{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T18:49:26Z","timestamp":1792003766359,"version":"4.4.0"},"reference-count":43,"publisher":"American Chemical Society (ACS)","issue":"9","license":[{"start":{"date-parts":[[2015,8,13]],"date-time":"2015-08-13T00:00:00Z","timestamp":1439424000000},"content-version":"vor","delay-in-days":365,"URL":"https:\/\/pubs.acs.org\/page\/policy\/authorchoice_termsofuse.html"}],"funder":[{"DOI":"10.13039\/100000025","name":"National Institute of Mental Health","doi-asserted-by":"publisher","award":["MH067880"],"award-info":[{"award-number":["MH067880"]}],"id":[{"id":"10.13039\/100000025","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000025","name":"National Institute of Mental Health","doi-asserted-by":"publisher","award":["MH091676"],"award-info":[{"award-number":["MH091676"]}],"id":[{"id":"10.13039\/100000025","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000025","name":"National Institute of Mental Health","doi-asserted-by":"publisher","award":["MH099799"],"award-info":[{"award-number":["MH099799"]}],"id":[{"id":"10.13039\/100000025","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000050","name":"National Heart, Lung, and Blood Institute","doi-asserted-by":"publisher","award":["HHSN268201000035C"],"award-info":[{"award-number":["HHSN268201000035C"]}],"id":[{"id":"10.13039\/100000050","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000052","name":"NIH Office of the Director","doi-asserted-by":"publisher","award":["OD000458"],"award-info":[{"award-number":["OD000458"]}],"id":[{"id":"10.13039\/100000052","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["P41 GM103533"],"award-info":[{"award-number":["P41 GM103533"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/na","name":"Hahn Family Foundation","doi-asserted-by":"publisher","award":["NA"],"award-info":[{"award-number":["NA"]}],"id":[{"id":"10.13039\/na","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,9,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Mass spectrometric strategies to identify protein subpopulations involved in specific biological functions rely on covalently tagging biotin to proteins using various chemical modification methods. The biotin tag is primarily used for enrichment of the targeted subpopulation for subsequent mass spectrometry (MS) analysis. A limitation of these strategies is that MS analysis does not easily discriminate unlabeled contaminants from the labeled protein subpopulation under study. To solve this problem, we developed a flexible method that only relies on direct MS detection of biotin-tagged proteins called \u201cDirect Detection of Biotin-containing Tags\u201d (DiDBiT). Compared with conventional targeted proteomic strategies, DiDBiT improves direct detection of biotinylated proteins \u223c200 fold. We show that DiDBiT is applicable to several protein labeling protocols in cell culture and in vivo using cell permeable NHS-biotin and incorporation of the noncanonical amino acid, azidohomoalanine (AHA), into newly synthesized proteins, followed by click chemistry tagging with biotin. We demonstrate that DiDBiT improves the direct detection of biotin-tagged newly synthesized peptides more than 20-fold compared to conventional methods. With the increased sensitivity afforded by DiDBiT, we demonstrate the MS detection of newly synthesized proteins labeled in vivo in the rodent nervous system with unprecedented temporal resolution as short as 3 h.<\/jats:p>","DOI":"10.1021\/pr5002862","type":"journal-article","created":{"date-parts":[[2014,8,13]],"date-time":"2014-08-13T06:11:08Z","timestamp":1407910268000},"page":"3966-3978","source":"Crossref","is-referenced-by-count":138,"title":["Direct Detection of Biotinylated\nProteins by Mass\nSpectrometry"],"prefix":"10.1021","volume":"13","author":[{"given":"Lucio Matias","family":"Schiapparelli","sequence":"first","affiliation":[{"name":"The Scripps Research Institute , , , ,","place":["La Jolla, California, United States, 92037"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel B.","family":"McClatchy","sequence":"additional","affiliation":[{"name":"The Scripps Research Institute , , , ,","place":["La Jolla, California, United States, 92037"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Han-Hsuan","family":"Liu","sequence":"additional","affiliation":[{"name":"The Scripps Research Institute , , , ,","place":["La Jolla, California, United States, 92037"]},{"name":"The Scripps Research Institute , , , ,","place":["La Jolla, California, United States, 92037"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pranav","family":"Sharma","sequence":"additional","affiliation":[{"name":"The Scripps Research Institute , , , ,","place":["La Jolla, California, United States, 92037"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"suffix":"III","given":"John R.","family":"Yates","sequence":"additional","affiliation":[{"name":"The Scripps Research Institute , , , ,","place":["La Jolla, California, United States, 92037"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hollis T.","family":"Cline","sequence":"additional","affiliation":[{"name":"The Scripps Research Institute , , , ,","place":["La Jolla, California, United States, 92037"]},{"name":"The Scripps Research Institute , , , ,","place":["La Jolla, California, United States, 92037"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2014,8,13]]},"reference":[{"issue":"39","key":"2026090223330048100_cit1","doi-asserted-by":"crossref","first-page":"26518","DOI":"10.1074\/jbc.M803337200","article-title":"Cell surface proteomics identifies molecules functionally\nlinked to tumor cell intravasation","volume":"283","author":"Conn","year":"2008","journal-title":"J. Biol.