2,610
Views
0
CrossRef citations to date
0
Altmetric
Reviews

Enhancing precision medicine through clinical mass spectrometry platform

ORCID Icon &
Pages 107-117 | Received 03 Jan 2022, Accepted 10 Mar 2022, Published online: 23 Mar 2022

References

  • Clarke NJ. Mass spectrometry in precision medicine: phenotypic measurements alongside pharmacogenomics. Clin Chem. 2016;62(1):70–76.
  • Hu Y, Wang Z, Liu L, et al. Mass spectrometry-based chemical mapping and profiling toward molecular understanding of diseases in precision medicine. Chem Sci. 2021;12(23):7993–8009.
  • Ashrafian H, Sounderajah V, Glen R, et al. Metabolomics: the stethoscope for the twenty-first century. Med Princ Pract. 2021;30(4):301–310.
  • Rajeev KA, Shulaev V. Metabolomics technology and bioinformatics for precision medicine. Brief Bioinform. 2019;20(6):1957–1971.
  • Annesley TM, Cooks RG, Herold DA, et al. Clinical mass spectrometry-achieving prominence in laboratory medicine. Clin Chem. 2016;62(1):1–3.
  • Clarke W. Mass spectrometry in the clinical laboratory: determining the need and avoiding pitfalls. In: Nair H, Clarke W, editors. Mass spectrometry for the clinical laboratory. Amsterdam: Elsevier; 2017. p. 1–15.
  • Breaud AB, Straseski JA, Clarke W. Mass spectrometry. In: Clarke W, editor. Contemporary practice in clinical chemistry. 3rd ed. Washington (DC): AACC Press; 2016. p. 127–136.
  • Kobold U. Approaches to measurement of vitamin D concentrations – mass spectrometry. Scand J Clin Lab Invest Suppl. 2012;243:54–59.
  • Brown SM, Lo SF. Inborn errors of metabolism. In: Clarke W, editor. Contemporary practice in clinical chemistry. 3rd ed. Washington (DC): AACC Press; 2016. p. 651–664.
  • Brown SM, Dickerson J. Pediatric laboratory medicine. In: Clarke W, editor. Contemporary practice in clinical chemistry. 3rd ed. Washington (DC): AACC Press; 2016. p. 763–770.
  • Tebani A, Afonso C, Marret S, et al. Omics-based strategies in precision medicine: toward a paradigm shift in inborn errors of metabolism investigations. Int J Mol Sci. 2016;17(9):1555.
  • Jannetto PJ. Therapeutic drug monitoring using mass spectrometry. In: Nair H, Clarke W, editors. Mass spectrometry for the clinical laboratory. Amsterdam: Elsevier; 2017. p. 165–179.
  • Wong SH, Marquet P, Cattaneo D, et al. Therapeutic drug monitoring in the era of precision medicine: achievements, gaps, and perspectives – an interview in Honor of Professor Charles Pippenger. Ther Drug Monit. 2021;43(6):719–727.
  • Shipkova M, Svinarov D. LC-MS/MS as a tool for TDM services: where are we? Clin Biochem. 2016;49(13–14):1009–1023.
  • Lynch KL. Toxicology: liquid chromatography mass spectrometry. In: Nair H, Clarke W, editors. Mass spectrometry for the clinical laboratory. Amsterdam: Elsevier; 2017. p. 109–130.
  • Kyle PB. Toxicology: GCMS. In: Nair H, Clarke W, editors. Mass spectrometry for the clinical laboratory. Amsterdam: Elsevier; 2017. p. 131–163.
  • Soldin S, Soldin OP. Steroid hormone analysis by tandem mass spectrometry. Clin Chem. 2009;55(6):1061–1066.
  • Cook-Botelho JC, Bachmann LM, French D. Steroid hormones. In: Nair H, Clarke W, editors. Mass spectrometry for the clinical laboratory. Amsterdam: Elsevier; 2017. p. 205–230.
  • Ketha H, Singh RJ. Vitamin D metabolite quantitation by LC-MS/MS. In: Nair H, Clarke W, editors. Mass spectrometry for the clinical laboratory. Amsterdam: Elsevier; 2017. p. 181–204.
