{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T13:00:21Z","timestamp":1790600421440,"version":"4.1.0"},"reference-count":68,"publisher":"American Chemical Society (ACS)","issue":"9","license":[{"start":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T00:00:00Z","timestamp":1788912000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/100018703","name":"HORIZON EUROPE European Innovation Council","doi-asserted-by":"publisher","award":["101161281"],"award-info":[{"award-number":["101161281"]}],"id":[{"id":"10.13039\/100018703","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100018703","name":"HORIZON EUROPE European Innovation Council","doi-asserted-by":"publisher","award":["101161509"],"award-info":[{"award-number":["101161509"]}],"id":[{"id":"10.13039\/100018703","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000780","name":"European Commission","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001823","name":"Ministerstvo ?kolstv?, Ml?de?e a Telov?chovy","doi-asserted-by":"publisher","award":["00022985"],"award-info":[{"award-number":["00022985"]}],"id":[{"id":"10.13039\/501100001823","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Ministerstvo ?kolstv?, Ml?de?e a Telov?chovy","award":["CZ.02.01.01\/00\/ 22_008\/0004644"],"award-info":[{"award-number":["CZ.02.01.01\/00\/ 22_008\/0004644"]}]},{"name":"Ministerstvo ?kolstv?, Ml?de?e a Telov?chovy","award":["LM2023033"],"award-info":[{"award-number":["LM2023033"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Given the significant role of glycosylation in modulating protein structure and activity, glycoproteomics is gaining increased interest from the broad scientific community. Large-scale site-resolved N-glycoproteomics relies on automated MS2-based searches, but candidate glycopeptide assignments can remain ambiguous when isomeric or isobaric glycan structures, adducts, chemical modifications, in-source fragments, or incomplete MS2 evidence support more than one plausible interpretation. Here, we systematically categorize common challenges and misassignments in glycoproteomics and present a post-search validation workflow using Skyline software to identify and correct these. The workflow matches search-engine-derived candidate assignments to LC\u2013MS\/MS evidence for correct precursor monoisotope assignment, retention time behavior, and glycosite context. The workflow is demonstrated with Byonic-derived glycopeptide candidate lists and converts automated search results into curated, verifiable, site-resolved N-glycopeptide features for downstream quantification and reporting. We applied the workflow to data from 52 human serum samples, and reviewed 3,071 candidate N-glycopeptide IDs. From these, 1,722 MS2 candidate IDs were refuted as inconsistent with chromatographic and\/or precursor-level evidence. Curation added 320 glycopeptide features, comprising 152 MS1-supported composition-level assignments and 168 additional LC-resolved isomer features, yielding a final curated feature set of 1,436 N-glycopeptides across the serum N-glycoproteome. Together, these results show that reviewing the raw LC-MS\/MS data associated with search-engine results improves both the accuracy and comprehensiveness of detectable N-glycopeptides, supporting more transparent and reliable reporting. The curated dataset provides a resource for future method development, benchmarking and machine\u2013learning efforts directed at automated glycopeptide validation.