Applicability of selected reaction monitoring for precise screening tests

References

• Schroeder LF, Guarner J, Amukele TK. Essential dagnostics for the use of world health organization essential medicines. Clin Chem. 2018;64(8):1148–1157. doi:10.1373/clinchem.2017.275339
   PubMed Web of Science ®Google Scholar
• Thierry AR. A step closer to cancer screening by blood test. Clin Chem. 2018;64(10):1420–1422. doi:10.1373/clinchem.2018.287847
   PubMed Web of Science ®Google Scholar
• Pavlou MP, Diamandis EP, Blasutig IM. The long journey of cancer biomarkers from the bench to the clinic. Clin Chem. 2013;59(1):147–157. doi:10.1373/clinchem.2012.184614
   PubMed Web of Science ®Google Scholar
• Martin-Timon I, Sevillano-Collantes C, Segura-Galindo A, et al. Type 2 diabetes and cardiovascular disease: have all risk factors the same strength? World J Diabetes. 2014;5(4):444–470. doi: 10.4239/wjd.v5.i4.444
   PubMedGoogle Scholar
• Tagliafico AS, Calabrese M, Mariscotti G, et al. Adjunct screening with tomosynthesis or ultrasound in women with mammography-negative dense breasts: interim report of a prospective comparative trial. J Clin Oncol. 2016;34(16):1882–1888. doi: 10.1200/JCO.2015.63.4147
   PubMed Web of Science ®Google Scholar
• Arbyn M, Simon M, Peeters E, et al. 2020 list of human papillomavirus assays suitable for primary cervical cancer screening. Clin Microbiol Infect. 2021;27(8):1083–1095. doi: 10.1016/j.cmi.2021.04.031
   PubMed Web of Science ®Google Scholar
• Kachuri L, Hoffmann TJ, Jiang Y, et al. Genetically adjusted PSA levels for prostate cancer screening. Nat Med. 2023;29(6):1412–1423. doi: 10.1038/s41591-023-02277-9
   PubMed Web of Science ®Google Scholar
• Pickhardt PJ, Hassan C, Halligan S, et al. Colorectal cancer: CT colonography and colonoscopy for detection–systematic review and meta-analysis. Radiology. 2011;259(2):393–405. doi: 10.1148/radiol.11101887
   PubMed Web of Science ®Google Scholar
• Hunger T, Wanka-Pail E, Brix G, et al. Lung cancer screening with low-dose CT in smokers: a systematic review and meta-analysis. Diagn (Basel). 2021;11(6):1040. doi: 10.3390/diagnostics11061040
   PubMedGoogle Scholar
• Johnson MM, Leachman SA, Aspinwall LG, et al. Skin cancer screening: recommendations for data-driven screening guidelines and a review of the US Preventive Services Task Force controversy. Melanoma Manag. 2017;4(1):13–37. doi: 10.2217/mmt-2016-0022
   PubMed Web of Science ®Google Scholar
• Carter SM, Barratt A. What is overdiagnosis and why should we take it seriously in cancer screening? Public Health Res Pract. 2017;27(3). doi: 10.17061/phrp2731722
   Google Scholar
• Singh H, Dickinson JA, Theriault G, et al. Overdiagnosis: causes and consequences in primary health care. Can Fam Physician. 2018;64(9):654–659.
   PubMed Web of Science ®Google Scholar
• Picotti P, Aebersold R. Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. Nat Methods. 2012;9(6):555–566. doi: 10.1038/nmeth.2015
   PubMed Web of Science ®Google Scholar
• Fuzery AK, Levin J, Chan MM, et al. Translation of proteomic biomarkers into FDA approved cancer diagnostics: issues and challenges. Clin Proteomics. 2013;10(1):13. doi:10.1186/1559-0275-10-13
   PubMed Web of Science ®Google Scholar
• Li XJ, Hayward C, Fong PY, et al. A blood-based proteomic classifier for the molecular characterization of pulmonary nodules. Sci Transl Med. 2013;5(207):207ra142. doi: 10.1126/scitranslmed.3007013
   PubMed Web of Science ®Google Scholar
• Meyer JG, Schilling B. Clinical applications of quantitative proteomics using targeted and untargeted data-independent acquisition techniques. Expert Rev Proteomics. 2017;14(5):419–429. doi:10.1080/14789450.2017.1322904
   PubMed Web of Science ®Google Scholar
• Shi T, Song E, Nie S, et al. Advances in targeted proteomics and applications to biomedical research. Proteomics. 2016;16(15–16):2160–2182. doi: 10.1002/pmic.201500449
   PubMed Web of Science ®Google Scholar
• Kusebauch U, Campbell DS, Deutsch EW, et al. Human SRMAtlas: a resource of targeted assays to quantify the complete human proteome. Cell. 2016;166(3):766–778. doi: 10.1016/j.cell.2016.06.041
   PubMed Web of Science ®Google Scholar
• Luan YY, Yao YM. The clinical significance and potential role of C-Reactive protein in chronic inflammatory and neurodegenerative diseases. Front Immunol. 2018;9:1302. doi:10.3389/fimmu.2018.01302
   PubMed Web of Science ®Google Scholar
• Tellez-Avila FI, Garcia-Osogobio SM. The carcinoembryonic antigen: apropos of an old friend. Rev Invest Clin. 2005;57(6):814–819.
