{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,12]],"date-time":"2026-11-12T03:45:02Z","timestamp":1794455102133,"version":"4.9.1"},"reference-count":88,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,7,3]],"date-time":"2024-07-03T00:00:00Z","timestamp":1719964800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2024,7,3]],"date-time":"2024-07-03T00:00:00Z","timestamp":1719964800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Clin Proteom"],"published-print":{"date-parts":[[2024,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Amyloidosis is a disease characterized by local and systemic extracellular deposition of amyloid protein fibrils where its excessive accumulation in tissues and resistance to degradation can lead to organ failure. Diagnosis is challenging because of approximately 36 different amyloid protein subtypes. Imaging methods like immunohistochemistry and the use of Congo red staining of amyloid proteins for laser capture microdissection combined with liquid chromatography tandem mass spectrometry (LMD\/LC\u2013MS\/MS) are two diagnostic methods currently used depending on the expertise of the pathology laboratory. Here, we demonstrate a streamlined in situ amyloid peptide spatial mapping by Matrix Assisted Laser Desorption Ionization\u2013Mass Spectrometry Imaging (MALDI-MSI) combined with Trapped Ion Mobility Spectrometry for potential transthyretin (ATTR) amyloidosis subtyping. While we utilized the standard LMD\/LC\u2013MS\/MS workflow for amyloid subtyping of 31 specimens from different organs, we also evaluated the potential introduction in the MS workflow variations in data acquisition parameters like dynamic exclusion, or testing Data Dependent Acquisition combined with High-Field Asymmetric Waveform Ion Mobility Spectrometry (DDA FAIMS) versus Data Independent Acquisition (DIA) for enhanced amyloid protein identification at shorter acquisition times. We also demonstrate the use of Mascot\u2019s Error Tolerant Search and PEAKS de novo sequencing for the sequence variant analysis of amyloidosis specimens.<\/jats:p>","DOI":"10.1186\/s12014-024-09500-w","type":"journal-article","created":{"date-parts":[[2024,7,3]],"date-time":"2024-07-03T14:13:50Z","timestamp":1720016030000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Effect of dynamic exclusion and the use of FAIMS, DIA and MALDI-mass spectrometry imaging with ion mobility on amyloid protein identification"],"prefix":"10.1186","volume":"21","author":[{"given":"Jennifer T.","family":"Aguilan","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jihyeon","family":"Lim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sabrina","family":"Racine-Brzostek","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joshua","family":"Fischer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cristina","family":"Silvescu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shannon","family":"Cornett","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Edward","family":"Nieves","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Damodara Rao","family":"Mendu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carlos-Madrid","family":"Aliste","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stacia","family":"Semple","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruth","family":"Angeletti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Louis M.","family":"Weiss","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adam","family":"Cole","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Prystowsky","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James","family":"Pullman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simone","family":"Sidoli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,7,3]]},"reference":[{"issue":"4","key":"9500_CR1","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1080\/13506129.2018.1549825","volume":"25","author":"MD Benson","year":"2018","unstructured":"Benson MD, et al. Amyloid nomenclature 2018: recommendations by the International Society of Amyloidosis (ISA) nomenclature committee. Amyloid. 2018;25(4):215\u20139.","journal-title":"Amyloid"},{"issue":"4","key":"9500_CR2","doi-asserted-by":"publisher","first-page":"322","DOI":"10.1159\/000506696","volume":"143","author":"MM Picken","year":"2020","unstructured":"Picken MM. The pathology of amyloidosis in classification: a review. Acta Haematol. 