{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T13:04:33Z","timestamp":1785243873016,"version":"3.55.0"},"reference-count":75,"publisher":"American Chemical Society (ACS)","issue":"29","license":[{"start":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T00:00:00Z","timestamp":1784160000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["R01CA218500"],"award-info":[{"award-number":["R01CA218500"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100011033","name":"Thermo Fisher Scientific","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100011033","id-type":"DOI","asserted-by":"publisher"}]},{"name":"DFCI\/NU Program in Cancer Drug Development at Northeastern University"},{"name":"ASMS Research Award"},{"DOI":"10.13039\/100000002","name":"National Institutes of Health (NIH)","doi-asserted-by":"crossref","award":["R35GM136421"],"award-info":[{"award-number":["R35GM136421"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health (NIH)","doi-asserted-by":"crossref","award":["R41GM156145"],"award-info":[{"award-number":["R41GM156145"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,7,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The advantages of top-down proteomics (TDP) in the characterization of proteoforms, resulting from genetic variations, alternative splicing, and post-translational modifications (PTMs), have been well documented. However, TDP applications on limited samples have been less explored, and no direct comparison with the bottom-up proteomics (BUP) approach for the same scarce amounts of samples has been conducted to date. In this work, we processed \u223c100\u20131000 HeLa cells using bottom-up and top-down workflows and subjected sample volumes equivalent to \u223c25 and up to \u223c250 HeLa cells to liquid chromatography\u2013mass spectrometry (LC\u2013MS)-based TDP and BUP analyses. Porous layer open-tubular (PLOT) columns were used for the separation of intact proteins in TDP MS, while traditional bead-packed columns were used for the BUP workflow. Up to 500 proteoforms and nearly 1300 proteins from cell lysates equivalent to \u223c25 HeLa cells were identified in TDP and BUP, respectively. Interestingly, among all the unambiguously identified proteins from both \u223c25 HeLa and \u223c250 HeLa cell lysates in TDP, \u223c20\u201330% were not identified in BUP under the same sample loading, suggesting significant complementarity between TDP and BUP approaches. Additionally, biologically relevant PTMs (e.g., acetylation, phosphorylation, and methylation) were reliably characterized in TDP as different proteoforms. We anticipate that TDP, enhanced by ultralow-flow PLOT chromatography columns coupled to MS, could be a supplementary or an alternative approach for limited-sample analysis, as it eliminates the need for protein digestion and minimizes sample cleanup, enabling rapid sample preparation while preserving proteoform information.<\/jats:p>","DOI":"10.1021\/acs.analchem.6c01310","type":"journal-article","created":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T15:20:31Z","timestamp":1784215231000},"page":"21319-21332","source":"Crossref","is-referenced-by-count":0,"title":["Top-Down versus\nBottom-Up Proteomics in Highly Sensitive\nLC-MS-Based Profiling of Limited Samples"],"prefix":"10.1021","volume":"98","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2132-582X","authenticated-orcid":true,"given":"Yunfan","family":"Gao","sequence":"first","affiliation":[{"name":"Barnett Institute of Chemical and Biological Analysis , , Northeastern University, 360 Huntington Avenue , , ,","place":["Boston, Massachusetts, United States, 02115"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3815-1448","authenticated-orcid":true,"given":"Michal","family":"Gregus\u030c","sequence":"additional","affiliation":[{"name":"Barnett Institute of Chemical and Biological Analysis , , Northeastern University, 360 Huntington Avenue , , ,","place":["Boston, Massachusetts, United