{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T21:33:05Z","timestamp":1791495185900,"version":"4.3.4"},"reference-count":86,"publisher":"Wiley","issue":"2-3","license":[{"start":{"date-parts":[[2025,9,16]],"date-time":"2025-09-16T00:00:00Z","timestamp":1757980800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2025,9,16]],"date-time":"2025-09-16T00:00:00Z","timestamp":1757980800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/100000062","name":"National Institute of Diabetes and Digestive and Kidney Diseases","doi-asserted-by":"publisher","award":["R01 DK138335"],"award-info":[{"award-number":["R01 DK138335"]}],"id":[{"id":"10.13039\/100000062","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000062","name":"National Institute of Diabetes and Digestive and Kidney Diseases","doi-asserted-by":"publisher","award":["R01 DK133881"],"award-info":[{"award-number":["R01 DK133881"]}],"id":[{"id":"10.13039\/100000062","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000062","name":"National Institute of Diabetes and Digestive and Kidney Diseases","doi-asserted-by":"publisher","award":["U01 DK127505"],"award-info":[{"award-number":["U01 DK127505"]}],"id":[{"id":"10.13039\/100000062","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000062","name":"National Institute of Diabetes and Digestive and Kidney Diseases","doi-asserted-by":"publisher","award":["U01 DK127786"],"award-info":[{"award-number":["U01 DK127786"]}],"id":[{"id":"10.13039\/100000062","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000062","name":"National Institute of Diabetes and Digestive and Kidney Diseases","doi-asserted-by":"publisher","award":["R01 DK060581"],"award-info":[{"award-number":["R01 DK060581"]}],"id":[{"id":"10.13039\/100000062","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["analyticalsciencejournals.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Proteomics"],"published-print":{"date-parts":[[2026,2]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:label\/>\n                    <jats:p>Extracellular vesicles (EVs) are membrane\u2010bound particles secreted by cells, playing crucial roles in intercellular communication. The composition of EVs can undergo changes in response to stress and disease conditions, making them excellent biomarker candidates. However, extracting protein information from EVs can be challenging due to their low abundance in complex biofluids and copurification with contaminant proteins and particles. Techniques to enrich EVs have their strengths and limitations, without one being able to purify EVs to complete homogeneity. This can lead to compromised recovery rates and increased complexity, making data interpretation difficult. In this viewpoint article, we explore the concept that better characterization of EV composition, followed by quantification of EV proteins in complex samples, might be a more viable route for biomarker development. Mass spectrometers can provide reproducible deep coverage of the EV proteome, despite sample impurities. This paradigm shift presents opportunities to integrate advanced bioinformatics tools to refine the EV proteome landscape, identify novel biomarkers, and streamline validation processes in biomarker development. By focusing on leveraging technology rather than achieving absolute purity, this approach can transform current practices and open opportunities for robust biomarker discovery. Herein, we highlight not only such opportunities but also challenges to implement this concept.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>\n                      <jats:list list-type=\"bullet\">\n                        <jats:list-item>\n                          <jats:p>Extracellular vesicles (EVs) have enormous potential as biomarkers of diseases, as they can carry signatures of the cells they are derived from and the pathogenesis process.<\/jats:p>\n                        <\/jats:list-item>\n                        <jats:list-item>\n                          <jats:p>Biofluids, such as blood plasma, are highly complex and contain many components with physicochemical properties similar to those of EVs, making it challenging to obtain pure EV fractions.<\/jats:p>\n                        <\/jats:list-item>\n                        <jats:list-item>\n                          <jats:p>Challenges in obtaining pure preparations\u00a0represent a main hurdle for studying EVs, and their components are potential biomarkers.