<\/jats:p>","DOI":"10.1021\/jacsau.6c00875","type":"journal-article","created":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T16:02:02Z","timestamp":1788969722000},"page":"5478-5493","source":"Crossref","is-referenced-by-count":0,"title":["Post-Search Validation\nand Curation of Site-Resolved\nN-Glycoproteomics Data"],"prefix":"10.1021","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0009-0001-7199-6517","authenticated-orcid":true,"given":"Adam P.","family":"Urminsky","sequence":"first","affiliation":[{"name":"Masaryk Memorial Cancer Institute , , ,","place":["Brno, Czech Republic, 65653"]},{"name":"Masaryk University , , ,","place":["Brno, Czech Republic, 62500"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4440-9580","authenticated-orcid":true,"given":"Juan C.","family":"Rojas E.","sequence":"additional","affiliation":[{"name":"Leiden University Medical Centre , , ,","place":["Leiden, The Netherlands, 2333 ZA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lenka","family":"Hernychova","sequence":"additional","affiliation":[{"name":"Masaryk Memorial Cancer Institute , , ,","place":["Brno, Czech Republic, 65653"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7026-6750","authenticated-orcid":true,"given":"Noortje","family":"de Haan","sequence":"additional","affiliation":[{"name":"Leiden University Medical Centre , , ,","place":["Leiden, The Netherlands, 2333 ZA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,9,9]]},"reference":[{"key":"2026092808091846200_cit1","doi-asserted-by":"publisher","first-page":"48","DOI":"10.1038\/s43586-022-00128-4","article-title":"Glycoproteomics","volume":"2","author":"Bagdonaite","year":"2022","journal-title":"Nature Reviews Methods Primers"},{"key":"2026092808091846200_cit2","doi-asserted-by":"publisher","first-page":"346","DOI":"10.1038\/s41581-019-0129-4","article-title":"Glycosylation in health\nand disease","volume":"15","author":"Reily","year":"2019","journal-title":"Nature Reviews Nephrology"},{"key":"2026092808091846200_cit3","doi-asserted-by":"publisher","first-page":"267","DOI":"10.1021\/acs.analchem.9b04651","article-title":"Recent Advances\nin Glycoproteomic Analysis by Mass\nSpectrometry","volume":"92","author":"Suttapitugsakul","year":"2020","journal-title":"Analytical Chemistry"},{"key":"2026092808091846200_cit4","doi-asserted-by":"publisher","first-page":"56","DOI":"10.1007\/s00292-024-01390-x","article-title":"Advancements\nin mass spectrometry-based\nproteomics: a new era in pathology research and diagnostics","volume":"45","author":"Werner","year":"2024","journal-title":"Pathologie"},{"key":"2026092808091846200_cit5","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1186\/s12014-024-09452-1","article-title":"Recent developments in mass-spectrometry-based\ntargeted proteomics of clinical cancer biomarkers","volume":"21","author":"Wenk","year":"2024","journal-title":"Clinical Proteomics"},{"key":"2026092808091846200_cit6","doi-asserted-by":"publisher","first-page":"285","DOI":"10.1007\/s10719-015-9633-3","article-title":"A review of\nmethods for interpretation of glycopeptide tandem mass spectral data","volume":"33","author":"Hu","year":"2016","journal-title":"Glycoconjugate Journal"},{"key":"2026092808091846200_cit7","doi-asserted-by":"publisher","first-page":"540","DOI":"10.1038\/nrc3982","article-title":"Glycosylation in cancer: mechanisms\nand clinical implications","volume":"15","author":"Pinho","year":"2015","journal-title":"Nature Reviews Cancer"},{"key":"2026092808091846200_cit8","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1186\/s13045-024-01532-x","article-title":"Decoding the glycoproteome:\na new frontier for biomarker discovery in cancer","volume":"17","author":"He","year":"2024","journal-title":"Journal of Hematology & Oncology"},{"key":"2026092808091846200_cit9","doi-asserted-by":"publisher","first-page":"205","DOI":"10.1080\/19420862.2015.1117719","article-title":"Glycan analysis of\ntherapeutic glycoproteins","volume":"8","author":"Zhang","year":"2016","journal-title":"mAbs"},{"key":"2026092808091846200_cit10","doi-asserted-by":"publisher","DOI":"10.1016\/j.mcpro.2022.100205","article-title":"Multiattribute\nGlycan Identification and FDR Control for Glycoproteomics","volume":"21","author":"Polasky","year":"2022","journal-title":"Molecular & Cellular Proteomics"},{"key":"2026092808091846200_cit11","doi-asserted-by":"publisher","first-page":"345","DOI":"10.1093\/nsr\/nww019","article-title":"Advancements\nin mass spectrometry-based\nglycoproteomics and glycomics","volume":"3","author":"Lu","year":"2016","journal-title":"National Science\nReview"},{"key":"2026092808091846200_cit12","doi-asserted-by":"publisher","first-page":"6297","DOI":"10.1021\/acs.analchem.5b01121","article-title":"Carbamidomethylation\nSide Reactions May Lead to Glycan\nMisassignments in Glycopeptide Analysis","volume":"87","author":"Darula","year":"2015","journal-title":"Anal.\nChem."},{"key":"2026092808091846200_cit13","doi-asserted-by":"publisher","first-page":"2113","DOI":"10.1021\/acs.jproteome.0c00051","article-title":"Relative Retention Time Estimation Improves N-Glycopeptide Identifications\nby LC\u2013MS\/MS","volume":"19","author":"Klein","year":"2020","journal-title":"J. Proteome Res."},{"key":"2026092808091846200_cit14","doi-asserted-by":"publisher","first-page":"1515","DOI":"10.1038\/s41592-021-01306-0","article-title":"Precise,\nfast and comprehensive analysis of intact glycopeptides and modified\nglycans with pGlyco3","volume":"18","author":"Zeng","year":"2021","journal-title":"Nat. Methods"},{"key":"2026092808091846200_cit15","doi-asserted-by":"publisher","first-page":"13.20.1","DOI":"10.1002\/0471250953.bi1320s40","article-title":"Byonic: Advanced\nPeptide and Protein\nIdentification Software","volume":"40","author":"Bern","year":"2012","journal-title":"Current Protocols in\nBioinformatics"},{"key":"2026092808091846200_cit16","doi-asserted-by":"publisher","first-page":"438","DOI":"10.1038\/s41467-017-00535-2","article-title":"pGlyco\n2.0 Enables Precision N-Glycoproteomics with Comprehensive\nQuality Control and One-Step Mass Spectrometry for Intact Glycopeptide\nIdentification","volume":"8","author":"Liu","year":"2017","journal-title":"Nat. Commun."},{"key":"2026092808091846200_cit17","doi-asserted-by":"publisher","first-page":"1125","DOI":"10.1038\/s41592-020-0967-9","article-title":"Fast and\ncomprehensive N- and O-glycoproteomics\nanalysis with MSFragger-Glyco","volume":"17","author":"Polasky","year":"2020","journal-title":"Nat. Methods"},{"key":"2026092808091846200_cit18","doi-asserted-by":"publisher","first-page":"1900","DOI":"10.1038\/s41467-022-29530-y","article-title":"Glyco-Decipher enables\nglycan database-independent peptide matching and in-depth characterization\nof site-specific N-glycosylation","volume":"13","author":"Fang","year":"2022","journal-title":"Nat. Commun."},{"key":"2026092808091846200_cit19","doi-asserted-by":"publisher","first-page":"4046","DOI":"10.1038\/s41467-023-39699-5","article-title":"Glycopeptide database search and\nde novo sequencing with PEAKS GlycanFinder enable highly sensitive\nglycoproteomics","volume":"14","author":"Sun","year":"2023","journal-title":"Nat. Commun."},{"key":"2026092808091846200_cit20","doi-asserted-by":"publisher","first-page":"921","DOI":"10.1038\/s41592-021-01209-0","article-title":"StrucGP: de novo structural\nsequencing of site-specific N-glycan\non glycoproteins using a modularization strategy","volume":"18","author":"Shen","year":"2021","journal-title":"Nat. Methods"},{"key":"2026092808091846200_cit21","doi-asserted-by":"publisher","DOI":"10.1016\/j.mcpro.2025.100903","article-title":"Improving the Depth and Reliability of Glycopeptide\nIdentification Using Protein Prospector","volume":"24","author":"Chalkley","year":"2025","journal-title":"Molecular\n& Cellular Proteomics"},{"key":"2026092808091846200_cit22","doi-asserted-by":"publisher","first-page":"6168","DOI":"10.1038\/s41467-024-50338-5","article-title":"Expanding N-glycopeptide\nidentifications\nby modeling fragmentation, elution, and glycome connectivity","volume":"15","author":"Klein","year":"2024","journal-title":"Nat. Commun."