States, 02115"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James C.","family":"Kostas","sequence":"additional","affiliation":[{"name":"Barnett Institute of Chemical and Biological Analysis , , Northeastern University, 360 Huntington Avenue , , ,","place":["Boston, Massachusetts, United States, 02115"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7461-1838","authenticated-orcid":true,"given":"Anne-Lise","family":"Marie","sequence":"additional","affiliation":[{"name":"Barnett Institute of Chemical and Biological Analysis , , Northeastern University, 360 Huntington Avenue , , ,","place":["Boston, Massachusetts, United States, 02115"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4691-8488","authenticated-orcid":true,"given":"Alexander R.","family":"Ivanov","sequence":"additional","affiliation":[{"name":"Barnett Institute of Chemical and Biological Analysis , , Northeastern University, 360 Huntington Avenue , , ,","place":["Boston, Massachusetts, United States, 02115"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,7,16]]},"reference":[{"issue":"6","key":"2026072808073615800_cit1","doi-asserted-by":"publisher","first-page":"551","DOI":"10.1038\/nbt.3854","article-title":"Single-cell topological RNA-seq analysis\nreveals insights into cellular differentiation and development","volume":"35","author":"Rizvi","year":"2017","journal-title":"Nat. Biotechnol."},{"issue":"1","key":"2026072808073615800_cit2","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1681\/ASN.2018090912","article-title":"Advantages\nof Single-Nucleus over Single-Cell RNA Sequencing of Adult Kidney:\nRare Cell Types and Novel Cell States Revealed in Fibrosis","volume":"30","author":"Wu","year":"2019","journal-title":"J. Am. Soc. Nephrol."},{"issue":"Suppl_1","key":"2026072808073615800_cit3","doi-asserted-by":"publisher","first-page":"i248","DOI":"10.1093\/bioinformatics\/bth941","article-title":"Inferring quantitative models of\nregulatory networks from expression data","volume":"20","author":"Nachman","year":"2004","journal-title":"Bioinformatics"},{"issue":"3","key":"2026072808073615800_cit4","doi-asserted-by":"publisher","first-page":"535","DOI":"10.1016\/j.cell.2016.03.014","article-title":"On the Dependency\nof Cellular Protein\nLevels on mRNA Abundance","volume":"165","author":"Liu","year":"2016","journal-title":"Cell"},{"issue":"6959","key":"2026072808073615800_cit5","doi-asserted-by":"publisher","first-page":"737","DOI":"10.1038\/nature02046","article-title":"Global analysis\nof protein expression in yeast","volume":"425","author":"Ghaemmaghami","year":"2003","journal-title":"Nature"},{"issue":"1","key":"2026072808073615800_cit6","doi-asserted-by":"publisher","first-page":"50","DOI":"10.1186\/s13059-021-02267-5","article-title":"Single-cell\nproteomic and transcriptomic analysis of macrophage heterogeneity\nusing SCoPE2","volume":"22","author":"Specht","year":"2021","journal-title":"Genome Biol."},{"issue":"2","key":"2026072808073615800_cit7","doi-asserted-by":"publisher","first-page":"91","DOI":"10.2174\/1389202911314020003","article-title":"Integrated analysis of transcriptomic\nand proteomic data","volume":"14","author":"Haider","year":"2013","journal-title":"Curr. Genomics"},{"issue":"1","key":"2026072808073615800_cit8","doi-asserted-by":"publisher","DOI":"10.1002\/smtd.202301179","article-title":"Microfluidics Coupled\nMass Spectrometry for Single Cell Multi-Omics","volume":"8","author":"Zhang","year":"2024","journal-title":"Small Methods"},{"issue":"3","key":"2026072808073615800_cit9","doi-asserted-by":"publisher","first-page":"363","DOI":"10.1038\/s41592-023-01791-5","article-title":"Single-cell proteomics\nenabled by next-generation sequencing or mass spectrometry","volume":"20","author":"Bennett","year":"2023","journal-title":"Nat. Methods"},{"issue":"1","key":"2026072808073615800_cit10","doi-asserted-by":"publisher","first-page":"882","DOI":"10.1038\/s41467-018-03367-w","article-title":"Nanodroplet\nprocessing platform for deep and quantitative proteome profiling of\n10\u2013100 mammalian cells","volume":"9","author":"Zhu","year":"2018","journal-title":"Nat. Commun."