Moradian, A., Goonatilleke, E., Lin, T.-T., Hatten-Beck, M., Emrick, M., Schepmoes, A. A., Fillmore, T. L., MacCoss, M. J., Sechi, S., Sobhani, K., Little, R., Kabytaev, K., van Eyk, J. E., Qian, W.-J., & Hoofnagle, A. N. Interlaboratory Comparison of Antibody-Free LC-MS/MS Measurements of C-peptide and Insulin. Clinical Chemistry 2024 May 29 Epub ahead of print PMID: 38549041 doi: 10.1093/clinchem/hvae034

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Lidgard B, Hoofnagle AN, Zelnick LR, de Boer IH, Fretts AM, Kestenbaum BR, Lemaitre RN, Robinson-Cohen C, Bansal N. High-Density Lipoprotein Lipidomics and Mortality in CKD. Kidney Med 2023 Aug 6 6;5(10):100708 PMCID: PMC10507644 doi: 10.1016/j.xkme.2023.100708

Phipps WS, Kilgore MR, Kennedy JJ, Whiteaker JR, Hoofnagle AN, Paulovich AG. Clinical Proteomics for Solid Organ Tissues. Mol Cell Proteomics 2023 November 22(11):100648 PMCID: PMC10692389 doi: 10.1016/j.mcpro.2023.100648

Huynh HH, Kuch K, Orquillas A, Forrest K, Barahona-Carrillo L, Keene D, Henderson VW, Wagner AD, Poston KL, Montine TJ, Lin A, Tian L, MacCoss MJ, Emrick MA, Hoofnagle AN. Metrologically Traceable Quantification of 3 Apolipoprotein E Isoforms in Cerebrospinal Fluid. Clin Chem 2023 Jul 5 69(7):734-745 PMCID: PMC10320014 doi: 10.1093/clinchem/hvad056

Lidgard B, Hoofnagle AN, Zelnick LR, de Boer IH, Fretts AM, Kestenbaum BR, Lemaitre RN, Robinson-Cohen C, Bansal N. High-Density Lipoprotein Lipidomics in Chronic Kidney Disease. Clin Chem 2023 Mar 1 69(3):273-282 PMCID: PMC10069017 doi: 10.1093/clinchem/hvac216

Best CM, Thummel KE, Hsu S, Lin Y, Zelnick LR, Kestenbaum B, Kushnir MM, de Boer IH, Hoofnagle AN. The plasma free fraction of 25-hydroxyvitamin D3 is not strongly associated with 25-hydroxyvitamin D3 clearance in kidney disease patients and controls. J Steroid Biochem Mol Biol 2023 Feb 226:106206 PMID: 36404469 doi: 10.1016/j.jsbmb.2022.106206

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Shi J, Phipps WS, Owusu BY, Henderson CM, Laha TJ, Becker JO, Razavi M, Emrick MA, Hoofnagle AN. A distributable LC-MS/MS method for the measurement of serum thyroglobulin. J Mass Spectrom Adv Clin Lab 2022 Sep 19 26:28-33 PMCID: PMC9641599 doi: 10.1016/j.jmsacl.2022.09.005

Andrews M, Yoshida T, Henderson CM, Pflaum H, McGregor A, Lieberman JA, de Boer IH, Vaisar T, Himmelfarb J, Kestenbaum B, Chung JY, Hewitt SM, Santo BA, Ginley B, Sarder P, Rosenberg AZ, Murakami T, Kopp JB, Kuklenyik Z, Hoofnagle AN. Variant APOL1 protein in plasma associates with larger particles in humans and mouse models of kidney injury. PLoS One 2022 Oct 24 17(10):e0276649 PMCID: PMC9591058 doi: 10.1371/journal.pone.0276649

Kilpatrick LE, Bouillon R, Davis WC, Henderson CM, Hoofnagle AN, Pauwels S, Vanderschueren D, Waelkens E, Wildiers H, Yen JH, Phinney KW. The influence of proteoforms: assessing the accuracy of total vitamin D-binding protein quantification by proteolysis and LC-MS/MS. Clin Chem Lab Med 2022 Oct 24 61(1):78-85 PMID: 36279170 doi: 10.1515/cclm-2022-0642

Huynh HH, Forrest K, Becker JO, Emrick MA, Miller GD, Moncrieffe D, Cowan DA, Thomas A, Thevis M, MacCoss MJ, Hoffstrom B, Byers PH, Eichner D, Hoofnagle AN. A Targeted Liquid Chromatography-Tandem Mass Spectrometry Method for Simultaneous Quantification of Peptides from the Carboxyl-terminal Region of Type III Procollagen, Biomarkers of Collagen Turnover. Clin Chem 2022 Oct 6 68(10):1281-1291 PMID: 35906802 doi: 10.1093/clinchem/hvac119