\nChem."},{"issue":"29","key":"2026090223330048100_cit2","doi-asserted-by":"crossref","first-page":"9251","DOI":"10.1021\/ja801445p","article-title":"Protein\u2013protein interaction\ndetection in vitro and in cells by proximity biotinylation","volume":"130","author":"Fernandez-Suarez","year":"2008","journal-title":"J. Am. Chem. Soc."},{"issue":"2","key":"2026090223330048100_cit3","doi-asserted-by":"crossref","first-page":"e52823","DOI":"10.1371\/journal.pone.0052823","article-title":"Imaging\ntrans-cellular neurexin-neuroligin interactions by enzymatic probe\nligation","volume":"8","author":"Liu","year":"2013","journal-title":"PLoS One"},{"issue":"4","key":"2026090223330048100_cit4","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1016\/j.jprot.2011.01.010","article-title":"The accessible cerebral vascular\nproteome in a mouse model of cerebral beta-amyloidosis","volume":"74","author":"Roesli","year":"2011","journal-title":"J. Proteomics"},{"issue":"1","key":"2026090223330048100_cit5","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1038\/nprot.2006.29","article-title":"In vivo protein biotinylation and\nsample preparation for the proteomic identification of organ- and\ndisease-specific antigens accessible from the vasculature","volume":"1","author":"Roesli","year":"2006","journal-title":"Nat. Protoc."},{"issue":"3","key":"2026090223330048100_cit6","doi-asserted-by":"crossref","first-page":"508","DOI":"10.1016\/j.cell.2008.05.054","article-title":"Experience-dependent transfer of\nOtx2 homeoprotein into the visual cortex activates postnatal plasticity","volume":"134","author":"Sugiyama","year":"2008","journal-title":"Cell"},{"issue":"1","key":"2026090223330048100_cit7","doi-asserted-by":"crossref","first-page":"e85119","DOI":"10.1371\/journal.pone.0085119","article-title":"Membrane labeling of coral gastrodermal\ncells by biotinylation: the proteomic identification of surface proteins\ninvolving cnidaria-dinoflagellate endosymbiosis","volume":"9","author":"Li","year":"2014","journal-title":"PLoS One"},{"issue":"6","key":"2026090223330048100_cit8","doi-asserted-by":"crossref","first-page":"1155","DOI":"10.1038\/nprot.2013.065","article-title":"Relative quantification of proteasome\nactivity by activity-based protein profiling and LC-MS\/MS","volume":"8","author":"Li","year":"2013","journal-title":"Nat. Protoc."},{"issue":"3","key":"2026090223330048100_cit9","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1038\/nmeth.2368","article-title":"Proteome-wide\nmapping of cholesterol-interacting proteins in mammalian cells","volume":"10","author":"Hulce","year":"2013","journal-title":"Nat. Methods"},{"issue":"13","key":"2026090223330048100_cit10","doi-asserted-by":"crossref","first-page":"5406","DOI":"10.1158\/0008-5472.CAN-08-0999","article-title":"Comparative analysis of the membrane\nproteome of closely related metastatic and nonmetastatic tumor cells","volume":"69","author":"Roesli","year":"2009","journal-title":"Cancer Res."},{"issue":"3","key":"2026090223330048100_cit11","first-page":"108","article-title":"Comparative analysis of techniques to purify plasma\nmembrane proteins","volume":"21","author":"Weekes","year":"2010","journal-title":"J. Biomol. 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Cell Biol."},{"issue":"28","key":"2026090223330048100_cit15","doi-asserted-by":"crossref","first-page":"6571","DOI":"10.1021\/bi9007726","article-title":"Click chemistry\nand bioorthogonal reactions: unprecedented selectivity in the labeling\nof biological molecules","volume":"48","author":"Best","year":"2009","journal-title":"Biochemistry"},{"issue":"3","key":"2026090223330048100_cit16","doi-asserted-by":"crossref","first-page":"532","DOI":"10.1038\/nprot.2007.52","article-title":"Labeling,\ndetection and identification of newly synthesized\nproteomes with bioorthogonal non-canonical amino-acid tagging","volume":"2","author":"Dieterich","year":"2007","journal-title":"Nat. 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U.S.A."},{"issue":"4","key":"2026090223330048100_cit21","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1038\/nmeth.2401","article-title":"QuaNCAT: Quantitating\nproteome dynamics in primary cells","volume":"10","author":"Howden","year":"2013","journal-title":"Nat. Methods"},{"issue":"15\u201316","key":"2026090223330048100_cit22","doi-asserted-by":"crossref","first-page":"2464","DOI":"10.1002\/pmic.201200112","article-title":"Dopaminergic modulation of the hippocampal\nneuropil\nproteome identified by bioorthogonal noncanonical amino acid tagging\n(BONCAT)","volume":"12","author":"Hodas","year":"2012","journal-title":"Proteomics"},{"issue":"6","key":"2026090223330048100_cit23","doi-asserted-by":"crossref","first-page":"1502","DOI":"10.1074\/mcp.M111.015594","article-title":"Stable isotope labeling\nin zebrafish allows in vivo\nmonitoring of cardiac morphogenesis","volume":"12","author":"Konzer","year":"2013","journal-title":"Mol. 