},{"key":"2026092808091846200_cit23","doi-asserted-by":"publisher","first-page":"5268","DOI":"10.1038\/s41467-020-19052-w","article-title":"A Streamlined Pipeline\nfor Multiplexed Quantitative Site-Specific N-Glycoproteomics","volume":"11","author":"Fang","year":"2020","journal-title":"Nat. Commun."},{"key":"2026092808091846200_cit24","doi-asserted-by":"publisher","first-page":"7539","DOI":"10.1038\/s41467-022-35172-x","article-title":"pGlycoQuant with a\nDeep Residual Network for Quantitative\nGlycoproteomics at Intact Glycopeptide Level","volume":"13","author":"Kong","year":"2022","journal-title":"Nat. Commun."},{"key":"2026092808091846200_cit25","doi-asserted-by":"publisher","first-page":"2198","DOI":"10.1021\/acs.jproteome.6b00171","article-title":"LaCyTools:\nA Targeted\nLiquid Chromatography\u2013Mass Spectrometry Data Processing Package\nfor Relative Quantitation of Glycopeptides","volume":"15","author":"Jansen","year":"2016","journal-title":"J. Proteome Res."},{"key":"2026092808091846200_cit26","doi-asserted-by":"publisher","first-page":"2003","DOI":"10.1007\/s00216-025-05794-3","article-title":"GlycoDash: automated, visually assisted curation of\nglycoproteomics datasets for large sample numbers","volume":"417","author":"Pongracz","year":"2025","journal-title":"Anal. Bioanal. Chem."},{"key":"2026092808091846200_cit27","doi-asserted-by":"publisher","first-page":"2579","DOI":"10.1038\/s41467-026-70560-7","article-title":"StrucGAP: a modular,\nstreamlined and traceable data mining platform for structural and\nsite-specific glycoproteomics","volume":"17","author":"Yang","year":"2026","journal-title":"Nat. Commun."},{"key":"2026092808091846200_cit28","doi-asserted-by":"publisher","first-page":"1304","DOI":"10.1038\/s41592-021-01309-x","article-title":"Community evaluation\nof glycoproteomics informatics solutions reveals\nhigh-performance search strategies for serum glycopeptide analysis","volume":"18","author":"Kawahara","year":"2021","journal-title":"Nat. Methods"},{"key":"2026092808091846200_cit29","doi-asserted-by":"publisher","first-page":"1985","DOI":"10.1007\/s00216-025-05780-9","article-title":"Comparative\nanalysis\nof glycoproteomic software using a tailored glycan database","volume":"417","author":"Hogan","year":"2025","journal-title":"Anal. Bioanal. Chem."},{"key":"2026092808091846200_cit30","doi-asserted-by":"publisher","first-page":"966","DOI":"10.1093\/bioinformatics\/btq054","article-title":"Skyline: an open source document\neditor for creating\nand analyzing targeted proteomics experiments","volume":"26","author":"MacLean","year":"2010","journal-title":"Bioinformatics"},{"key":"2026092808091846200_cit31","doi-asserted-by":"publisher","first-page":"672","DOI":"10.1074\/mcp.RA119.001791","article-title":"Large-scale Identification of N-linked Intact Glycopeptides in Human\nSerum using HILIC Enrichment and Spectral Library Search","volume":"19","author":"Shu","year":"2020","journal-title":"Molecular & Cellular Proteomics"},{"key":"2026092808091846200_cit32","doi-asserted-by":"publisher","first-page":"5478","DOI":"10.1021\/ac500945m","article-title":"Novel LC-MS2 Product\nDependent Parallel Data Acquisition Function and Data Analysis Workflow\nfor Sequencing and Identification of Intact Glycopeptides","volume":"86","author":"Wu","year":"2014","journal-title":"Analytical Chemistry"},{"key":"2026092808091846200_cit33","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1016\/j.eng.2024.11.039","article-title":"New Avenues for Human\nBlood Plasma Biomarker Discovery via Improved In-Depth Analysis of\nthe Low-Abundant N-Glycoproteome","volume":"57","author":"Zuniga-Banuelos","year":"2026","journal-title":"Engineering"},{"key":"2026092808091846200_cit34","doi-asserted-by":"publisher","first-page":"1323","DOI":"10.1093\/glycob\/cwv091","article-title":"Symbol Nomenclature\nfor Graphical Representations of Glycans","volume":"25","author":"Varki","year":"2015","journal-title":"Glycobiology"},{"key":"2026092808091846200_cit35","doi-asserted-by":"publisher","first-page":"22706","DOI":"10.1039\/c3ra42969e","article-title":"LC-MS based\ndetection of glycoprotein sialylation \u2013 part II: Structural\nanalysis","volume":"3","author":"Palmisano","year":"2013","journal-title":"RSC Adv."