Foulon N, Goonatilleke E, MacCoss MJ, Emrick MA, Hoofnagle AN. Multiplexed quantification of insulin and C-peptide by LC-MS/MS without the use of antibodies. J Mass Spectrom Adv Clin Lab 2022 Jun 10 25:19-26 PMCID: PMC9207678 doi: 10.1016/j.jmsacl.2022.06.003

Phipps WS, Smith KD, Yang HY, Henderson CM, Pflaum H, Lerch ML, Fondrie WE, Emrick MA, Wu CC, MacCoss MJ, Noble WS, Hoofnagle AN. Tandem Mass Spectrometry-Based Amyloid Typing Using Manual Microdissection and Open-Source Data Processing. Am J Clin Pathol 2022 May 4 157(5):748-757 PMCID: PMC9071319 doi: 10.1093/ajcp/aqab185

Limonte CP, Valo E, Drel V, Natarajan L, Darshi M, Forsblom C, Henderson CM, Hoofnagle AN, Ju W, Kretzler M, Montemayor D, Nair V, Nelson RG, O'Toole JF, Toto RD, Rosas SE, Ruzinski J, Sandholm N, Schmidt IM, Vaisar T, Waikar SS, Zhang J, Rossing P, Ahluwalia TS, Groop PH, Pennathur S, Snell-Bergeon JK, Costacou T, Orchard TJ, Sharma K, de Boer IH. Kidney Precision Medicine Project. Urinary Proteomics Identifies Cathepsin D as a Biomarker of Rapid eGFR Decline in Type 1 Diabetes. Diabetes Care 2022 Jun 2 45(6):1416-1427 PMCID: PMC9210873 doi: 10.2337/dc21-2204

Phipps WS, Greene DN, Pflaum H, Laha TJ, Dickerson JA, Irvine J, Merrill AE, Ranjitkar P, Henderson CM, Hoofnagle AN. Small volume retinol binding protein measurement by liquid chromatography-tandem mass spectrometry. Clin Biochem 2022 Jan 99:111-117 PMCID: PMC8671195 doi: 10.1016/j.clinbiochem.2021.10.005

Best CM, Zelnick LR, Thummel KE, Hsu S, Limonte C, Thadhani R, Sesso HD, Manson JE, Buring JE, Mora S, Lee IM, Cook NR, Friedenberg G, Luttmann-Gibson H, de Boer IH, Hoofnagle AN. Serum Vitamin D: Correlates of Baseline Concentration and Response to Supplementation in VITAL-DKD. J Clin Endocrinol Metab 2022 Jan 18 107(2):525-537 PMCID: PMC8764322 doi: 10.1210/clinem/dgab693

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Owusu BY, Pflaum H, Garner R, Foulon N, Laha TJ, Hoofnagle AN. Development and Validation of a Novel LC-MS/MS Assay for C-Peptide in Human Serum. J Mass Spectrom Adv Clin Lab 2021 Jan 19:1-6 PMCID: PMC8553002 doi: 10.1016/j.jmsacl.2020.12.001

Shi J, Bird R, Schmeling MW, Hoofnagle AN. Using mass spectrometry to overcome the longstanding inaccuracy of a commercially-available clinical testosterone immunoassay. J Chromatogr B Analyt Technol Biomed Life Sci 2021 Oct 15 1183:122969 PMCID: PMC8589107 doi: 10.1016/j.jchromb.2021.122969

Banerjee RR, Spence T, Frank SJ, Pandian R, Hoofnagle AN, Argiropoulos B, Marcadier JL. Very Low Vitamin D in a Patient With a Novel Pathogenic Variant in the GC Gene That Encodes Vitamin D-Binding Protein. J Endocr Soc 2021 Jun 5 5(9):bvab104 PMCID: PMC8362819 doi: 10.1210/jendso/bvab104

Fretts AM, Jensen PN, Hoofnagle AN, McKnight B, Sitlani CM, Siscovick DS, King IB, Psaty BM, Sotoodehnia N, Lemaitre RN. Circulating Ceramides and Sphingomyelins and Risk of Mortality: The Cardiovascular Health Study. Clin Chem 2021 Nov 26 67(12):1650-1659 PMCID goes here doi: 10.1093/clinchem/hvab182

Hendelman T, Chaudhary A, LeClair AC, van Leuven K, Chee J, Fink SL, Welch EJ, Berthier E, Quist BA, Wald A, Wener MH, Hoofnagle AN, Morishima C. Self-collection of capillary blood using Tasso-SST devices for Anti-SARS-CoV-2 IgG antibody testing. PLoS One 2021 Sep 2 16(9):e0255841 PMCID: PMC8412246 doi: 10.1371/journal.pone.0255841