2020;143(4):322\u201334.","journal-title":"Acta Haematol"},{"issue":"10","key":"9500_CR3","doi-asserted-by":"publisher","first-page":"1046","DOI":"10.1182\/bloodadvances.2018016402","volume":"2","author":"TP Quock","year":"2018","unstructured":"Quock TP, et al. Epidemiology of AL amyloidosis: a real-world study using US claims data. Blood Adv. 2018;2(10):1046\u201353.","journal-title":"Blood Adv"},{"issue":"8","key":"9500_CR4","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1038\/s41408-021-00529-w","volume":"11","author":"A Staron","year":"2021","unstructured":"Staron A, et al. Marked progress in AL amyloidosis survival: a 40-year longitudinal natural history study. Blood Cancer J. 2021;11(8):139.","journal-title":"Blood Cancer J"},{"issue":"9","key":"9500_CR5","doi-asserted-by":"publisher","first-page":"865","DOI":"10.1001\/jamacardio.2018.2093","volume":"3","author":"KM Alexander","year":"2018","unstructured":"Alexander KM, et al. Geographic disparities in reported US amyloidosis mortality from 1979 to 2015: potential underdetection of cardiac amyloidosis. JAMA Cardiol. 2018;3(9):865\u201370.","journal-title":"JAMA Cardiol"},{"issue":"6","key":"9500_CR6","doi-asserted-by":"publisher","DOI":"10.1161\/CIRCHEARTFAILURE.118.005407","volume":"12","author":"LG Gilstrap","year":"2019","unstructured":"Gilstrap LG, et al. Epidemiology of cardiac amyloidosis-associated heart failure hospitalizations among fee-for-service medicare beneficiaries in the United States. Circ Heart Fail. 2019;12(6): e005407.","journal-title":"Circ Heart Fail"},{"issue":"5","key":"9500_CR7","doi-asserted-by":"publisher","first-page":"1994","DOI":"10.1111\/j.1523-1755.2005.00653.x","volume":"68","author":"HG Kang","year":"2005","unstructured":"Kang HG, et al. Hereditary amyloidosis in early childhood associated with a novel insertion-deletion (indel) in the fibrinogen Aalpha chain gene. Kidney Int. 2005;68(5):1994\u20138.","journal-title":"Kidney Int"},{"issue":"2","key":"9500_CR8","doi-asserted-by":"publisher","first-page":"126","DOI":"10.1111\/joim.12383","volume":"278","author":"KS Patel","year":"2015","unstructured":"Patel KS, Hawkins PN. Cardiac amyloidosis: where are we today? J Intern Med. 2015;278(2):126\u201344.","journal-title":"J Intern Med"},{"issue":"5","key":"9500_CR9","doi-asserted-by":"publisher","first-page":"1085","DOI":"10.4103\/1319-2442.301175","volume":"31","author":"N Garg","year":"2020","unstructured":"Garg N, et al. Clinicopathological spectrum of renal amyloidosis in young. Saudi J Kidney Dis Transpl. 2020;31(5):1085\u201390.","journal-title":"Saudi J Kidney Dis Transpl"},{"issue":"3","key":"9500_CR10","doi-asserted-by":"publisher","first-page":"160","DOI":"10.3109\/13506120308998998","volume":"10","author":"LH Connors","year":"2003","unstructured":"Connors LH, et al. Tabulation of human transthyretin (TTR) variants, 2003. Amyloid. 2003;10(3):160\u201384.","journal-title":"Amyloid"},{"issue":"6","key":"9500_CR11","doi-asserted-by":"publisher","first-page":"1223","DOI":"10.1016\/j.ekir.2017.07.009","volume":"2","author":"T Prokaeva","year":"2017","unstructured":"Prokaeva T, et al. Hereditary renal amyloidosis associated with a novel apolipoprotein A-II variant. Kidney Int Rep. 2017;2(6):1223\u201332.","journal-title":"Kidney Int Rep"},{"issue":"3","key":"9500_CR12","doi-asserted-by":"publisher","first-page":"461","DOI":"10.1016\/j.ekir.2016.11.005","volume":"2","author":"D Rowczenio","year":"2017","unstructured":"Rowczenio D, et al. Renal amyloidosis associated with 5 novel variants in the fibrinogen A alpha chain protein. Kidney Int Rep. 2017;2(3):461\u20139.","journal-title":"Kidney Int Rep"},{"issue":"1","key":"9500_CR13","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1016\/j.kint.2020.03.033","volume":"98","author":"M Colombat","year":"2020","unstructured":"Colombat M, et al. New clinical forms of hereditary apoA-I amyloidosis entail both glomerular and retinal amyloidosis. Kidney Int. 2020;98(1):195\u2013208.","journal-title":"Kidney Int"},{"issue":"2","key":"9500_CR14","doi-asserted-by":"publisher","first-page":"431","DOI":"10.1681\/ASN.2016090951","volume":"28","author":"SH Nasr","year":"2017","unstructured":"Nasr SH, et al. Hereditary lysozyme amyloidosis variant p.Leu102Ser associates with unique phenotype. J Am Soc Nephrol. 2017;28(2):431\u20138.","journal-title":"J Am Soc Nephrol"},{"key":"9500_CR15","doi-asserted-by":"publisher","first-page":"659","DOI":"10.1016\/B978-0-444-52902-2.00039-4","volume":"115","author":"S Kiuru-Enari","year":"2013","unstructured":"Kiuru-Enari S, Haltia M. Hereditary gelsolin amyloidosis. Handb Clin Neurol. 2013;115:659\u201381.","journal-title":"Handb Clin Neurol"},{"issue":"5","key":"9500_CR16","doi-asserted-by":"publisher","first-page":"1416","DOI":"10.1053\/j.gastro.2004.03.003","volume":"126","author":"L Obici","year":"2004","unstructured":"Obici L, et al. Liver biopsy discloses a new apolipoprotein A-I hereditary amyloidosis in several unrelated Italian families. Gastroenterology. 