},{"issue":"1","key":"2026072808073615800_cit11","doi-asserted-by":"publisher","first-page":"161","DOI":"10.1186\/s13059-018-1547-5","article-title":"SCoPE-MS: mass spectrometry\nof single mammalian cells quantifies proteome heterogeneity during\ncell differentiation","volume":"19","author":"Budnik","year":"2018","journal-title":"Genome Biol."},{"issue":"3","key":"2026072808073615800_cit12","doi-asserted-by":"publisher","first-page":"1676","DOI":"10.1021\/acs.jproteome.0c00890","article-title":"Simple\nand Efficient Microsolid-Phase Extraction Tip-Based Sample Preparation\nWorkflow to Enable Sensitive Proteomic Profiling of Limited Samples\n(200 to 10,000 Cells)","volume":"20","author":"Kostas","year":"2021","journal-title":"J. Proteome Res."},{"issue":"2","key":"2026072808073615800_cit13","doi-asserted-by":"publisher","first-page":"704","DOI":"10.1021\/acs.analchem.1c02929","article-title":"Capillary Electrophoresis\nCoupled to Electrospray Ionization Tandem Mass Spectrometry for Ultra-Sensitive\nProteomic Analysis of Limited Samples","volume":"94","author":"Johnson","year":"2022","journal-title":"Anal.\nChem."},{"issue":"6","key":"2026072808073615800_cit14","doi-asserted-by":"publisher","first-page":"1672","DOI":"10.1074\/mcp.M114.045724","article-title":"An Integrated\nPlatform\nfor Isolation, Processing, and Mass Spectrometry-based Proteomic Profiling\nof Rare Cells in Whole Blood","volume":"14","author":"Li","year":"2015","journal-title":"Mol. Cell. Proteomics"},{"issue":"21","key":"2026072808073615800_cit15","doi-asserted-by":"publisher","first-page":"14702","DOI":"10.1021\/acs.analchem.0c03262","article-title":"Improved Sensitivity of Ultralow\nFlow LC-MS-Based Proteomic\nProfiling of Limited Samples Using Monolithic Capillary Columns and\nFAIMS Technology","volume":"92","author":"Gregus","year":"2020","journal-title":"Anal. Chem."},{"issue":"3","key":"2026072808073615800_cit16","doi-asserted-by":"publisher","first-page":"2665","DOI":"10.1021\/acs.analchem.9b04631","article-title":"Improved Single-Cell\nProteome Coverage Using Narrow-Bore\nPacked NanoLC Columns and Ultrasensitive Mass Spectrometry","volume":"92","author":"Cong","year":"2020","journal-title":"Anal. Chem."},{"issue":"1","key":"2026072808073615800_cit17","doi-asserted-by":"publisher","first-page":"50","DOI":"10.1038\/s41587-022-01389-w","article-title":"Increasing the throughput of sensitive\nproteomics by\nplexDIA","volume":"41","author":"Derks","year":"2023","journal-title":"Nat. Biotechnol."},{"issue":"15","key":"2026072808073615800_cit18","doi-asserted-by":"publisher","first-page":"6017","DOI":"10.1021\/acs.analchem.2c00646","article-title":"Label-Free\nProfiling of up to 200 Single-Cell Proteomes per Day Using a Dual-Column\nNanoflow Liquid Chromatography Platform","volume":"94","author":"Webber","year":"2022","journal-title":"Anal.\nChem."},{"issue":"11","key":"2026072808073615800_cit19","doi-asserted-by":"crossref","first-page":"197A","DOI":"10.1021\/ac0415657","article-title":"Top-down\nproteomics","volume":"76","author":"Kelleher","year":"2004","journal-title":"Anal. Chem."},{"issue":"3","key":"2026072808073615800_cit20","doi-asserted-by":"publisher","first-page":"186","DOI":"10.1038\/nmeth.2369","article-title":"Proteoform: a single\nterm describing protein complexity","volume":"10","author":"Smith","year":"2013","journal-title":"Nat. Methods"},{"issue":"4","key":"2026072808073615800_cit21","doi-asserted-by":"publisher","first-page":"683","DOI":"10.1016\/j.bbrc.2014.02.041","article-title":"Top Down\nproteomics: facts and perspectives","volume":"445","author":"Catherman","year":"2014","journal-title":"Biochem.\nBiophys. Res. Commun."