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Protoc."},{"issue":"1","key":"2026090223330048100_cit28","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1158\/0008-5472.CAN-09-2939","article-title":"A proteomic\napproach\nfor the identification of vascular markers of liver metastasis","volume":"70","author":"Borgia","year":"2010","journal-title":"Cancer Res."},{"issue":"5","key":"2026090223330048100_cit29","doi-asserted-by":"crossref","first-page":"584, 586,\n588","DOI":"10.2144\/000112171","article-title":"Differential recovery of biotinylated microbial proteins\nusing monomeric or polymeric avidin","volume":"40","author":"Khare","year":"2006","journal-title":"Biotechniques"},{"issue":"5","key":"2026090223330048100_cit30","doi-asserted-by":"crossref","first-page":"1654","DOI":"10.1002\/pmic.200500240","article-title":"Identification\nof S-nitrosylated proteins after chronic exposure of colon epithelial\ncells to deoxycholate","volume":"6","author":"Dall\u2019Agnol","year":"2006","journal-title":"Proteomics"},{"issue":"1\u20132","key":"2026090223330048100_cit31","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1016\/j.jim.2012.06.003","article-title":"Defining TNF-alpha\nand IL-1beta induced nascent proteins: combining bio-orthogonal non-canonical\namino acid tagging and proteomics","volume":"382","author":"Choi","year":"2012","journal-title":"J. Immunol.\nMethods"},{"issue":"3","key":"2026090223330048100_cit32","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1038\/85686","article-title":"Large-scale analysis\nof the yeast proteome by multidimensional protein identification technology","volume":"19","author":"Washburn","year":"2001","journal-title":"Nat. Biotechnol."},{"issue":"10","key":"2026090223330048100_cit33","first-page":"S174","article-title":"ProLuCID,\na fast and sensitive tandem mass spectra-based protein identification\nprogram","volume":"5","author":"Xu","year":"2006","journal-title":"Mol. Cell. Proteomics"},{"issue":"1","key":"2026090223330048100_cit34","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1021\/pr025556v","article-title":"Evaluation of multidimensional chromatography\ncoupled\nwith tandem mass spectrometry (LC\/LC-MS\/MS) for large-scale protein\nanalysis: the yeast proteome","volume":"2","author":"Peng","year":"2003","journal-title":"J. Proteome Res."},{"issue":"3","key":"2026090223330048100_cit35","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1021\/pr015514r","article-title":"Code developments to improve the\nefficiency of automated MS\/MS spectra interpretation","volume":"1","author":"Sadygov","year":"2002","journal-title":"J. Proteome Res."},{"key":"2026090223330048100_cit36","doi-asserted-by":"publisher","DOI":"10.1002\/0471250953.bi1304s16","article-title":"Validation of tandem mass spectrometry\ndatabase search results using DTASelect","author":"Cociorva","year":"2007","journal-title":"Curr.\nProtoc. Bioinf."},{"issue":"1","key":"2026090223330048100_cit37","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1021\/pr015504q","article-title":"DTASelect and\nContrast: tools for assembling and comparing protein identifications\nfrom shotgun proteomics","volume":"1","author":"Tabb","year":"2002","journal-title":"J. Proteome Res."},{"issue":"23","key":"2026090223330048100_cit38","doi-asserted-by":"crossref","first-page":"9819","DOI":"10.1021\/ac901335x","article-title":"Software tool for\nresearching annotations of proteins: open-source protein annotation\nsoftware with data visualization","volume":"81","author":"Bhatia","year":"2009","journal-title":"Anal. Chem."},{"issue":"3","key":"2026090223330048100_cit39","doi-asserted-by":"crossref","first-page":"736","DOI":"10.1182\/blood-2009-08-239004","article-title":"In vivo biotinylation of the vasculature\nin B-cell lymphoma identifies BST-2 as a target for antibody-based\ntherapy","volume":"115","author":"Schliemann","year":"2010","journal-title":"Blood"},{"issue":"5","key":"2026090223330048100_cit40","doi-asserted-by":"crossref","first-page":"e63191","DOI":"10.1371\/journal.pone.0063191","article-title":"Metabolic turnover\nof synaptic proteins: kinetics, interdependencies and implications\nfor synaptic maintenance","volume":"8","author":"Cohen","year":"2013","journal-title":"PLoS One"},{"issue":"14","key":"2026090223330048100_cit41","doi-asserted-by":"crossref","first-page":"4193","DOI":"10.1021\/ac0498563","article-title":"A model for\nrandom sampling and estimation of relative protein abundance in shotgun\nproteomics","volume":"76","author":"Liu","year":"2004","journal-title":"Anal. Chem."},{"issue":"10","key":"2026090223330048100_cit42","doi-asserted-by":"crossref","first-page":"715","DOI":"10.1038\/nchembio.200","article-title":"Cell-selective metabolic\nlabeling\nof proteins","volume":"5","author":"Ngo","year":"2009","journal-title":"Nat. Chem. 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