2004;126(5):1416\u201322.","journal-title":"Gastroenterology"},{"issue":"9","key":"9500_CR17","doi-asserted-by":"publisher","first-page":"1852","DOI":"10.1016\/j.mayocp.2020.06.029","volume":"95","author":"S Dasari","year":"2020","unstructured":"Dasari S, et al. Amyloid typing by mass spectrometry in clinical practice: a comprehensive review of 16,175 samples. Mayo Clin Proc. 2020;95(9):1852\u201364.","journal-title":"Mayo Clin Proc"},{"issue":"24","key":"9500_CR18","doi-asserted-by":"publisher","first-page":"9629","DOI":"10.1073\/pnas.1121005109","volume":"109","author":"CE Bulawa","year":"2012","unstructured":"Bulawa CE, et al. Tafamidis, a potent and selective transthyretin kinetic stabilizer that inhibits the amyloid cascade. Proc Natl Acad Sci USA. 2012;109(24):9629\u201334.","journal-title":"Proc Natl Acad Sci USA"},{"issue":"11","key":"9500_CR19","doi-asserted-by":"publisher","first-page":"1007","DOI":"10.1056\/NEJMoa1805689","volume":"379","author":"MS Maurer","year":"2018","unstructured":"Maurer MS, et al. Tafamidis treatment for patients with transthyretin amyloid cardiomyopathy. N Engl J Med. 2018;379(11):1007\u201316.","journal-title":"N Engl J Med"},{"key":"9500_CR20","doi-asserted-by":"publisher","DOI":"10.15761\/TiM.1000206","author":"L Pedro","year":"2019","unstructured":"Pedro L, Pinho R, Marques N. Amyloidosis \u2013 a review. Trends Med. 2019. https:\/\/doi.org\/10.15761\/TiM.1000206.","journal-title":"Trends Med"},{"issue":"1","key":"9500_CR21","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1038\/s41572-018-0034-3","volume":"4","author":"G Merlini","year":"2018","unstructured":"Merlini G, et al. Systemic immunoglobulin light chain amyloidosis. Nat Rev Dis Primers. 2018;4(1):38.","journal-title":"Nat Rev Dis Primers"},{"issue":"12","key":"9500_CR22","doi-asserted-by":"publisher","first-page":"1106","DOI":"10.1056\/NEJMoa1504942","volume":"373","author":"DB Richards","year":"2015","unstructured":"Richards DB, et al. Therapeutic clearance of amyloid by antibodies to serum amyloid P component. N Engl J Med. 2015;373(12):1106\u201314.","journal-title":"N Engl J Med"},{"issue":"6","key":"9500_CR23","doi-asserted-by":"publisher","first-page":"948","DOI":"10.1515\/cclm-2019-1007","volume":"58","author":"D Canetti","year":"2020","unstructured":"Canetti D, et al. Diagnostic amyloid proteomics: experience of the UK National Amyloidosis Centre. Clin Chem Lab Med. 2020;58(6):948\u201357.","journal-title":"Clin Chem Lab Med"},{"issue":"20","key":"9500_CR24","doi-asserted-by":"publisher","first-page":"12662","DOI":"10.3390\/ijms232012662","volume":"23","author":"SA Fedotov","year":"2022","unstructured":"Fedotov SA, et al. Noninvasive diagnostics of renal amyloidosis: current state and perspectives. Int J Mol Sci. 2022;23(20):12662.","journal-title":"Int J Mol Sci"},{"key":"9500_CR25","doi-asserted-by":"publisher","first-page":"385","DOI":"10.1146\/annurev-bioeng-071114-040723","volume":"17","author":"JJ Vaquero","year":"2015","unstructured":"Vaquero JJ, Kinahan P. Positron emission tomography: current challenges and opportunities for technological advances in clinical and preclinical imaging systems. Annu Rev Biomed Eng. 2015;17:385\u2013414.","journal-title":"Annu Rev Biomed Eng"},{"issue":"13","key":"9500_CR26","doi-asserted-by":"publisher","first-page":"2241","DOI":"10.1182\/blood-2010-03-273797","volume":"116","author":"JS Wall","year":"2010","unstructured":"Wall JS, et al. Radioimmunodetection of amyloid deposits in patients with AL amyloidosis. Blood. 2010;116(13):2241\u20134.","journal-title":"Blood"},{"issue":"46","key":"9500_CR27","doi-asserted-by":"publisher","first-page":"E10839","DOI":"10.1073\/pnas.1805515115","volume":"115","author":"JS Wall","year":"2018","unstructured":"Wall JS, et al. Bifunctional amyloid-reactive peptide promotes binding of antibody 11\u20131F4 to diverse amyloid types and enhances therapeutic efficacy. Proc Natl Acad Sci USA. 2018;115(46):E10839\u201348.","journal-title":"Proc Natl Acad Sci USA"},{"issue":"14","key":"9500_CR28","doi-asserted-by":"publisher","first-page":"1065","DOI":"10.1136\/heartjnl-2016-310704","volume":"103","author":"M Grogan","year":"2017","unstructured":"Grogan M, Dispenzieri A, Gertz MA. Light-chain cardiac amyloidosis: strategies to promote early diagnosis and cardiac response. Heart. 