  • Martin IW. Mass spectrometry in clinical microbiology laboratory. In: Nair H, Clarke W, editors. Mass spectrometry for the clinical laboratory. Amsterdam: Elsevier; 2017. p. 231–245.
  • Chen XF, Hou X, Xiao M, et al. Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) analysis for the identification of pathogenic microorganisms: a review. Microorganisms. 2021;9(7):1536.
  • Beebe K, Kennedy AD. Sharpening precision medicine by a thorough interrogation of metabolic individuality. Comput Struct Biotechnol J. 2016;14:97–105.
  • Omenn GS, Lane L, Overall CM, et al. Progress on identifying and characterizing the human proteome: 2018 metrics from the HUPO Human Proteome Project. J Proteome Res. 2018;17(12):4031–4041.
  • Pino LK, Rose J, O’Broin A, et al. Emerging mass spectrometry-based proteomics methodologies for novel biomedical applications. Biochem Soc Trans. 2020;48(5):1953–1966.
  • Nassar SF, Raddassi K, Ubhi B, et al. Precision medicine: steps along the road to combat human cancer. Cells. 2020;9(9):2056.
  • Bai B, Vanderwall D, Li Y, et al. Proteomic landscape of Alzheimer’s disease: novel insights into pathogenesis and biomarker discovery. Mol Neurodegener. 2021;16(1):55.
  • Koussiouris J, Looby N, Anderson M, et al. Metabolomics studies in psoriatic disease: a review. Metabolites. 2021;11(6):375.
  • Gibson DA, Simitsidellis I, Collins F, et al. Endometrial intracrinology: oestrogens, androgens and endometrial disorders. Int J Mol Sci. 2018;19(10):3276.
  • Bjerrum JT, Wang YL, Seidelin JB, et al. IBD metabonomics predicts phenotype, disease course, and treatment response. EBioMedicine. 2021;71:103551.
  • Shevchuk O, Begonja AJ, Gambaryan S, et al. Proteomics: a tool to study platelet function. Int J Mol Sci. 2021;22(9):4776.
  • Pandey R, Caflisch L, Lodi A, et al. Metabolomic signature of brain cancer. Mol Carcinog. 2017;56(11):2355–2371.
  • Flores-Morales A, Iglesias-Gato D. Quantitative mass spectrometry-based proteomic profiling for precision medicine in prostate cancer. Front Oncol. 2017;7:267.
  • Sirolli V, Pieroni L, Di Liberato L, et al. Urinary peptidomic biomarkers in kidney diseases. Int J Mol Sci. 2019;21(1):96.
  • Saez-Rodriguez J, Rinschen MM, Floege J, et al. Big science and big data in nephrology. Kidney Int. 2019;95(6):1326–1337.
  • Gross RW. The evolution of lipidomics through space and time. Biochim Biophys Acta Mol Cell Biol Lipids. 2017;1862(8):731–739.
  • Ruhaak LR, Van der Laarse A, Cobbaert CM. Apolipoprotein profiling as a personalized approach to the diagnosis and treatment of dyslipidaemia. Ann Clin Biochem. 2019;56(3):338–356.
  • Fert-Bober J, Murray CI, Parker SJ, et al. Precision profiling of the cardiovascular post-translationally modified proteome: where there is a will, there is a way. Circ Res. 2018;122(9):1221–1237.
  • Sumi MP, Mahajan B, Sattar RSA, et al. Elucidation of epigenetic land scape in coronary artery disease: a review on basic concept to personalized medicine. Epigenet Insights. 2021;14:1–18.
  • Chen MX, Wang SY, Kuo CH, et al. Metabolome analysis for investigating host-gut microbiota interactions. J Formos Med Assoc. 2019;118(Suppl 1):S10–S22.
  • Tsunoda SM, Gonzales C, Jarmusch AK, et al. Contribution of the gut microbiome to drug disposition, pharmacokinetic and pharmacodynamic variability. Clin Pharmacokinet. 2021;60(8):971–984.
  • Couvillion SP, Zhu Y, Nagy G, et al. New mass spectrometry technologies contributing towards comprehensive and high throughput omics analyses of single cells. Analyst. 2019;144(3):794–807.