},{"key":"2026092808091846200_cit36","doi-asserted-by":"publisher","DOI":"10.1002\/anie.202302883","article-title":"Decoding the Fucose\nMigration Product during Mass-Spectrometric Analysis\nof Blood Group Epitopes","volume":"62","author":"Lettow","year":"2023","journal-title":"Angew. Chem., Int.\nEd."},{"key":"2026092808091846200_cit37","doi-asserted-by":"publisher","first-page":"9605","DOI":"10.1021\/acs.analchem.3c01319","article-title":"Glycoproteomics-Compatible\nMS\/MS-Based Quantification of Glycopeptide Isomers","volume":"95","author":"Maliepaard","year":"2023","journal-title":"Analytical Chemistry"},{"key":"2026092808091846200_cit38","doi-asserted-by":"publisher","first-page":"6024","DOI":"10.1021\/pr500898r","article-title":"Assignment of Saccharide Identities\nthrough Analysis of Oxonium Ion Fragmentation Profiles in LC\u2013MS\/MS\nof Glycopeptides","volume":"13","author":"Halim","year":"2014","journal-title":"J. Proteome Res."},{"key":"2026092808091846200_cit39","doi-asserted-by":"publisher","first-page":"887","DOI":"10.1007\/s13361-017-1626-y","article-title":"Adduct Formation in\nESI\/MS by Mobile Phase Additives","volume":"28","author":"Kruve","year":"2017","journal-title":"Journal of\nthe American Society for Mass Spectrometry"},{"key":"2026092808091846200_cit40","doi-asserted-by":"publisher","first-page":"1173","DOI":"10.1074\/mcp.M116.064048","article-title":"Systematic Evaluation\nof Protein Reduction and Alkylation\nReveals Massive Unspecific Side Effects by Iodine-containing Reagents","volume":"16","author":"Mu\u0308ller","year":"2017","journal-title":"Molecular & Cellular Proteomics"},{"key":"2026092808091846200_cit41","doi-asserted-by":"publisher","first-page":"3064","DOI":"10.1021\/ac504725r","article-title":"Characterizing\nsialic acid variants\nat the glycopeptide level","volume":"87","author":"Medzihradszky","year":"2015","journal-title":"Analytical Chemistry"},{"key":"2026092808091846200_cit42","doi-asserted-by":"publisher","first-page":"1472","DOI":"10.1021\/acs.jproteome.5b01046","article-title":"In-Depth Characterization and Spectral\nLibrary Building of Glycopeptides in the Tryptic Digest of a Monoclonal\nAntibody Using 1D and 2D LC\u2013MS\/MS","volume":"15","author":"Dong","year":"2016","journal-title":"J.\nProteome Res."},{"key":"2026092808091846200_cit43","doi-asserted-by":"publisher","first-page":"893","DOI":"10.1074\/mcp.R112.026567","article-title":"Glycopeptide\nanalysis, recent developments and applications","volume":"12","author":"Desaire","year":"2013","journal-title":"Molecular & Cellular Proteomics"},{"key":"2026092808091846200_cit44","doi-asserted-by":"publisher","first-page":"7236","DOI":"10.1021\/acs.analchem.9b00594","article-title":"GlycopeptideGraphMS: Improved Glycopeptide\nDetection and Identification by Exploiting Graph Theoretical Patterns\nin Mass and Retention Time","volume":"91","author":"Choo","year":"2019","journal-title":"Analytical Chemistry"},{"key":"2026092808091846200_cit45","doi-asserted-by":"publisher","first-page":"664","DOI":"10.1021\/acs.jproteome.8b00766","article-title":"GlyConnect:\nGlycoproteomics Goes Visual, Interactive, and Analytical","volume":"18","author":"Alocci","year":"2019","journal-title":"J. Proteome Res."},{"key":"2026092808091846200_cit46","doi-asserted-by":"publisher","first-page":"229","DOI":"10.1002\/mas.21540","article-title":"The Skyline ecosystem:\nInformatics for quantitative\nmass spectrometry proteomics","volume":"39","author":"Pino","year":"2020","journal-title":"Mass Spectrom.