2017;103(14):1065\u201372.","journal-title":"Heart"},{"issue":"3","key":"9500_CR29","doi-asserted-by":"publisher","first-page":"3","DOI":"10.14797\/mdcj-8-3-3","volume":"8","author":"KR Baker","year":"2012","unstructured":"Baker KR, Rice L. The amyloidoses: clinical features, diagnosis and treatment. Methodist Debakey Cardiovasc J. 2012;8(3):3\u20137.","journal-title":"Methodist Debakey Cardiovasc J"},{"issue":"7","key":"9500_CR30","doi-asserted-by":"publisher","first-page":"1239","DOI":"10.3324\/haematol.2013.102764","volume":"99","author":"JA Vrana","year":"2014","unstructured":"Vrana JA, et al. Clinical diagnosis and typing of systemic amyloidosis in subcutaneous fat aspirates by mass spectrometry-based proteomics. Haematologica. 2014;99(7):1239\u201347.","journal-title":"Haematologica"},{"issue":"3","key":"9500_CR31","doi-asserted-by":"publisher","first-page":"529","DOI":"10.1046\/j.1365-2141.2001.02999.x","volume":"114","author":"RA Kyle","year":"2001","unstructured":"Kyle RA. Amyloidosis: a convoluted story. Br J Haematol. 2001;114(3):529\u201338.","journal-title":"Br J Haematol"},{"key":"9500_CR32","doi-asserted-by":"publisher","DOI":"10.1042\/BSR20181415","author":"EI Yakupova","year":"2019","unstructured":"Yakupova EI, et al. Congo Red and amyloids: history and relationship. 2019. Biosci Rep. https:\/\/doi.org\/10.1042\/BSR20181415."},{"issue":"7","key":"9500_CR33","doi-asserted-by":"publisher","first-page":"1710","DOI":"10.1110\/ps.051997606","volume":"15","author":"RW McLaughlin","year":"2006","unstructured":"McLaughlin RW, et al. The effects of sodium sulfate, glycosaminoglycans, and Congo red on the structure, stability, and amyloid formation of an immunoglobulin light-chain protein. Protein Sci. 2006;15(7):1710\u201322.","journal-title":"Protein Sci"},{"issue":"2","key":"9500_CR34","first-page":"284","volume":"38","author":"MB Pepys","year":"1979","unstructured":"Pepys MB, et al. Binding of serum amyloid P-component (SAP) by amyloid fibrils. Clin Exp Immunol. 1979;38(2):284\u201393.","journal-title":"Clin Exp Immunol"},{"issue":"2","key":"9500_CR35","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1016\/j.proghi.2012.03.001","volume":"47","author":"RP Linke","year":"2012","unstructured":"Linke RP. On typing amyloidosis using immunohistochemistry. Detailled illustrations, review and a note on mass spectrometry. Prog Histochem Cytochem. 2012;47(2):61\u2013132.","journal-title":"Prog Histochem Cytochem"},{"issue":"4","key":"9500_CR36","doi-asserted-by":"publisher","first-page":"373","DOI":"10.1078\/0065-1281-00726","volume":"105","author":"RP Linke","year":"2003","unstructured":"Linke RP. Severe problems in diagnosing amyloid diseases. Acta Histochem. 2003;105(4):373\u20135.","journal-title":"Acta Histochem"},{"issue":"3","key":"9500_CR37","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1016\/j.acthis.2006.03.010","volume":"108","author":"RP Linke","year":"2006","unstructured":"Linke RP, et al. Classification of amyloidosis: misdiagnosing by way of incomplete immunohistochemistry and how to prevent it. Acta Histochem. 2006;108(3):197\u2013208.","journal-title":"Acta Histochem"},{"issue":"8","key":"9500_CR38","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0256306","volume":"16","author":"A Barreca","year":"2021","unstructured":"Barreca A, et al. Immunohistochemical typing of amyloid in fixed paraffin-embedded samples by an automatic procedure: Comparison with immunofluorescence data on fresh-frozen tissue. PLoS ONE. 2021;16(8): e0256306.","journal-title":"PLoS ONE"},{"issue":"23","key":"9500_CR39","doi-asserted-by":"publisher","first-page":"1786","DOI":"10.1056\/NEJMoa013354","volume":"346","author":"HJ Lachmann","year":"2002","unstructured":"Lachmann HJ, et al. Misdiagnosis of hereditary amyloidosis as AL (primary) amyloidosis. N Engl J Med. 2002;346(23):1786\u201391.","journal-title":"N Engl J Med"},{"issue":"10","key":"9500_CR40","doi-asserted-by":"publisher","first-page":"1067","DOI":"10.1002\/jms.3264","volume":"48","author":"JD Theis","year":"2013","unstructured":"Theis JD, et al. Shotgun-proteomics-based clinical testing for diagnosis and classification of amyloidosis. J Mass Spectrom. 2013;48(10):1067\u201377.","journal-title":"J Mass Spectrom"},{"issue":"10","key":"9500_CR41","doi-asserted-by":"publisher","first-page":"1024","DOI":"10.1038\/labinvest.2008.72","volume":"88","author":"FJ Rodriguez","year":"2008","unstructured":"Rodriguez FJ, et al. Immunoglobulin derived depositions in the nervous system: novel mass spectrometry application for protein characterization in formalin-fixed tissues. Lab Invest. 