   PubMedGoogle Scholar
• Zhang X, Han X, Zuo P, et al. CEACAM5 stimulates the progression of non-small-cell lung cancer by promoting cell proliferation and migration. J Int Med Res. 2020;48(9):300060520959478. doi:10.1177/0300060520959478
   PubMed Web of Science ®Google Scholar
• Thompson JA, Grunert F, Zimmermann W. Carcinoembryonic antigen gene family: molecular biology and clinical perspectives. J Clin Lab Anal. 1991;5(5):344–366. doi:10.1002/jcla.1860050510
   PubMed Web of Science ®Google Scholar
• Vachatova S, Andrys C, Krejsek J, et al. Metabolic syndrome and selective inflammatory markers in psoriatic patients. J Immunol Res. 2016;2016:1–8. doi: 10.1155/2016/5380792
   Web of Science ®Google Scholar
• Lynch KL. A case series evaluation of comprehensive drug testing in the pediatric acute care setting. J Mass Spectrom Adv Clin Lab. 2023;28:75–79. doi: 10.1016/j.jmsacl.2023.02.011
   PubMedGoogle Scholar
• Millington DS, Kodo N, Norwood DL, et al. Tandem mass spectrometry: a new method for acylcarnitine profiling with potential for neonatal screening for inborn errors of metabolism. J Inherit Metab Dis. 1990;13(3):321–324. doi:10.1007/BF01799385
   PubMed Web of Science ®Google Scholar
• Fitzgerald RL, Herold DA. Serum total testosterone: immunoassay compared with negative chemical ionization gas chromatography-mass spectrometry. Clin Chem. 1996;42(5):749–755. doi:10.1093/clinchem/42.5.749
   PubMed Web of Science ®Google Scholar
• Holland RD, Wilkes JG, Rafii F, et al. Rapid identification of intact whole bacteria based on spectral patterns using matrix-assisted laser desorption/ionization with time-of-flight mass spectrometry. Rapid Commun Mass Spectrom. 1996;10(10):1227–1232. doi: 10.1002/(SICI)1097-0231(19960731)10:10<1227:AID-RCM659>3.0.CO;2-6
   PubMed Web of Science ®Google Scholar
• Croxatto A, Prod’hom G, Greub G. Applications of MALDI-TOF mass spectrometry in clinical diagnostic microbiology. FEMS Microbiol Rev. 2012;36(2):380–407. doi:10.1111/j.1574-6976.2011.00298.x
   PubMed Web of Science ®Google Scholar
• Soldin SJ, Soukhova N, Janicic N, et al. The measurement of free thyroxine by isotope dilution tandem mass spectrometry. Clin Chim Acta. 2005;358(1–2):113–118. doi:10.1016/j.cccn.2005.02.010
   PubMed Web of Science ®Google Scholar
• Grebe SK, Singh RJ. LC-MS/MS in the Clinical Laboratory - where to from here? Clin Biochem Rev. 2011;32(1):5–31. doi:10.1373/clinchem.2010.157115
   PubMedGoogle Scholar
• Lange V, Picotti P, Domon B, et al. Selected reaction monitoring for quantitative proteomics: a tutorial. Mol Syst Biol. 2008;4(1):222. doi: 10.1038/msb.2008.61
   PubMed Web of Science ®Google Scholar
• Strathmann FG, Hoofnagle AN. Current and future applications of mass spectrometry to the clinical laboratory. Am J Clin Pathol. 2011;136(4):609–616. doi:10.1309/AJCPW0TA8OBBNGCK
   PubMed Web of Science ®Google Scholar
• Thomas L. Emerging applications in clinical mass spectrometry. MLO Med Lab Obs. 2016;48(4):24, 28 (2016).