  • Zhang P, Carlsten C, Chaleckis R, et al. Defining the scope of exposome studies and research needs from a multidisciplinary perspective. Environ Sci Technol Lett. 2021;8(10):839–852.
  • Doll S, Gnad F, Mann M. The case for proteomics and phosphor-proteomics in personalized cancer medicine. Prot Clin Appl. 2019;13(2):1800113.
  • Kuznetsov A, Voronina A, Govorun V, et al. Critical review of existing MHC I immunopeptidome isolation methods. Molecules. 2020;25(22):5409.
  • Freudenmann LK, Marcu A, Stevanović S. Mapping the tumour human leukocyte antigen (HLA) ligandome by mass spectrometry. Immunology. 2018;154(3):331–345.
  • Zhang B, Whiteaker JR, Hoofnagle AN, et al. Clinical potential of mass spectrometry-based proteogenomics. Nat Rev Clin Oncol. 2019;16(4):256–268.
  • Ferreira JA, Relvas-Santos M, Peixoto A, et al. Glycoproteogenomics: setting the course for next-generation cancer neoantigen discovery for cancer vaccines. Genomics Proteomics Bioinform. 2021;19(1):25–43.
  • Caprioli RM. Imaging mass spectrometry: a perspective. J Biomol Tech. 2019;30(1):7–11.
  • Chen K, Baluya D, Tosun M, et al. Imaging mass spectrometry: a new tool to assess molecular underpinnings of neurodegeneration. Metabolites. 2019;9(7):135.
  • Spraggins JM, Schwamborn K, Heeren RMA, et al. The importance of clinical tissue imaging. Clin Mass Spectrom. 2019;12:47–49.
  • Momcilovic M, Shackelford DB. Imaging cancer metabolism. Biomol Ther. 2018;26(1):81–92.
  • Yang FY, Chen JH, Ruan QQ, et al. Mass spectrometry imaging: an emerging technology for the analysis of metabolites in insects. Arch Insect Biochem Physiol. 2020;103(4):e21643.
  • Pietkiewicz D, Horała A, Plewa S, et al. MALDI-MSI-a step forward in overcoming the diagnostic challenges in ovarian tumors. Int J Environ Res Public Health. 2020;17(20):7564.
  • Longuespée R, Alberts D, Baiwir D, et al. MALDI imaging combined with laser microdissection-based microproteomics for protein identification: application to intratumor heterogeneity studies. Methods Mol Biol. 2018;1788:297–312.
  • Serafim V, Shah A, Puiu M, et al. Classification of cancer cell lines using matrix-assisted laser desorption/ionization time‑of‑flight mass spectrometry and statistical analysis. Int J Mol Med. 2017;40(4):1096–1104.
  • Schwartz SA, Weil RJ, Thompson RC, et al. Proteomic-based prognosis of brain tumor patients using direct-tissue matrix-assisted laser desorption ionization mass spectrometry. Cancer Res. 2005;65(17):7674–7681.
  • Agar NY, Malcolm JG, Mohan V, et al. Imaging of meningioma progression by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Anal Chem. 2010;82(7):2621–2625.
  • Nguyen SN, Sontag RL, Carson JP, et al. Towards high-resolution tissue imaging using nanospray desorption electrospray ionization mass spectrometry coupled to shear force microscopy. J Am Soc Mass Spectrom. 2018;29(2):316–322.
  • Groseclose MR, Massion PP, Chaurand P, et al. High-throughput proteomic analysis of formalin-fixed paraffin-embedded tissue microarrays using MALDI imaging mass spectrometry. Proteomics. 2008;8(18):3715–3724.
  • Sadeesh N, Scaravilli M, Latonen L. Proteomic landscape of prostate cancer: the view provided by quantitative proteomics, integrative analyses, and protein interactomes. Cancers. 2021;13(19):4829.
  • Witzke KE, Großerueschkamp F, Gerwert K, et al. Application of label-free proteomics for quantitative analysis of urothelial carcinoma and cystitis tissue. Methods Mol Biol. 2021;2228:283–292.
  • Chughtai K, Jiang L, Greenwood TR, et al. Mass spectrometry images acylcarnitines, phosphatidylcholines, and sphingomyelin in MDA-MB-231 breast tumor models. J Lipid Res. 2013;54(2):333–344.