},{"issue":"1","key":"2026072808073615800_cit22","doi-asserted-by":"publisher","first-page":"499","DOI":"10.1146\/annurev-anchem-071015-041550","article-title":"Progress in Top-Down\nProteomics and\nthe Analysis of Proteoforms","volume":"9","author":"Toby","year":"2016","journal-title":"Annu. Rev. Anal\nChem. (Palo Alto Calif)"},{"issue":"10","key":"2026072808073615800_cit23","doi-asserted-by":"publisher","first-page":"1195","DOI":"10.1002\/pmic.201300432","article-title":"Top-down proteomics\nin health and disease: challenges and opportunities","volume":"14","author":"Gregorich","year":"2014","journal-title":"Proteomics"},{"issue":"6579","key":"2026072808073615800_cit24","doi-asserted-by":"publisher","first-page":"411","DOI":"10.1126\/science.aaz5284","article-title":"The Blood Proteoform Atlas: A reference\nmap of proteoforms in human hematopoietic cells","volume":"375","author":"Melani","year":"2022","journal-title":"Science"},{"issue":"10","key":"2026072808073615800_cit25","doi-asserted-by":"publisher","first-page":"1617","DOI":"10.1007\/s13361-012-0469-9","article-title":"A Cell-Based\nApproach to the Human Proteome Project","volume":"23","author":"Kelleher","year":"2012","journal-title":"J. Am.\nSoc. Mass Spectrom."},{"issue":"5","key":"2026072808073615800_cit26","doi-asserted-by":"publisher","first-page":"1299","DOI":"10.1021\/acs.jproteome.2c00034","article-title":"Mapping the Proteoform Landscape\nof Five Human Tissues","volume":"21","author":"Drown","year":"2022","journal-title":"J. Proteome Res."},{"issue":"9","key":"2026072808073615800_cit27","doi-asserted-by":"publisher","first-page":"4054","DOI":"10.1021\/pr200258m","article-title":"Top-Down Quantitative\nProteomics Identified Phosphorylation of Cardiac Troponin I as a Candidate\nBiomarker for Chronic Heart Failure","volume":"10","author":"Zhang","year":"2011","journal-title":"J. Proteome\nRes."},{"issue":"45","key":"2026072808073615800_cit28","doi-asserted-by":"publisher","first-page":"30965","DOI":"10.1074\/jbc.M109.023945","article-title":"A Common\nProperty of Amyotrophic Lateral Sclerosis-associated Variants DESTABILIZATION\nOF THE COPPER\/ZINC SUPEROXIDE DISMUTASE ELECTROSTATIC LOOP","volume":"284","author":"Molnar","year":"2009","journal-title":"J. Biol. Chem."},{"issue":"16","key":"2026072808073615800_cit29","doi-asserted-by":"publisher","first-page":"4140","DOI":"10.1073\/pnas.1716122115","article-title":"Precise characterization\nof KRAS4b proteoforms in human colorectal cells and tumors reveals\nmutation\/modification cross-talk","volume":"115","author":"Ntai","year":"2018","journal-title":"Proc. Natl.\nAcad. Sci. U. S. A."},{"key":"2026072808073615800_cit30","doi-asserted-by":"publisher","first-page":"5797","DOI":"10.1038\/srep05797","article-title":"Quantitative Measurement\nof Intact Alpha-Synuclein Proteoforms from Post-Mortem Control and\nParkinson\u2019s Disease Brain Tissue by Intact Protein Mass Spectrometry","volume":"4","author":"Kellie","year":"2014","journal-title":"Sci. Rep."},{"issue":"1","key":"2026072808073615800_cit31","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1021\/pr050278w","article-title":"Integration\nof multidimensional chromatographic protein separations with a combined\n\u2033top-down\u2033 and \u2033bottom-up\u2033 proteomic strategy","volume":"5","author":"Millea","year":"2006","journal-title":"J. Proteome Res."},{"issue":"1","key":"2026072808073615800_cit32","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1074\/mcp.M114.047480","article-title":"Integrated Bottom-Up and Top-Down\nProteomics of Patient-Derived Breast Tumor Xenografts","volume":"15","author":"Ntai","year":"2016","journal-title":"Mol. Cell. Proteomics"},{"issue":"3","key":"2026072808073615800_cit33","doi-asserted-by":"publisher","first-page":"1347","DOI":"10.1021\/pr800720d","article-title":"An integrated\ntop-down and bottom-up strategy for broadly characterizing protein\nisoforms and modifications","volume":"8","author":"Wu","year":"2009","journal-title":"J. Proteome Res."