   PubMedGoogle Scholar
• Addona TA, Abbatiello SE, Schilling B, et al. Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat Biotechnol. 2009;27(7):633–641. doi: 10.1038/nbt.1546
   PubMed Web of Science ®Google Scholar
• Costenoble R, Picotti P, Reiter L, et al. Comprehensive quantitative analysis of central carbon and amino-acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics. Mol Syst Biol. 2011;7(1):464. doi: 10.1038/msb.2010.122
   PubMedGoogle Scholar
• Wang Q, Chaerkady R, Wu J, et al. Mutant proteins as cancer-specific biomarkers. Proc Natl Acad Sci USA. 2011;108(6):2444–2449. doi: 10.1073/pnas.1019203108
   PubMed Web of Science ®Google Scholar
• Yocum AK, Gratsch TE, Leff N, et al. Coupled global and targeted proteomics of human embryonic stem cells during induced differentiation. Mol & Cell Proteomics. 2008;7(4):750–767. doi: 10.1074/mcp.M700399-MCP200
   PubMed Web of Science ®Google Scholar
• Kuhn E, Wu J, Karl J, et al. Quantification of C-reactive protein in the serum of patients with rheumatoid arthritis using multiple reaction monitoring mass spectrometry and 13C-labeled peptide standards. Proteomics. 2004;4(4):1175–1186. doi:10.1002/pmic.200300670
   PubMed Web of Science ®Google Scholar
• Fortin T, Salvador A, Charrier JP, et al. Clinical quantitation of prostate-specific antigen biomarker in the low nanogram/milliliter range by conventional bore liquid chromatography-tandem mass spectrometry (multiple reaction monitoring) coupling and correlation with ELISA tests. Mol Cell Proteomics. 2009;8(5):1006–1015. doi: 10.1074/mcp.M800238-MCP200
   PubMed Web of Science ®Google Scholar
• Keshishian H, Addona T, Burgess M, et al. Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution. Mol Cell Proteomics. 2007;6(12):2212–2229. doi:10.1074/mcp.M700354-MCP200
   PubMed Web of Science ®Google Scholar
• Pawlak M, Schick E, Bopp MA, et al. Zeptosens’ protein microarrays: a novel high performance microarray platform for low abundance protein analysis. Proteomics. 2002;2(4):383–393. doi:10.1002/1615-9861(200204)2:4<383:AID-PROT383>3.0.CO;2-E
   PubMed Web of Science ®Google Scholar
• Hoofnagle AN, Becker JO, Wener MH, et al. Quantification of thyroglobulin, a low-abundance serum protein, by immunoaffinity peptide enrichment and tandem mass spectrometry. Clin Chem. 2008;54(11):1796–1804. doi:10.1373/clinchem.2008.109652
   PubMed Web of Science ®Google Scholar
• Kim H, Sohn A, Yeo I, et al. Clinical assay for AFP-L3 by using multiple reaction monitoring-mass spectrometry for diagnosing hepatocellular carcinoma. Clin Chem. 2018;64(8):1230–1238. doi: 10.1373/clinchem.2018.289702
   PubMed Web of Science ®Google Scholar
• Ellington AA, Kullo IJ, Bailey KR, et al. Antibody-based protein multiplex platforms: technical and operational challenges. Clin Chem. 2010;56(2):186–193. doi:10.1373/clinchem.2009.127514
   PubMed Web of Science ®Google Scholar
• Segurado OG, Sasso EH. Vectra DA for the objective measurement of disease activity in patients with rheumatoid arthritis. Clin Exp Rheumatol. 2014;32(5 Suppl 85):S-29–34.
   Web of Science ®Google Scholar
• Hwang D, Lee IY, Yoo H, et al. A systems approach to prion disease. Mol Syst Biol. 2009;5(1):252. doi: 10.1038/msb.2009.10
   PubMedGoogle Scholar
• Vachani A, Hammoud Z, Springmeyer S, et al. Clinical utility of a plasma protein Classifier for indeterminate lung nodules. Lung. 2015;193(6):1023–1027. doi: 10.1007/s00408-015-9800-0
   PubMed Web of Science ®Google Scholar
• Saade GR, Boggess KA, Sullivan SA, et al. Development and validation of a spontaneous preterm delivery predictor in asymptomatic women. Am J Obstet Gynecol. 2016;214(5):e633 631–e633 624. doi: 10.1016/j.ajog.2016.02.001
   Web of Science ®Google Scholar
• Lung Screening Trial Research T N, Aberle DR, Adams AM, et al. Reduced lung-cancer mortality with low-dose computed tomographic screening. N Engl J Med. 2011;365(5):395–409.