  • Caprioli RM, Farmer TB, Gile J. Molecular imaging of biological samples: localization of peptides and proteins using MALDI-TOF MS. Anal Chem. 1997;69(23):4751–4760.
  • Sun C, Wang F, Zhang Y, et al. Mass spectrometry imaging-based metabolomics to visualize the spatially resolved reprogramming of carnitine metabolism in breast cancer. Theranostics. 2020;10(16):7070–7082.
  • Chagovets VV, Starodubtseva NL, Tokareva AO, et al. Validation of breast cancer margins by tissue spray mass spectrometry. Int J Mol Sci. 2020;21(12):4568.
  • Menendez J, Lupu R. Fatty acid synthase and the lipogenic phenotype in cancer pathogenesis. Nat Rev Cancer. 2007;7(10):763–777.
  • Vallianatou T, Shariatgorji R, Nilsson A, et al. Integration of mass spectrometry imaging and machine learning visualizes region-specific age-induced and drug-target metabolic perturbations in the brain. ACS Chem Neurosci. 2021;12(10):1811–1823.
  • Bogusiewicz J, Burlikowska K, Jaroch K, et al. Profiling of carnitine shuttle system intermediates in gliomas using solid-phase microextraction (SPME). Molecules. 2021;26(20):6112.
  • Eberlin LS, Norton I, Orringer D, et al. Ambient mass spectrometry for the intraoperative molecular diagnosis of human brain tumors. Proc Natl Acad Sci U S A. 2013;110(5):1611–1616.
  • Dória ML, McKenzie JS, Mroz A, et al. Epithelial ovarian carcinoma diagnosis by desorption electrospray ionization mass spectrometry imaging. Sci Rep. 2016;6:39219.
  • Cipollo JF, Parsons LM. Glycomics and glycoproteomics of viruses: Mass spectrometry applications and insights toward structure-function relationships. Mass Spectrom Rev. 2020;39(4):371–409.
  • Hasan MM, Mimi MA, Mamun MA, et al. Mass spectrometry imaging for glycome in the brain. Front Neuroanat. 2021;15:711955.
  • Kailemia MJ, Xu G, Wong M, et al. Recent advances in the mass spectrometry methods for glycomics and cancer. Anal Chem. 2018;90(1):208–224.
  • Drake RR, Powers TW, Jones EE, et al. MALDI mass spectrometry imaging of N-linked glycans in cancer tissues. Adv Cancer Res. 2017;134:85–116.
  • Mezger STP, Mingels AMA, Bekers O, et al. Trends in mass spectrometry imaging for cardiovascular diseases. Anal Bioanal Chem. 2019;411(17):3709–3720.
  • Lim J, Aguilan JT, Sellers RS, et al. Lipid mass spectrometry imaging and proteomic analysis of severe aortic stenosis. J Mol Histol. 2020;51(5):559–571.
  • Takahashi S, Murata K, Ozawa K, et al. Moraxella species: infectious microbes identified by use of time-of-flight mass spectrometry. Jpn J Ophthalmol. 2019;63(4):328–336.
  • Lahiri S, Aftab W, Walenta L, et al. MALDI-IMS combined with shotgun proteomics identify and localize new factors in male infertility [published correction appears in Life Sci Alliance. 2021;4(3)]. Life Sci Alliance. 2021;4(3):e202000672.
  • Gou J, Jia J, Zhao X, et al. Identification of stathmin 1 during peri-implantation period in mouse endometrium by a proteomics-based analysis. Biochem Biophys Res Commun. 2015;461(2):211–216.
  • Feider CL, Woody S, Ledet S, et al. Molecular imaging of endometriosis tissues using desorption electrospray ionization mass spectrometry. Sci Rep. 2019;9(1):15690.
  • Groseclose MR, Castellino S. A mimetic tissue model for the quantification of drug distributions by MALDI imaging mass spectrometry. Anal Chem. 2013;85(21):10099–10106.
  • Lee RFS, Theiner S, Meibom A, et al. Application of imaging mass spectrometry approaches to facilitate metal-based anticancer drug research. Metallomics. 2017;9(4):365–381.
