{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,28]],"date-time":"2026-10-28T02:42:13Z","timestamp":1793155333237,"version":"4.5.0"},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2021,11,22]],"date-time":"2021-11-22T00:00:00Z","timestamp":1637539200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"name":"University of Washington\u2019s (UW\u2019s) Proteomics Resource","award":["UWPR95794"],"award-info":[{"award-number":["UWPR95794"]}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 GM121818"],"award-info":[{"award-number":["R01 GM121818"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["P41 GM103533"],"award-info":[{"award-number":["P41 GM103533"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,5,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Objectives<\/jats:title>\n                  <jats:p>Standard implementations of amyloid typing by liquid chromatography\u2013tandem mass spectrometry use capabilities unavailable to most clinical laboratories. To improve accessibility of this testing, we explored easier approaches to tissue sampling and data processing.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>We validated a typing method using manual sampling in place of laser microdissection, pairing the technique with a semiquantitative measure of sampling adequacy. In addition, we created an open-source data processing workflow (Crux Pipeline) for clinical users.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Cases of amyloidosis spanning the major types were distinguishable with 100% specificity using measurements of individual amyloidogenic proteins or in combination with the ratio of \u03bb and \u03ba constant regions. Crux Pipeline allowed for rapid, batched data processing, integrating the steps of peptide identification, statistical confidence estimation, and label-free protein quantification.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>Accurate mass spectrometry\u2013based amyloid typing is possible without laser microdissection. To facilitate entry into solid tissue proteomics, newcomers can leverage manual sampling approaches in combination with Crux Pipeline and related tools.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/ajcp\/aqab185","type":"journal-article","created":{"date-parts":[[2021,9,21]],"date-time":"2021-09-21T03:11:22Z","timestamp":1632193882000},"page":"748-757","source":"Crossref","is-referenced-by-count":12,"title":["Tandem Mass Spectrometry\u2013Based Amyloid Typing Using Manual Microdissection and Open-Source Data Processing"],"prefix":"10.1093","volume":"157","author":[{"given":"William S","family":"Phipps","sequence":"first","affiliation":[{"name":"Department of Laboratory Medicine and Pathology , Seattle, WA , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kelly D","family":"Smith","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine and Pathology , Seattle, WA , USA"},{"name":"Department of Medicine , Seattle, WA , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Han-Yin","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of Genome Sciences, University of Washington , Seattle, WA , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Clark M","family":"Henderson","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine and Pathology , Seattle, WA , USA"},{"name":"Seagen , Bothel, WA , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hannah","family":"Pflaum","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine and Pathology , Seattle, WA , USA"},{"name":"Seattle Children\u2019s Hospital , Seattle, WA , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Melissa L","family":"Lerch","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine and Pathology , Seattle, WA , 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