},{"issue":"1","key":"2026072808073615800_cit34","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1016\/j.jpha.2022.11.003","article-title":"Integrated top-down\nand bottom-up proteomics mass spectrometry for the characterization\nof endogenous ribosomal protein heterogeneity","volume":"13","author":"Zhang","year":"2023","journal-title":"J. Pharm. Anal."},{"issue":"24","key":"2026072808073615800_cit35","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1002\/pmic.202400338","article-title":"Top-Down Proteomics: Why and When?","volume":"25","author":"Kaulich","year":"2025","journal-title":"Proteomics"},{"issue":"10","key":"2026072808073615800_cit36","doi-asserted-by":"publisher","first-page":"7087","DOI":"10.1021\/acs.analchem.0c00467","article-title":"Sensitive Top-Down Proteomics Analysis of a Low Number of Mammalian\nCells Using a Nanodroplet Sample Processing Platform","volume":"92","author":"Zhou","year":"2020","journal-title":"Anal. Chem."},{"issue":"6","key":"2026072808073615800_cit37","doi-asserted-by":"publisher","first-page":"1361","DOI":"10.1021\/jasms.0c00484","article-title":"Capillary\nZone Electrophoresis-Electron-Capture\nCollision-Induced Dissociation on a Quadrupole Time-of-Flight Mass\nSpectrometer for Top-Down Characterization of Intact Proteins","volume":"32","author":"Shen","year":"2021","journal-title":"J. Am. Soc. Mass Spectrom."},{"issue":"41","key":"2026072808073615800_cit38","doi-asserted-by":"publisher","first-page":"14358","DOI":"10.1021\/acs.analchem.2c03045","article-title":"On-capillary Cell\nLysis Enables Top-down Proteomic Analysis of Single Mammalian Cells\nby CE-MS\/MS","volume":"94","author":"Johnson","year":"2022","journal-title":"Anal. Chem."},{"issue":"2","key":"2026072808073615800_cit39","doi-asserted-by":"publisher","first-page":"100491","DOI":"10.1016\/j.mcpro.2022.100491","article-title":"Spatially Resolved\nTop-Down Proteomics of Tissue Sections\nBased on a Microfluidic Nanodroplet Sample Preparation Platform","volume":"22","author":"Liao","year":"2023","journal-title":"Mol. Cell. Proteomics"},{"issue":"3","key":"2026072808073615800_cit40","doi-asserted-by":"publisher","first-page":"1346","DOI":"10.1021\/acs.jproteome.9b00797","article-title":"Individual Ion Mass\nSpectrometry Enhances the Sensitivity and Sequence Coverage of Top-Down\nMass Spectrometry","volume":"19","author":"Kafader","year":"2020","journal-title":"J. Proteome Res."},{"issue":"19","key":"2026072808073615800_cit41","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2222081120","article-title":"High sensitivity\ntop-down proteomics captures single muscle cell heterogeneity in large\nproteoforms","volume":"120","author":"Melby","year":"2023","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"issue":"27","key":"2026072808073615800_cit42","doi-asserted-by":"publisher","first-page":"14189","DOI":"10.1021\/acs.analchem.4c06727","article-title":"Top-Down\nProteomic Analysis of Limited Samples Using Porous Layer Open Tubular\nColumns and High-Field Asymmetric Ion Mobility Spectrometry Coupled\nto Mass Spectrometry","volume":"97","author":"Gregus","year":"2025","journal-title":"Anal. Chem."},{"issue":"1","key":"2026072808073615800_cit43","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1002\/jssc.202000936","article-title":"Sample preparation\nand fractionation techniques for intact proteins for mass spectrometric\nanalysis","volume":"44","author":"Thomas","year":"2021","journal-title":"J. Sep. Sci."},{"issue":"28","key":"2026072808073615800_cit44","doi-asserted-by":"publisher","first-page":"4664","DOI":"10.1039\/D4AY00651H","article-title":"Mass spectrometry-intensive\ntop-down proteomics: an update on technology advancements and biomedical\napplications","volume":"16","author":"Xu","year":"2024","journal-title":"Anal. Methods"},{"issue":"1","key":"2026072808073615800_cit45","doi-asserted-by":"publisher","first-page":"303","DOI":"10.1021\/acs.jproteome.4c00778","article-title":"Quantitative Top-down Proteomics\nRevealed Kinase Inhibitor-Induced Proteoform-Level Changes in Cancer\nCells","volume":"24","author":"Chowdhury","year":"2025","journal-title":"J. Proteome Res."