2008;88(10):1024\u201337.","journal-title":"Lab Invest"},{"issue":"7","key":"9500_CR42","doi-asserted-by":"publisher","first-page":"901","DOI":"10.1016\/j.jmoldx.2020.04.002","volume":"22","author":"CO Martins","year":"2020","unstructured":"Martins CO, et al. Mass spectrometry-based method targeting Ig variable regions for assessment of minimal residual disease in multiple myeloma. J Mol Diagn. 2020;22(7):901\u201311.","journal-title":"J Mol Diagn"},{"issue":"24","key":"9500_CR43","doi-asserted-by":"publisher","first-page":"4957","DOI":"10.1182\/blood-2009-07-230722","volume":"114","author":"JA Vrana","year":"2009","unstructured":"Vrana JA, et al. Classification of amyloidosis by laser microdissection and mass spectrometry-based proteomic analysis in clinical biopsy specimens. Blood. 2009;114(24):4957\u20139.","journal-title":"Blood"},{"issue":"1","key":"9500_CR44","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1038\/nmeth705","volume":"1","author":"JD Venable","year":"2004","unstructured":"Venable JD, et al. Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra. Nat Methods. 2004;1(1):39\u201345.","journal-title":"Nat Methods"},{"issue":"6","key":"9500_CR45","doi-asserted-by":"publisher","first-page":"O111016717","DOI":"10.1074\/mcp.O111.016717","volume":"11","author":"LC Gillet","year":"2012","unstructured":"Gillet LC, et al. Targeted data extraction of the MS\/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol Cell Proteomics. 2012;11(6):O111016717.","journal-title":"Mol Cell Proteomics"},{"issue":"7","key":"9500_CR46","doi-asserted-by":"publisher","first-page":"1088","DOI":"10.1074\/mcp.P119.001913","volume":"19","author":"LK Pino","year":"2020","unstructured":"Pino LK, et al. Acquiring and analyzing data independent acquisition proteomics experiments without spectrum libraries. Mol Cell Proteomics. 2020;19(7):1088\u2013103.","journal-title":"Mol Cell Proteomics"},{"issue":"12","key":"9500_CR47","doi-asserted-by":"publisher","first-page":"1563","DOI":"10.1038\/s41587-021-00968-7","volume":"39","author":"P Sinitcyn","year":"2021","unstructured":"Sinitcyn P, et al. MaxDIA enables library-based and library-free data-independent acquisition proteomics. Nat Biotechnol. 2021;39(12):1563\u201373.","journal-title":"Nat Biotechnol"},{"issue":"5","key":"9500_CR48","doi-asserted-by":"publisher","first-page":"419","DOI":"10.1080\/14789450.2017.1322904","volume":"14","author":"JG Meyer","year":"2017","unstructured":"Meyer JG, Schilling B. Clinical applications of quantitative proteomics using targeted and untargeted data-independent acquisition techniques. Expert Rev Proteomics. 2017;14(5):419\u201329.","journal-title":"Expert Rev Proteomics"},{"issue":"1","key":"9500_CR49","doi-asserted-by":"publisher","first-page":"2622","DOI":"10.1038\/s41467-022-30094-0","volume":"13","author":"K Frohlich","year":"2022","unstructured":"Frohlich K, et al. Benchmarking of analysis strategies for data-independent acquisition proteomics using a large-scale dataset comprising inter-patient heterogeneity. Nat Commun. 2022;13(1):2622.","journal-title":"Nat Commun"},{"key":"9500_CR50","doi-asserted-by":"publisher","first-page":"117727191771094","DOI":"10.1177\/1177271917710948","volume":"12","author":"N Rauniyar","year":"2017","unstructured":"Rauniyar N, et al. Data-independent acquisition and parallel reaction monitoring mass spectrometry identification of serum biomarkers for ovarian cancer. Biomark Insights. 2017;12:1177271917710948.","journal-title":"Biomark Insights"},{"issue":"1","key":"9500_CR51","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1038\/nmeth.2309","volume":"10","author":"MA Gillette","year":"2013","unstructured":"Gillette MA, Carr SA. Quantitative analysis of peptides and proteins in biomedicine by targeted mass spectrometry. Nat Methods. 2013;10(1):28\u201334.","journal-title":"Nat Methods"},{"issue":"3","key":"9500_CR52","doi-asserted-by":"publisher","DOI":"10.1002\/prca.201700106","volume":"12","author":"J Park","year":"2018","unstructured":"Park J, et al. Development and validation of mass spectrometry-based targeted analysis for amyloid proteins. Proteomics Clin Appl. 2018;12(3): e1700106.","journal-title":"Proteomics Clin Appl"},{"issue":"7","key":"9500_CR53","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0235143","volume":"15","author":"M Ogawa","year":"2020","unstructured":"Ogawa M, et al. Mass spectrometry-based absolute quantification of amyloid proteins in pathology tissue specimens: merits and limitations. PLoS ONE. 2020;15(7): e0235143.","journal-title":"PLoS ONE"},{"issue":"18","key":"9500_CR54","doi-asserted-by":"publisher","first-page":"5323","DOI":"10.1007\/s00216-015-8689-z","volume":"407","author":"R Casadonte","year":"2015","unstructured":"Casadonte R, et al. Imaging mass spectrometry analysis of renal amyloidosis biopsies reveals protein co-localization with amyloid deposits. Anal Bioanal Chem. 2015;407(18):5323\u201331.","journal-title":"Anal Bioanal Chem"},{"issue":"15","key":"9500_CR55","doi-asserted-by":"publisher","first-page":"1595","DOI":"10.1016\/j.clinbiochem.2013.05.063","volume":"46","author":"T Nakanishi","year":"2013","unstructured":"Nakanishi T, et al. Topologies of amyloidogenic proteins in Congo red-positive sliced sections of formalin-fixed paraffin embedded tissues by MALDI-MS imaging coupled with on-tissue tryptic digestion. Clin Biochem. 