiwan.
¹¹ Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.
¹² School of Post-Baccalaureate Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.
¹³ Department of Biological Science and Technology, College of Biological Science and Technology, National Yang Ming Chiao Tung University, Taiwan.

PMID: 41280735
PMCID: PMC12637081
DOI: 10.1016/j.jmsacl.2025.10.005

Abstract

Background: Typing Mycobacterium tuberculosis (MTB) isolates is important for identifying clusters and guiding infection control measures. Although whole-genome sequencing (WGS) and 24-loci mycobacterial interspersed repetitive units-variable-number tandem repeat (MIRU-VNTR) are widely used for molecular typing, they may not capture phenotypic or metabolic variation. Alternative approaches, such as mass spectrometric-based profiling, could provide complementary insights.

Methods: A total of 247 clinical MTB isolates were analyzed by thermal desorption-electrospray ionization mass spectrometry (TD-ESI/MS). The resulting mass spectral profiles were evaluated using principal component analysis (PCA) and hierarchical clustering analysis (HCA). Results were compared with lineage classifications based on WGS and MIRU-VNTR to assess concordance.

Results: While WGS and MIRU-VNTR were highly concordant for lineage classification (98.8%; 244/247), TD-ESI/MS revealed diverse spectral profiles that did not align consistently with genetic lineages. However, HCA showed isolate-level clustering, including among genetically similar strains, suggesting that TD-ESI/MS may detect metabolic or lipidomic differences not captured by genome-based methods.

Conclusion: Although TD-ESI/MS does not generate similar results from MTB molecular typing, it shows potential for identifying specific spectral signatures. The technique may be useful in future investigations into phenotypic diversity and other clinically relevant features not captured by genotyping alone.

Keywords: Analysis; Genome; Mass spectrometry; Mycobacterium tuberculosis.

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Conflict of interest statement

the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Figures

**Fig. 1**
(a) PCA score plots of the lipid ion signals from TD-ESI mass spectra for five randomly-selected clinical MTB isolates and a laboratory strain, H37Rv; (b) HCA analysis of the mass spectra for 247 clinical MTB isolates. Each isolate was analyzed in at least 3 biological replicates. Roman Numerals indicated the groups of TD-ESI/MS typing.

**Fig. 2**
Representative TD-ESI mass spectra of samples extracted from (a) Group I, (b) Group II, or (c) Group III.

**Fig. 3**
**Phylogenetic tree of 247 clinical MTB isolates and 1 *M. bovis* based on the molecular results of whole-genome sequencing.** The phylogeny between isolates was deduced using the Neighbor-Joining method, and the evolutionary distances were computed via the Maximum Composite Likelihood method.

See this image and copyright information in PMC

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Evaluation of thermal desorption-electrospray ionization mass spectrometry for characterization of Mycobacterium tuberculosis: Comparison with MIRU-VNTR and whole-genome sequencing

Affiliations

Evaluation of thermal desorption-electrospray ionization mass spectrometry for characterization of Mycobacterium tuberculosis: Comparison with MIRU-VNTR and whole-genome sequencing

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

LinkOut - more resources

Full Text Sources