<\/jats:p>\n                        <\/jats:list-item>\n                        <jats:list-item>\n                          <jats:p>This article\u00a0explores the concept of studying EV proteins within complex samples, discussing opportunities and needs to move this field forward.<\/jats:p>\n                        <\/jats:list-item>\n                      <\/jats:list>\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1002\/pmic.70036","type":"journal-article","created":{"date-parts":[[2025,9,16]],"date-time":"2025-09-16T09:45:29Z","timestamp":1758015929000},"page":"9-20","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Challenges and Opportunities in State\u2010of\u2010the\u2010Art Proteomics Analysis for Biomarker Development From Plasma Extracellular Vesicles"],"prefix":"10.1002","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3534-7744","authenticated-orcid":false,"given":"Panshak P.","family":"Dakup","sequence":"first","affiliation":[{"name":"Biological Sciences Division Pacific Northwest National Laboratory  Richland Washington USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3475-5191","authenticated-orcid":false,"given":"Ivo Diaz","family":"Ludovico","sequence":"additional","affiliation":[{"name":"Biological Sciences Division Pacific Northwest National Laboratory  Richland Washington USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2189-9049","authenticated-orcid":false,"given":"Youngki","family":"You","sequence":"additional","affiliation":[{"name":"Biological Sciences Division Pacific Northwest National Laboratory  Richland Washington USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2834-7458","authenticated-orcid":false,"given":"Chaitra","family":"Rao","sequence":"additional","affiliation":[{"name":"Department of Pediatrics Indiana University School of Medicine  Indianapolis Indiana USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1550-1655","authenticated-orcid":false,"given":"Javier","family":"Flores","sequence":"additional","affiliation":[{"name":"Biological Sciences Division Pacific Northwest National Laboratory  Richland Washington USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8384-1926","authenticated-orcid":false,"given":"Lisa M.","family":"Bramer","sequence":"additional","affiliation":[{"name":"Biological Sciences Division Pacific Northwest National Laboratory  Richland Washington USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3829-9207","authenticated-orcid":false,"given":"Marian","family":"Rewers","sequence":"additional","affiliation":[{"name":"Barbara Davis Center For Diabetes School of Medicine University of Colorado Anschutz Medical Campus  Aurora Colorado USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4744-2397","authenticated-orcid":false,"given":"Bobbie\u2010Jo M.","family":"Webb\u2010Robertson","sequence":"additional","affiliation":[{"name":"Biological Sciences Division Pacific Northwest National Laboratory  Richland Washington USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6049-3968","authenticated-orcid":false,"given":"Thomas O.","family":"Metz","sequence":"additional","affiliation":[{"name":"Biological Sciences Division Pacific Northwest National Laboratory  Richland Washington USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5013-6075","authenticated-orcid":false,"given":"Raghavendra G.","family":"Mirmira","sequence":"additional","affiliation":[{"name":"Department of Medicine and the Kovler Diabetes Center The University of Chicago  Chicago Illinois USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4393-954X","authenticated-orcid":false,"given":"Emily K.","family":"Sims","sequence":"additional","affiliation":[{"name":"Department of Pediatrics Indiana University School of Medicine  Indianapolis Indiana USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4056-2695","authenticated-orcid":false,"given":"Ernesto S.","family":"Nakayasu","sequence":"additional","affiliation":[{"name":"Biological Sciences Division Pacific Northwest National Laboratory  Richland Washington USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2025,9,16]]},"reference":[{"key":"e_1_2_12_2_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41577-022-00763-8"},{"key":"e_1_2_12_3_1","doi-asserted-by":"publisher","DOI":"10.3390\/ijms20225695"},{"key":"e_1_2_12_4_1","article-title":"Extracellular Vesicles\u2010Connecting Kingdoms","volume":"10","author":"Ciferri M. C.","year":"2021","journal-title":"International Journal of Molecular