2013;46(15):1595\u2013600.","journal-title":"Clin Biochem"},{"issue":"10","key":"9500_CR56","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1369\/0022155415595264","volume":"63","author":"M Winter","year":"2015","unstructured":"Winter M, et al. MALDI-mass spectrometry imaging identifies vitronectin as a common constituent of amyloid deposits. J Histochem Cytochem. 2015;63(10):772\u20139.","journal-title":"J Histochem Cytochem"},{"issue":"6","key":"9500_CR57","doi-asserted-by":"publisher","first-page":"573","DOI":"10.1039\/D0MO00087F","volume":"16","author":"JT Aguilan","year":"2020","unstructured":"Aguilan JT, Kulej K, Sidoli S. Guide for protein fold change and p-value calculation for non-experts in proteomics. Mol Omics. 2020;16(6):573\u201382.","journal-title":"Mol Omics"},{"issue":"1","key":"9500_CR58","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1038\/s41592-019-0638-x","volume":"17","author":"V Demichev","year":"2020","unstructured":"Demichev V, et al. DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput. Nat Methods. 2020;17(1):41\u20134.","journal-title":"Nat Methods"},{"issue":"9","key":"9500_CR59","doi-asserted-by":"publisher","first-page":"3489","DOI":"10.1182\/blood-2005-10-4148","volume":"107","author":"RL Comenzo","year":"2006","unstructured":"Comenzo RL, et al. Seeking confidence in the diagnosis of systemic AL (Ig light-chain) amyloidosis: patients can have both monoclonal gammopathies and hereditary amyloid proteins. Blood. 2006;107(9):3489\u201391.","journal-title":"Blood"},{"issue":"4","key":"9500_CR60","doi-asserted-by":"publisher","first-page":"491","DOI":"10.1016\/j.humpath.2014.12.009","volume":"46","author":"SM Said","year":"2015","unstructured":"Said SM, Grogg KL, Smyrk TC. Gastric amyloidosis: clinicopathological correlations in 79 cases from a single institution. Hum Pathol. 2015;46(4):491\u20138.","journal-title":"Hum Pathol"},{"issue":"Suppl 1","key":"9500_CR61","doi-asserted-by":"publisher","first-page":"219","DOI":"10.3109\/13506129.2011.574354082","volume":"18","author":"C Murphy","year":"2011","unstructured":"Murphy C, et al. Non-hereditary apolipoprotein AI-associated pulmonary amyloid. Amyloid. 2011;18(Suppl 1):219\u201320.","journal-title":"Amyloid"},{"issue":"3","key":"9500_CR62","doi-asserted-by":"publisher","first-page":"257","DOI":"10.2353\/jmoldx.2009.080161","volume":"11","author":"M Eriksson","year":"2009","unstructured":"Eriksson M, et al. Hereditary apolipoprotein AI-associated amyloidosis in surgical pathology specimens: identification of three novel mutations in the APOA1 gene. J Mol Diagn. 2009;11(3):257\u201362.","journal-title":"J Mol Diagn"},{"issue":"39","key":"9500_CR63","doi-asserted-by":"publisher","DOI":"10.1097\/MD.0000000000008148","volume":"96","author":"C Lu","year":"2017","unstructured":"Lu C, et al. Apolipoprotein A-1-related amyloidosis 2 case reports and review of the literature. Medicine. 2017;96(39): e8148.","journal-title":"Medicine"},{"issue":"2","key":"9500_CR64","doi-asserted-by":"publisher","first-page":"82","DOI":"10.1038\/nrrheum.2010.229","volume":"7","author":"MJ Ombrello","year":"2011","unstructured":"Ombrello MJ, Kastner DL. Autoinflammation in 2010: expanding clinical spectrum and broadening therapeutic horizons. Nat Rev Rheumatol. 2011;7(2):82\u20134.","journal-title":"Nat Rev Rheumatol"},{"issue":"1","key":"9500_CR65","doi-asserted-by":"publisher","first-page":"88","DOI":"10.1007\/s13730-020-00525-2","volume":"10","author":"J Borg","year":"2021","unstructured":"Borg J, et al. Treatment of renal AA-Amyloidosis associated with human immunodeficiency virus infection: a case report. CEN Case Rep. 2021;10(1):88\u201393.","journal-title":"CEN Case Rep"},{"issue":"2","key":"9500_CR66","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1093\/ckj\/sfu021","volume":"7","author":"MA Khalighi","year":"2014","unstructured":"Khalighi MA, Dean Wallace W, Palma-Diaz MF. Amyloid nephropathy. Clin Kidney J. 2014;7(2):97\u2013106.","journal-title":"Clin Kidney J"},{"key":"9500_CR67","doi-asserted-by":"crossref","unstructured":"Guevremont R. High-field asymmetric waveform ion mobility spectrometry: a new tool for mass spectrometry. J Chromatogr A. 2004;1058(1\u20132):3\u201319. https:\/\/pubmed.ncbi.nlm.nih.gov\/15595648\/","DOI":"10.1016\/S0021-9673(04)01478-5"},{"issue":"14","key":"9500_CR68","doi-asserted-by":"publisher","first-page":"4193","DOI":"10.1021\/ac0498563","volume":"76","author":"H Liu","year":"2004","unstructured":"Liu H, Sadygov RG, Yates JR 3rd. