{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T15:18:33Z","timestamp":1787066313176,"version":"build-2736575974"},"reference-count":95,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2020,12,1]],"date-time":"2020-12-01T00:00:00Z","timestamp":1606780800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"content-domain":{"domain":["www.atsjournals.org"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2020,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Sarcoidosis is a multisystem disease with heterogeneity in manifestations and outcomes. System-level studies leveraging \u201comics\u201d technologies are expected to define mechanisms contributing to sarcoidosis heterogeneous manifestations and course. With improvements in mass spectrometry (MS) and bioinformatics, it is possible to study protein abundance for a large number of proteins simultaneously. Contemporary fast-scanning MS enables the acquisition of spectral data for deep coverage of the proteins with data-dependent or data-independent acquisition MS modes. Studies leveraging MS-based proteomics in sarcoidosis have characterized BAL fluid (BALF), alveolar macrophages, plasma, and exosomes. These studies identified several differentially expressed proteins, including protocadherin-2 precursor, annexin A2, pulmonary surfactant A2, complement factors C3, vitamin-D\u2013binding protein, cystatin B, and amyloid P, comparing subjects with sarcoidosis with control subjects. Other studies identified ceruloplasmin, complement factors B, C3, and 1, and others with differential abundance in sarcoidosis compared with other interstitial lung diseases. Using quantitative proteomics, most recent studies found differences in PI3K\/Akt\/mTOR, MAP kinase, pluripotency-associated transcriptional factor, and hypoxia response pathways. Other studies identified increased clathrin-mediated endocytosis and Fc\u03b3 receptor\u2013mediated phagocytosis pathways in sarcoidosis alveolar macrophages. Although studies in mixed BAL and blood cells or plasma are limited, some of the changes in lung compartment are detected in the blood cells and plasma. We review proteomics for sarcoidosis with a focus on the existing MS data acquisition strategies, bioinformatics for spectral data analysis to infer protein identity and quantity, unique aspects about biospecimen collection and processing for lung-related proteomics, and proteomics studies conducted to date in sarcoidosis.<\/jats:p>","DOI":"10.1165\/rcmb.2020-0070ps","type":"journal-article","created":{"date-parts":[[2020,8,17]],"date-time":"2020-08-17T16:05:47Z","timestamp":1597680347000},"page":"727-738","update-policy":"https:\/\/doi.org\/10.1164\/crossmarkpolicies","source":"Crossref","is-referenced-by-count":23,"title":["Application of Proteomics in Sarcoidosis"],"prefix":"10.1093","volume":"63","author":[{"given":"Candance R.","family":"Guerrero","sequence":"first","affiliation":[{"name":"Department of Biochemistry, Molecular Biology, and Biophysics, College of Biological Sciences and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lisa A.","family":"Maier","sequence":"additional","affiliation":[{"name":"Division of Environmental and Occupational Health Sciences, National Jewish Health, Denver, Colorado"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timothy J.","family":"Griffin","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Molecular Biology, and Biophysics, College of Biological Sciences and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"LeeAnn","family":"Higgins","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Molecular Biology, and Biophysics, College of Biological Sciences and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charles P.","family":"Najt","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Molecular Biology, and Biophysics, College of Biological Sciences and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David M.","family":"Perlman","sequence":"additional","affiliation":[{"name":"Division of Pulmonary, Critical Care, and Sleep Medicine, University of Minnesota, Minneapolis, Minnesota; and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1294-6181","authenticated-orcid":false,"given":"Maneesh","family":"Bhargava","sequence":"additional","affiliation":[{"name":"Division of Pulmonary, Critical Care, and Sleep Medicine, University of Minnesota, Minneapolis, Minnesota; and"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,12,1]]},"reference":[{"key":"2026021100444590300_bib1","doi-asserted-by":"crossref","first-page":"S415","DOI":"10.1513\/AnnalsATS.201707-563OT","article-title":"Executive summary of the NHLBI workshop report: leveraging current scientific advancements to understand sarcoidosis variability and improve 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