Sciences"},{"key":"e_1_2_12_5_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0285440"},{"key":"e_1_2_12_6_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41419-024-07003-y"},{"key":"e_1_2_12_7_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41392-024-01735-1"},{"key":"e_1_2_12_8_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.molmet.2022.101545"},{"key":"e_1_2_12_9_1","doi-asserted-by":"publisher","DOI":"10.3201\/eid2608.191042"},{"key":"e_1_2_12_10_1","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms12010116"},{"key":"e_1_2_12_11_1","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.ado6894"},{"key":"e_1_2_12_12_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.xcrm.2025.101999"},{"key":"e_1_2_12_13_1","doi-asserted-by":"publisher","DOI":"10.1002\/mds.28639"},{"key":"e_1_2_12_14_1","doi-asserted-by":"publisher","DOI":"10.1001\/jamaneurol.2023.4398"},{"key":"e_1_2_12_15_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2408949121"},{"key":"e_1_2_12_16_1","doi-asserted-by":"publisher","DOI":"10.1212\/NXI.0000000000000866"},{"key":"e_1_2_12_17_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-024-02937-4"},{"key":"e_1_2_12_18_1","doi-asserted-by":"publisher","DOI":"10.3390\/bioengineering9030105"},{"key":"e_1_2_12_19_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.xcrm.2023.101093"},{"key":"e_1_2_12_20_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41597-023-02748-1"},{"key":"e_1_2_12_21_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00125-024-06313-2"},{"key":"e_1_2_12_22_1","doi-asserted-by":"publisher","DOI":"10.3389\/fendo.2022.971313"},{"key":"e_1_2_12_23_1","doi-asserted-by":"publisher","DOI":"10.18632\/oncotarget.26620"},{"key":"e_1_2_12_24_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature14581"},{"key":"e_1_2_12_25_1","doi-asserted-by":"publisher","DOI":"10.1080\/20013078.2020.1750202"},{"key":"e_1_2_12_26_1","doi-asserted-by":"publisher","DOI":"10.3390\/cancers15010177"},{"key":"e_1_2_12_27_1","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.M117.068577"},{"key":"e_1_2_12_28_1","doi-asserted-by":"publisher","DOI":"10.3109\/07357907.2015.1081921"},{"key":"e_1_2_12_29_1","first-page":"1719","article-title":"Proteomics Profiling of Plasma Exosomes in Epithelial Ovarian Cancer: A Potential Role in the Coagulation Cascade, Diagnosis and Prognosis","volume":"54","author":"Zhang W.","year":"2019","journal-title":"International Journal of Oncology"},{"key":"e_1_2_12_30_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1618088114"},{"key":"e_1_2_12_31_1","doi-asserted-by":"publisher","DOI":"10.1038\/s42003-022-04349-x"},{"key":"e_1_2_12_32_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-22913-7"},{"key":"e_1_2_12_33_1","doi-asserted-by":"publisher","DOI":"10.1080\/20013078.2018.1535750"},{"key":"e_1_2_12_34_1","doi-asserted-by":"publisher","DOI":"10.1002\/jev2.12404"},{"key":"e_1_2_12_35_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ymeth.2015.04.008"},{"key":"e_1_2_12_36_1","doi-asserted-by":"publisher","DOI":"10.1002\/jev2.12122"},{"key":"e_1_2_12_37_1","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.86394"},{"key":"e_1_2_12_38_1","doi-asserted-by":"publisher","DOI":"10.1002\/jex2.138"},{"key":"e_1_2_12_39_1","doi-asserted-by":"publisher","DOI":"10.3390\/proteomes7020018"},{"key":"e_1_2_12_40_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ejcb.2022.151227"},{"key":"e_1_2_12_41_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jproteome.5c00149"},{"key":"e_1_2_12_42_1","doi-asserted-by":"publisher","DOI":"10.3402\/jev.v4.29509"},{"key":"e_1_2_12_43_1","doi-asserted-by":"publisher","DOI":"10.1038\/srep23978"},{"key":"e_1_2_12_44_1","doi-asserted-by":"publisher","DOI":"10.1038\/srep14664"},{"key":"e_1_2_12_45_1","doi-asserted-by":"publisher","DOI":"10.1002\/cbic.201400043"},{"key":"e_1_2_12_46_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ymeth.2015.05.028"},{"key":"e_1_2_12_47_1","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2014.00442"},{"key":"e_1_2_12_48_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.trac.2019.06.037"},{"key":"e_1_2_12_49_1","doi-asserted-by":"publisher","DOI":"10.1021\/acsomega.3c07427"},{"key":"e_1_2_12_50_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-24163-y"},{"key":"e_1_2_12_51_1","doi-asserted-by":"publisher","DOI":"10.1002\/jev2.70024"},{"key":"e_1_2_12_52_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-025-60595-7"},{"key":"e_1_2_12_53_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jproteome.0c00151"},{"key":"e_1_2_12_54_1","doi-asserted-by":