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem. 2004;76(14):4193\u2013201.","journal-title":"Anal Chem"},{"issue":"1","key":"9500_CR69","doi-asserted-by":"publisher","first-page":"786","DOI":"10.15252\/msb.20145728","volume":"11","author":"Y Liu","year":"2015","unstructured":"Liu Y, et al. Quantitative variability of 342 plasma proteins in a human twin population. Mol Syst Biol. 2015;11(1):786.","journal-title":"Mol Syst Biol"},{"issue":"6","key":"9500_CR70","doi-asserted-by":"publisher","DOI":"10.15252\/msb.20199356","volume":"16","author":"JM Bader","year":"2020","unstructured":"Bader JM, et al. Proteome profiling in cerebrospinal fluid reveals novel biomarkers of Alzheimer\u2019s disease. Mol Syst Biol. 2020;16(6): e9356.","journal-title":"Mol Syst Biol"},{"issue":"11","key":"9500_CR71","doi-asserted-by":"publisher","first-page":"4752","DOI":"10.1021\/acs.jproteome.5b00826","volume":"14","author":"J Muntel","year":"2015","unstructured":"Muntel J, et al. Advancing urinary protein biomarker discovery by data-independent acquisition on a quadrupole-orbitrap mass spectrometer. J Proteome Res. 2015;14(11):4752\u201362.","journal-title":"J Proteome Res"},{"key":"9500_CR72","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1186\/s12014-018-9220-2","volume":"15","author":"L Lin","year":"2018","unstructured":"Lin L, et al. Fast quantitative urinary proteomic profiling workflow for biomarker discovery in kidney cancer. Clin Proteomics. 2018;15:42.","journal-title":"Clin Proteomics"},{"issue":"1","key":"9500_CR73","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1039\/D0MO00072H","volume":"17","author":"L Krasny","year":"2021","unstructured":"Krasny L, Huang PH. Data-independent acquisition mass spectrometry (DIA-MS) for proteomic applications in oncology. Mol Omics. 2021;17(1):29\u201342.","journal-title":"Mol Omics"},{"issue":"1","key":"9500_CR74","doi-asserted-by":"publisher","first-page":"2539","DOI":"10.1038\/s41467-021-22759-z","volume":"12","author":"RB Kitata","year":"2021","unstructured":"Kitata RB, et al. A data-independent acquisition-based global phosphoproteomics system enables deep profiling. Nat Commun. 2021;12(1):2539.","journal-title":"Nat Commun"},{"issue":"1","key":"9500_CR75","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1186\/s12014-022-09359-9","volume":"19","author":"Y Wang","year":"2022","unstructured":"Wang Y, et al. Optimized data-independent acquisition approach for proteomic analysis at single-cell level. Clin Proteomics. 2022;19(1):24.","journal-title":"Clin Proteomics"},{"issue":"15","key":"9500_CR76","doi-asserted-by":"publisher","first-page":"2568","DOI":"10.1002\/pmic.201400454","volume":"15","author":"Y Zhang","year":"2015","unstructured":"Zhang Y, et al. Unrestricted modification search reveals lysine methylation as major modification induced by tissue formalin fixation and paraffin embedding. Proteomics. 2015;15(15):2568\u201379.","journal-title":"Proteomics"},{"issue":"2","key":"9500_CR77","doi-asserted-by":"publisher","first-page":"O111014902","DOI":"10.1074\/mcp.O111.014902","volume":"11","author":"B Ma","year":"2012","unstructured":"Ma B, Johnson R. De novo sequencing and homology searching. Mol Cell Proteomics. 2012;11(2):O111014902.","journal-title":"Mol Cell Proteomics"},{"key":"9500_CR78","doi-asserted-by":"publisher","DOI":"10.1002\/mas.21775","author":"NV Zakharova","year":"2022","unstructured":"Zakharova NV, et al. Mass spectrometric studies of the variety of beta-amyloid proteoforms in Alzheimer\u2019s disease. Mass Spectrom Rev. 2022. https:\/\/doi.org\/10.1002\/mas.21775.","journal-title":"Mass Spectrom Rev"},{"issue":"1","key":"9500_CR79","doi-asserted-by":"publisher","first-page":"6434","DOI":"10.1038\/s41467-021-26553-9","volume":"12","author":"L Radamaker","year":"2021","unstructured":"Radamaker L, et al. Role of mutations and post-translational modifications in systemic AL amyloidosis studied by cryo-EM. Nat Commun. 