   PubMed Web of Science ®Google Scholar
• Tanner NT, Aggarwal J, Gould MK, et al. Management of pulmonary nodules by community pulmonologists: a multicenter observational study. Chest. 2015;148(6):1405–1414. doi: 10.1378/chest.15-0630
   PubMed Web of Science ®Google Scholar
• Wiener RS, Gould MK, Slatore CG, et al. Resource use and guideline concordance in evaluation of pulmonary nodules for cancer: too much and too little care. JAMA Intern Med. 2014;174(6):871–880. doi:10.1001/jamainternmed.2014.561
   PubMed Web of Science ®Google Scholar
• Dekker GA, Lee SY, North RA, et al. Risk factors for preterm birth in an international prospective cohort of nulliparous women. PLoS One. 2012;7(7):e39154. doi: 10.1371/journal.pone.0039154
   PubMed Web of Science ®Google Scholar
• Kalinich M, Haber DA. Cancer detection: seeking signals in blood. Science. 2018;359(6378):866–867. doi:10.1126/science.aas9102
   PubMed Web of Science ®Google Scholar
• Kim H, Kim Y, Han B, et al. Clinically applicable deep learning algorithm using quantitative proteomic data. J Proteome Res. 2019;18(8):3195–3202. doi: 10.1021/acs.jproteome.9b00268
   PubMed Web of Science ®Google Scholar
• Yu SJ, Kim H, Min H, et al. Targeted proteomics predicts a sustained complete-response after transarterial chemoembolization and clinical outcomes in patients with hepatocellular carcinoma: a prospective cohort study. J Proteome Res. 2017;16(3):1239–1248. doi: 10.1021/acs.jproteome.6b00833
   PubMed Web of Science ®Google Scholar
• Kim H, Yu SJ, Yeo I, et al. Prediction of response to Sorafenib in hepatocellular carcinoma: a putative Marker panel by multiple reaction monitoring-mass spectrometry (MRM-MS). Mol & Cell Proteomics. 2017;16(7):1312–1323. doi: 10.1074/mcp.M116.066704
   PubMed Web of Science ®Google Scholar
• Toghi Eshghi S, Auger P, Mathews WR. Quality assessment and interference detection in targeted mass spectrometry data using machine learning. Clin Proteomics. 2018;15(1):33. doi: 10.1186/s12014-018-9209-x
   PubMedGoogle Scholar
• Lee J, Kim H, Sohn A, et al. Cost-effective automated preparation of serum samples for reproducible quantitative clinical proteomics. J Proteome Res. 2019;18(5):2337–2345. doi: 10.1021/acs.jproteome.9b00023
   PubMed Web of Science ®Google Scholar
• Reiter L, Rinner O, Picotti P, et al. mProphet: automated data processing and statistical validation for large-scale SRM experiments. Nat Methods. 2011;8(5):430–435. doi: 10.1038/nmeth.1584
   PubMed Web of Science ®Google Scholar
• Surinova S, Huttenhain R, Chang CY, et al. Automated selected reaction monitoring data analysis workflow for large-scale targeted proteomic studies. Nat Protoc. 2013;8(8):1602–1619. doi:10.1038/nprot.2013.091
   PubMed Web of Science ®Google Scholar
• Bereman MS, Beri J, Sharma V, et al. An automated pipeline to monitor system performance in liquid chromatography–tandem Mass spectrometry proteomic experiments. J Proteome Res. 2016;15(12):4763–4769. doi: 10.1021/acs.jproteome.6b00744
   PubMed Web of Science ®Google Scholar
• Gallien S, Bourmaud A, Kim SY, et al. Technical considerations for large-scale parallel reaction monitoring analysis. J Proteomics. 2014;100:147–159. doi:10.1016/j.jprot.2013.10.029
   PubMed Web of Science ®Google Scholar
• Gillet LC, Navarro P, Tate S, et al. Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mo Cell Proteomics. 2012;11(6):O111 016717. doi: 10.1074/mcp.O111.016717
   PubMed Web of Science ®Google Scholar
• Shi C, Merchant N, Newsome G, et al. Differentiation of pancreatic ductal adenocarcinoma from chronic pancreatitis by PAM4 immunohistochemistry. Arch Pathol Lab Med. 2014;138(2):220–228. doi:10.5858/arpa.2013-0056-OA
   PubMed Web of Science ®Google Scholar
• Mayerle J, Kalthoff H, Reszka R, et al. Metabolic biomarker signature to differentiate pancreatic ductal adenocarcinoma from chronic pancreatitis. Gut. 2018;67(1):128–137. doi: 10.1136/gutjnl-2016-312432
   PubMed Web of Science ®Google Scholar
• Gutierrez DB, Gant-Branum RL, Romer CE, et al. An integrated, high-throughput strategy for multiomic systems level analysis. J Proteome Res. 2018;17(10):3396–3408. doi: 10.1021/acs.jproteome.8b00302
   PubMed Web of Science ®Google Scholar