Shi J, Lindo EG, Baird GS, Young B, Ryan M, Jefferson JA, Mehrotra R, Mathias PC, Hoofnagle AN. Calculating estimated glomerular filtration rate without the race correction factor: Observations at a large academic medical system. Clin Chim Acta 2021 Sep 520:16-22 PMCID: PMC8286343 doi: 10.1016/j.cca.2021.05.022

Ginsberg C, Hoofnagle AN, Katz R, Becker JO, Kritchevsky SB, Shlipak MG, Sarnak MJ, Ix JH. The Vitamin D Metabolite Ratio Is Independent of Vitamin D Binding Protein Concentration. Clin Chem 2021 Jan 30 67(2):385-393 PMCID: PMC8880257 doi: 10.1093/clinchem/hvaa238

Best CM, Riley DV, Laha TJ, Pflaum H, Zelnick LR, Hsu S, Thummel KE, Foster-Schubert KE, Kuzma JN, Cromer G, Larson I, Hagman DK, Heshelman K, Kratz M, de Boer IH, Hoofnagle AN. Vitamin D in human serum and adipose tissue after supplementation. Am J Clin Jutr 2021 Jan 4 113(1):83-91 PMCID: PMC7779222 doi: 10.1093/ajcn/nqaa295

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Hsu S, Hoofnagle AN, Gupta DK, Gutierrez OM, Peralta CA, Shea S, Allen NB, Burke G, Michos ED, Ix JH, Siscovick D, Psaty BM, Watson KE, Kestenbaum B, de Boer IH, Robinson-Cohen C. Race, Ancestry, and Vitamin D Metabolism: The Multi-Ethnic Study of Atherosclerosis. J Clin Endocrinol Metab 2020 Dec 1 105(12):e4337–50 PMCID: PMC7526733 doi: 10.1210/clinem/dgaa612

Moncrieffe D, Cox HD, Carletta S, Becker JO, Thomas A, Eichner D, Ahrens B, Thevis M, Bowers LD, Cowan DA, Hoofnagle AN. Inter-Laboratory Agreement of Insulin-like Growth Factor 1 Concentrations Measured Intact by Mass Spectrometry. Clin Chem 2020 April 1 66(4):579-586 PMID: 32232452 doi: 10.1093/clinchem/hvaa043

Chen Y, Zelnick LR, Wang K, Hoofnagle AN, Becker JO, Hsu CY, Feldman HI, Mehta RC, Lash JP, Waikar SS, Shafi T, Seliger SL, Shlipak MG, Rahman M, Kestenbaum BR. CRIC Study Investigators. Kidney Clearance of Secretory Solutes Is Associated with Progression of CKD: The CRIC Study. J Am Soc Nephrol 2020 Apr 31(4):817-827 PMCID: PMC7191931 doi: 10.1681/ASN.2019080811

Hoffman MA, Schmeling M, Dahlin JL, Bevins NJ, Cooper DP, Jarolim P, Fitzgerald RL, Hoofnagle AN. Calibrating from Within: Multipoint Internal Calibration of a Quantitative Mass Spectrometric Assay of Serum Methotrexate. Clin Chem 2020 Mar 1 66(3):474-482 PMID: 32057077 doi: 10.1093/clinchem/hvaa003

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Erdman P, Palmer-Toy DE, Horowitz G, Hoofnagle A. Accuracy-Based Vitamin D Survey: Six Years of Quality Improvement Guided by Proficiency Testing. Arch Pathol Lab Med 2019 Dec 143(12):1531-1538 PMID: 31116045 doi: 10.5858/arpa.2018-0625-CP

Henderson CM, Fink SL, Bassyouni H, Argiropoulos B, Brown L, Laha TJ, Jackson KJ, Lewkonia R, Ferreira P, Hoofnagle AN, Marcadier JL. Vitamin D-Binding Protein Deficiency and Homozygous Deletion of the GC Gene. N Engl J Med 2019 Mar 21 380(12):1150-1157 PMCID: PMC7898410 doi: 10.1056/NEJMoa1807841

Author names go here. Paper Title goes here. Journal Name goes here Publication Date Volume, issue, and page numbers go here PMCID goes here doi goes here

Lemaitre RN, Yu C, Hoofnagle A, Hari N, Jensen PN, Fretts AM, Umans JG, Howard BV, Sitlani CM, Siscovick DS, King IB, Sotoodehnia N, McKnight B. Circulating Sphingolipids, Insulin, HOMA-IR, and HOMA-B: The Strong Heart Family Study. Diabetes 2018 Aug 67(8):1663-1672 PMCID: PMC6054436 doi: 10.2337/db17-1449

Henderson CM, Shulman NJ, MacLean B, MacCoss MJ, Hoofnagle AN. Skyline Performs as Well as Vendor Software in the Quantitative Analysis of Serum 25-Hydroxy Vitamin D and Vitamin D Binding Globulin. Clin Chem 2018 Feb 64(2):408-410 PMCID: PMC6109398 doi: 10.1373/clinchem.2017.282293