2021;12(1):6434.","journal-title":"Nat Commun"},{"issue":"1","key":"9500_CR80","doi-asserted-by":"publisher","first-page":"254","DOI":"10.1038\/s41375-018-0194-x","volume":"33","author":"S Kumar","year":"2019","unstructured":"Kumar S, et al. Assay to rapidly screen for immunoglobulin light chain glycosylation: a potential path to earlier AL diagnosis for a subset of patients. Leukemia. 2019;33(1):254\u20137.","journal-title":"Leukemia"},{"issue":"4","key":"9500_CR81","doi-asserted-by":"publisher","first-page":"1060","DOI":"10.1038\/s41375-019-0405-0","volume":"33","author":"S Kumar","year":"2019","unstructured":"Kumar S, et al. Correction: assay to rapidly screen for immunoglobulin light chain glycosylation: a potential path to earlier AL diagnosis for a subset of patients. Leukemia. 2019;33(4):1060.","journal-title":"Leukemia"},{"issue":"1","key":"9500_CR82","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1080\/13506129.2022.2095618","volume":"30","author":"J Baur","year":"2023","unstructured":"Baur J, et al. Identification of AL proteins from 10 lambda-AL amyloidosis patients by mass spectrometry extracted from abdominal fat and heart tissue. Amyloid. 2023;30(1):27\u201337.","journal-title":"Amyloid"},{"issue":"Pt B","key":"9500_CR83","doi-asserted-by":"publisher","first-page":"234","DOI":"10.1016\/j.jprot.2015.04.016","volume":"127","author":"M Vila-Rico","year":"2015","unstructured":"Vila-Rico M, et al. Quantitative analysis of post-translational modifications in human serum transthyretin associated with familial amyloidotic polyneuropathy by targeted LC-MS and intact protein MS. J Proteomics. 2015;127(Pt B):234\u201346.","journal-title":"J Proteomics"},{"issue":"7","key":"9500_CR84","doi-asserted-by":"publisher","first-page":"1768","DOI":"10.3390\/cells10071768","volume":"10","author":"E Wieczorek","year":"2021","unstructured":"Wieczorek E, Ozyhar A. Transthyretin: from structural stability to osteoarticular and cardiovascular diseases. Cells. 2021;10(7):1768.","journal-title":"Cells"},{"issue":"4","key":"9500_CR85","doi-asserted-by":"publisher","first-page":"632","DOI":"10.1016\/j.jaccao.2020.08.013","volume":"2","author":"TV Kourelis","year":"2020","unstructured":"Kourelis TV, et al. A proteomic atlas of cardiac amyloid plaques. JACC CardioOncol. 2020;2(4):632\u201343.","journal-title":"JACC CardioOncol"},{"issue":"1","key":"9500_CR86","doi-asserted-by":"publisher","first-page":"146","DOI":"10.1186\/s12883-019-1369-4","volume":"19","author":"EP Azevedo","year":"2019","unstructured":"Azevedo EP, et al. Inflammatory profiling of patients with familial amyloid polyneuropathy. BMC Neurol. 2019;19(1):146.","journal-title":"BMC Neurol"},{"issue":"5","key":"9500_CR87","doi-asserted-by":"publisher","first-page":"399","DOI":"10.1093\/abbs\/gmv131","volume":"48","author":"J Sheng","year":"2016","unstructured":"Sheng J, Xu Z. Three decades of research on angiogenin: a review and perspective. Acta Biochim Biophys Sin. 2016;48(5):399\u2013410.","journal-title":"Acta Biochim Biophys Sin"},{"issue":"3","key":"9500_CR88","doi-asserted-by":"publisher","DOI":"10.1038\/cddis.2014.45","volume":"5","author":"R Del Giudice","year":"2014","unstructured":"Del Giudice R, et al. Amyloidogenic variant of apolipoprotein A-I elicits cellular stress by attenuating the protective activity of angiogenin. Cell Death Dis. 2014;5(3): e1097.","journal-title":"Cell Death Dis"}],"container-title":["Clinical Proteomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12014-024-09500-w.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12014-024-09500-w\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12014-024-09500-w.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,3]],"date-time":"2024-07-03T14:13:54Z","timestamp":1720016034000},"score":1,"resource":{"primary":{"URL":"https:\/\/clinicalproteomicsjournal.biomedcentral.com\/articles\/10.1186\/s12014-024-09500-w"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,7,3]]},"references-count":88,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2024,12]]}},"alternative-id":["9500"],"URL":"https:\/\/doi.org\/10.1186\/s12014-024-09500-w","relation":{"references":[{"id-type":"uri","id":"","asserted-by":"subject"}]},"ISSN":["1542-6416","1559-0275"],"issn-type":[{"value":"1542-6416","type":"print"},{"value":"1559-0275","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,7,3]]},"assertion":[{"value":"18 March 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 June 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 July 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Drs. Joshua Fischer, Cristina Silvescu, and Shannon Cornett work for the company Bruker, which commercializes the instrumentation utilized for Figure 6.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"47"}}