\nRev."},{"key":"2026092808091846200_cit47","doi-asserted-by":"publisher","first-page":"591","DOI":"10.1021\/acs.jproteome.0c00563","article-title":"Improved\nMonoisotopic Mass Estimation for Deeper Proteome Coverage","volume":"20","author":"Rad","year":"2021","journal-title":"J. Proteome Res."},{"key":"2026092808091846200_cit48","doi-asserted-by":"publisher","first-page":"5241","DOI":"10.1021\/acs.jproteome.1c00657","article-title":"Advances and Utility\nof the Human Plasma Proteome","volume":"20","author":"Deutsch","year":"2021","journal-title":"J. Proteome Res."},{"key":"2026092808091846200_cit49","doi-asserted-by":"publisher","first-page":"309","DOI":"10.1007\/s10719-015-9626-2","article-title":"Human Plasma Protein\nN-Glycosylation","volume":"33","author":"Clerc","year":"2016","journal-title":"Glycoconjugate J."},{"key":"2026092808091846200_cit50","doi-asserted-by":"publisher","first-page":"2497","DOI":"10.1038\/s41467-025-57916-1","article-title":"In-depth plasma\nN-glycoproteome profiling using narrow-window data-independent acquisition\non the Orbitrap Astral mass spectrometer","volume":"16","author":"Jager","year":"2025","journal-title":"Nat.\nCommun."},{"key":"2026092808091846200_cit51","doi-asserted-by":"publisher","first-page":"5279","DOI":"10.1021\/acs.jproteome.4c00586","article-title":"The Circulating Proteome\u2500Technological\nDevelopments, Current\nChallenges, and Future Trends","volume":"23","author":"Geyer","year":"2024","journal-title":"J. Proteome Res."},{"key":"2026092808091846200_cit52","doi-asserted-by":"publisher","first-page":"2137","DOI":"10.1038\/s41467-019-09910-7","article-title":"Highly sensitive CE-ESI-MS\nanalysis of N-glycans from complex biological samples","volume":"10","author":"Lageveen-Kammeijer","year":"2019","journal-title":"Nat. Commun."},{"key":"2026092808091846200_cit53","doi-asserted-by":"publisher","first-page":"320","DOI":"10.1038\/s41598-023-51021-3","article-title":"N-glycan profiling\nof tissue samples to aid breast cancer subtyping","volume":"14","author":"Benesova","year":"2024","journal-title":"Sci. Rep."},{"key":"2026092808091846200_cit54","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1007\/978-1-0716-2978-9_16","volume-title":"Serum\/Plasma Proteomics:\nMethods and Protocols","author":"Chau","year":"2023"},{"key":"2026092808091846200_cit55","doi-asserted-by":"publisher","first-page":"1602","DOI":"10.1074\/mcp.RA120.002041","article-title":"Examining and Fine-tuning the Selection\nof Glycan Compositions with GlyConnect Compozitor","volume":"19","author":"Robin","year":"2020","journal-title":"Molecular & Cellular Proteomics"},{"key":"2026092808091846200_cit56","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1038\/s41551-023-01067-5","article-title":"Oxonium ion scanning\nmass spectrometry for large-scale plasma glycoproteomics","volume":"8","author":"White","year":"2024","journal-title":"Nature Biomedical Engineering"},{"key":"2026092808091846200_cit57","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.M111.014381","article-title":"The mzIdentML Data Standard for Mass Spectrometry-Based\nProteomics\nResults","volume":"11","author":"Jones","year":"2012","journal-title":"Molecular & Cellular Proteomics"},{"key":"2026092808091846200_cit58","doi-asserted-by":"publisher","first-page":"1534","DOI":"10.1002\/pmic.200300744","article-title":"Unimod: Protein\nmodifications for mass spectrometry","volume":"4","author":"Creasy","year":"2004","journal-title":"PROTEOMICS"},{"key":"2026092808091846200_cit59","doi-asserted-by":"publisher","first-page":"2800","DOI":"10.1074\/mcp.O114.042267","article-title":"Identification\nof a Set of Conserved\nEukaryotic Internal Retention Time Standards for Data-independent\nAcquisition Mass Spectrometry","volume":"14","author":"Parker","year":"2015","journal-title":"Mol. 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