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Rubinow KB, Henderson CM, Robinson-Cohen C, Himmelfarb J, de Boer IH, Vaisar T, Kestenbaum B, Hoofnagle AN. Kidney function is associated with an altered protein composition of high-density lipoprotein. Kidney Int 2017 Dec 92(6):1526-1535 PMCID: PMC5696089 doi: 10.1016/j.kint.2017.05.020

Henderson CM, Lutsey PL, Misialek JR, Laha TJ, Selvin E, Eckfeldt JH, Hoofnagle AN. Measurement by a Novel LC-MS/MS Methodology Reveals Similar Serum Concentrations of Vitamin D-Binding Protein in Blacks and Whites. Clim Chem 2016 Jan 62(1):179-87 PMCID: PMC4698095 doi: 10.1373/clinchem.2015.244541

Hoofnagle AN, Eckfeldt JH, Lutsey PL. Vitamin D-Binding Protein Concentrations Quantified by Mass Spectrometry. N Engl J Med 2015 Oct 8 373(15):1480-2 PMCID: PMC4654614 doi: 10.1056/NEJMc1502602

Grant RP, Hoofnagle AN. From lost in translation to paradise found: enabling protein biomarker method transfer by mass spectrometry. Clin Chem 2014 Jul 60(7):941-4 PMCID: PMC4315805 doi: 10.1373/clinchem.2014.224840

Cox HD, Lopes F, Woldemariam GA, Becker JO, Parkin MC, Thomas A, Butch AW, Cowan DA, Thevis M, Bowers LD, Hoofnagle AN. Interlaboratory agreement of insulin-like growth factor 1 concentrations measured by mass spectrometry. Clin Chem 2014 Mar 60(3):541-8 PMID: 24323979 doi: 10.1373/clinchem.2013.208538

Laha TJ, Strathmann FG, Wang Z, de Boer IH, Thummel KE, Hoofnagle AN. Characterizing antibody cross-reactivity for immunoaffinity purification of analytes prior to multiplexed liquid chromatography-tandem mass spectrometry. Clin Chem 2012 Dec 58(12):1711-6 PMCID: PMC3731945 doi: 10.1373/clinchem.2012.185827

Hoofnagle AN, Becker JO, Oda MN, Cavigiolio G, Mayer P, Vaisar T. Multiple-reaction monitoring-mass spectrometric assays can accurately measure the relative protein abundance in complex mixtures. Clin Chem 2012 Apr 58(4):777-81 PMCID: PMC3665768 doi: 10.1373/clinchem.2011.173856

Strathmann FG, Laha TJ, Hoofnagle AN. Quantification of 1α,25-dihydroxy vitamin D by immunoextraction and liquid chromatography-tandem mass spectrometry. Clin Chem 2012 Sep 57(9):1279-85 PMCID: PMC3261234 doi: 10.1373/clinchem.2010.161174

Agger SA, Marney LC, Hoofnagle AN. Simultaneous quantification of apolipoprotein A-I and apolipoprotein B by liquid-chromatography-multiple- reaction-monitoring mass spectrometry. Clin Chem 2010 Dec 56(12):1804-13 PMCID: PMC3103773 doi: 10.1373/clinchem.2010.152264

Hoofnagle AN, Laha TJ, Donaldson TF. A rubber transfer gasket to improve the throughput of liquid-liquid extraction in 96-well plates: application to vitamin D testing. J Chromatogr B Analyt Technol Biomed Life Sci 2010 Jun 1 878(19):1639-42 PMCID: PMC2877171 doi: 10.1016/j.jchromb.2010.04.010

Hoofnagle AN. Quantitative clinical proteomics by liquid chromatography-tandem mass spectrometry: assessing the platform. Clin Chem 2010 Feb 56(2):161-4 PMID: 19959622 doi: 10.1373/clinchem.2009.134049

Hoofnagle AN, Wener MH. The fundamental flaws of immunoassays and potential solutions using tandem mass spectrometry. J Immunol Methods 2009 Aug 15 347(1-2):3-11 PMCID: PMC2720067 doi: 10.1016/j.jim.2009.06.00

Hoofnagle AN, Becker JO, Wener MH, Heinecke JW. Quantification of thyroglobulin, a low-abundance serum protein, by immunoaffinity peptide enrichment and tandem mass spectrometry. Clin Chem 2008 Nov 54(11):1796-804 PMCID: PMC2739673 doi: 10.1373/clinchem.2008.109652

Hoofnagle AN, Chou D, Astion ML. https://pubmed.ncbi.nlm.nih.gov/17040954/. Clin Chem 2007 Jan 53(1):134-7 PMID: 17040954 doi: 10.1373/clinchem.2006.078550