  • Morosi L, Matteo C, Ceruti T, et al. Quantitative determination of niraparib and olaparib tumor distribution by mass spectrometry imaging. Int J Biol Sci. 2020;16(8):1363–1375.
  • Prentice BM, Chumbley CW, Caprioli RM. Absolute quantification of rifampicin by MALDI imaging mass spectrometry using multiple TOF/TOF events in a single laser shot. J Am Soc Mass Spectrom. 2017;28(1):136–144.
  • Lv R, Shi R, Wu E, et al. Spatial-temporal profiling of antibiotic metabolites using graphite dots-assisted laser desorption ionization mass spectrometry. Talanta. 2020;220:121371.
  • Blaze MTM, Akhmetov A, Aydin B, et al. Quantification of antibiotic in biofilm-inhibiting multilayers by 7.87 eV laser desorption postionization MS imaging. Anal Chem. 2012;84(21):9410–9415.
  • Thompson CG, Bokhart MT, Sykes C, et al. Mass spectrometry imaging reveals heterogeneous efavirenz distribution within putative HIV reservoirs. Antimicrob Agents Chemother. 2015;59(5):2944–2948.
  • Heiss N, Rousson V, Ifticene-Treboux A, et al. Risk factors for positive resection margins of breast cancer tumorectomy specimen following breast-conserving surgery. Horm Mol Biol Clin Investig. 2017;32(2):20170023.
  • Santilli AML, Jamzad A, Sedghi A, et al. Domain adaptation and self-supervised learning for surgical margin detection. Int J Comput Assist Radiol Surg. 2021;16(5):861–869.
  • Alexander J, Gildea L, Balog J, et al. A novel methodology for in vivo endoscopic phenotyping of colorectal cancer based on real-time analysis of the mucosal lipidome: a prospective observational study of the iKnife. Surg Endosc. 2017;31(3):1361–1370.
  • Tzafetas M, Mitra A, Paraskevaidi M, et al. The intelligent knife (iKnife) and its intraoperative diagnostic advantage for the treatment of cervical disease [published correction appears in Proc Natl Acad Sci U S A. 2020;117(31):18892]. Proc Natl Acad Sci U S A. 2020;117(13):7338–7346.
  • Phelps DL, Balog J, Gildea LF, et al. The surgical intelligent knife distinguishes normal, borderline and malignant gynaecological tissues using rapid evaporative ionisation mass spectrometry (REIMS). Br J Cancer. 2018;118(10):1349–1358.
  • Santilli AML, Jamzad A, Janssen NNY, et al. Perioperative margin detection in basal cell carcinoma using a deep learning framework: a feasibility study. Int J Comput Assist Radiol Surg. 2020;15(5):887–896.
  • Hänel L, Kwiatkowski M, Heikaus L, et al. Mass spectrometry-based intraoperative tumor diagnostics. Future Sci OA. 2019;5(3):FSO373.
  • Garza KY, Feider CL, Klein DR, et al. Desorption electrospray ionization mass spectrometry imaging of proteins directly from biological tissue sections. Anal Chem. 2018;90(13):7785–7789.
  • Brown HM, Pirro V, Cooks RG. From DESI to the MasSpec pen: ambient ionization mass spectrometry for tissue analysis and intrasurgical cancer diagnosis. Clin Chem. 2018;64(4):628–630.
  • Keating MF, Zhang J, Feider CL, et al. Integrating the MasSpec pen to the da Vinci Surgical System for in vivo tissue analysis during a robotic assisted porcine surgery. Anal Chem. 2020;92(17):11535–11542.
  • Crutchfield CA, Clarke W. High resolution accurate mass (HRAM) mass spectrometry. In: Nair H, Clarke W, editors. Mass spectrometry for the clinical laboratory. Amsterdam: Elsevier; 2017. p. 247–259.
  • Yang JY, Herod DA. Evolving platforms for clinical mass spectrometry. In: Nair H, Clarke W, editors. Mass spectrometry for the clinical laboratory. Amsterdam: Elsevier; 2017. p. 261–276.
  • Patel SK, George B, Rai V. Artificial intelligence to decode cancer mechanism: beyond patient stratification for precision oncology. Front Pharmacol. 2020;11:1177.