"publisher","DOI":"10.1038\/srep33641"},{"key":"e_1_2_12_55_1","doi-asserted-by":"publisher","DOI":"10.1002\/pmic.202400025"},{"key":"e_1_2_12_56_1","doi-asserted-by":"publisher","DOI":"10.1021\/pr800225z"},{"key":"e_1_2_12_57_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.chroma.2011.04.063"},{"key":"e_1_2_12_58_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.langmuir.5b00095"},{"key":"e_1_2_12_59_1","doi-asserted-by":"publisher","DOI":"10.1002\/adbi.201900310"},{"key":"e_1_2_12_60_1","doi-asserted-by":"publisher","DOI":"10.1038\/s43586-023-00240-z"},{"key":"e_1_2_12_61_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-36932-z"},{"key":"e_1_2_12_62_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1462-5822.2009.01405.x"},{"key":"e_1_2_12_63_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.nano.2017.03.010"},{"key":"e_1_2_12_64_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0403453101"},{"key":"e_1_2_12_65_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12929-018-0494-5"},{"key":"e_1_2_12_66_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.rpth.2023.100177"},{"key":"e_1_2_12_67_1","doi-asserted-by":"publisher","DOI":"10.1002\/mas.21749"},{"key":"e_1_2_12_68_1","doi-asserted-by":"publisher","DOI":"10.1021\/acsmeasuresciau.3c00068"},{"key":"e_1_2_12_69_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.analchem.3c04497"},{"key":"e_1_2_12_70_1","doi-asserted-by":"publisher","DOI":"10.1021\/cr3003533"},{"key":"e_1_2_12_71_1","doi-asserted-by":"publisher","DOI":"10.1038\/msb.2008.61"},{"key":"e_1_2_12_72_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.2015"},{"key":"e_1_2_12_73_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.2329"},{"key":"e_1_2_12_74_1","doi-asserted-by":"publisher","DOI":"10.18632\/oncotarget.13634"},{"key":"e_1_2_12_75_1","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.O112.020131"},{"key":"e_1_2_12_76_1","doi-asserted-by":"publisher","DOI":"10.3390\/ijms161226120"},{"key":"e_1_2_12_77_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jprot.2014.10.017"},{"key":"e_1_2_12_78_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13054-024-05000-3"},{"key":"e_1_2_12_79_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-39347-y"},{"key":"e_1_2_12_80_1","doi-asserted-by":"publisher","DOI":"10.1214\/ss\/1009213726"},{"key":"e_1_2_12_81_1","doi-asserted-by":"publisher","DOI":"10.1002\/1878-0261.13362"},{"key":"e_1_2_12_82_1","article-title":"Integrating Machine Learning With Microfluidic Technologies for Proteomic Profiling of Extracellular Vesicles in Triple\u2010Negative Breast Cancer","volume":"84","author":"Kim M. W.","year":"2024","journal-title":"Cancer Research"},{"key":"e_1_2_12_83_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12964-023-01344-5"},{"key":"e_1_2_12_84_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.analchem.4c07016"},{"key":"e_1_2_12_85_1","doi-asserted-by":"publisher","DOI":"10.1053\/j.gastro.2020.11.046"},{"key":"e_1_2_12_86_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-03367-w"},{"key":"e_1_2_12_87_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-024-02559-1"}],"container-title":["PROTEOMICS"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/analyticalsciencejournals.onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/pmic.70036","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/analyticalsciencejournals.onlinelibrary.wiley.com\/doi\/full-xml\/10.1002\/pmic.70036","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/analyticalsciencejournals.onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/pmic.70036","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,2]],"date-time":"2026-07-02T17:45:00Z","timestamp":1783014300000},"score":1,"resource":{"primary":{"URL":"https:\/\/analyticalsciencejournals.onlinelibrary.wiley.com\/doi\/10.1002\/pmic.70036"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,9,16]]},"references-count":86,"journal-issue":{"issue":"2-3","published-print":{"date-parts":[[2026,2]]}},"alternative-id":["10.1002\/pmic.70036"],"URL":"https:\/\/doi.org\/10.1002\/pmic.70036","archive":["Portico"],"relation":{},"ISSN":["1615-9853","1615-9861"],"issn-type":[{"value":"1615-9853","type":"print"},{"value":"1615-9861","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,9,16]]},"assertion":[{"value":"2025-05-20","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-08-20","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-09-16","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}