},{"issue":"10","key":"2026072808073615800_cit46","doi-asserted-by":"publisher","first-page":"5467","DOI":"10.1021\/acs.analchem.7b00380","article-title":"Top-Down Proteomics\nof Large Proteins up to 223 kDa Enabled by Serial Size Exclusion Chromatography\nStrategy","volume":"89","author":"Cai","year":"2017","journal-title":"Anal. Chem."},{"issue":"7376","key":"2026072808073615800_cit47","doi-asserted-by":"publisher","first-page":"254","DOI":"10.1038\/nature10575","article-title":"Mapping intact protein\nisoforms in\ndiscovery mode using top-down proteomics","volume":"480","author":"Tran","year":"2011","journal-title":"Nature"},{"issue":"17","key":"2026072808073615800_cit48","doi-asserted-by":"publisher","DOI":"10.1002\/pmic.202300650","article-title":"Combining SDS-PAGE\nto capillary zone electrophoresis-tandem mass spectrometry for high-resolution\ntop-down proteomics analysis of intact histone proteoforms","volume":"24","author":"Fang","year":"2024","journal-title":"Proteomics"},{"issue":"81","key":"2026072808073615800_cit49","doi-asserted-by":"publisher","first-page":"11528","DOI":"10.1039\/D4CC02666G","article-title":"Deciphering nanoparticle\nprotein coronas by capillary isoelectric focusing-mass spectrometry-based\ntop-down proteomics","volume":"60","author":"Zhu","year":"2024","journal-title":"Chem. Commun. (Camb)"},{"key":"2026072808073615800_cit50","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1016\/j.chroma.2017.01.008","article-title":"High-resolution\nultrahigh-pressure long column reversed-phase\nliquid chromatography for top-down proteomics","volume":"1498","author":"Shen","year":"2017","journal-title":"J. Chromatogr. A"},{"issue":"2","key":"2026072808073615800_cit51","doi-asserted-by":"publisher","first-page":"457","DOI":"10.1002\/mas.21706","article-title":"Recent advances\nin top-down proteome sample processing ahead of MS analysis","volume":"42","author":"Nickerson","year":"2021","journal-title":"Mass Spectrom. Rev."},{"key":"2026072808073615800_cit52","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1016\/j.chroma.2018.02.002","article-title":"Dendritic\ncore-shell silica spheres with large pore size for separation of biomolecules","volume":"1540","author":"Qu","year":"2018","journal-title":"J. Chromatogr. A"},{"issue":"17","key":"2026072808073615800_cit53","doi-asserted-by":"publisher","first-page":"2788","DOI":"10.1002\/jssc.201900292","article-title":"Fast reversed-phase\nliquid chromatographic\nseparation of proteins by flow-through poly(styrene-co-divinylbenzene)\nmicrospheres","volume":"42","author":"Li","year":"2019","journal-title":"J. Sep. Sci."},{"key":"2026072808073615800_cit54","doi-asserted-by":"publisher","first-page":"48","DOI":"10.1016\/j.aca.2018.09.021","article-title":"Monolith columns for\nliquid chromatographic separations of intact proteins: A review of\nrecent advances and applications","volume":"1046","author":"Lynch","year":"2019","journal-title":"Anal. Chim.\nActa"},{"key":"2026072808073615800_cit55","doi-asserted-by":"publisher","first-page":"37507","DOI":"10.1038\/srep37507","article-title":"Versatile, sensitive liquid chromatography\nmass spectrometry - Implementation of 10 mum OT columns suitable for\nsmall molecules, peptides and proteins","volume":"6","author":"Vehus","year":"2016","journal-title":"Sci.\nRep"},{"key":"2026072808073615800_cit56","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1016\/j.chroma.2019.01.026","article-title":"Fabrication of a monolithic,\nmacroporous diallyl maleate-based material and its application for\nfast separation of intact proteins from human plasma with reversed-phase\nchromatography","volume":"1592","author":"Lan","year":"2019","journal-title":"J. Chromatogr. A"},{"issue":"17","key":"2026072808073615800_cit57","doi-asserted-by":"publisher","first-page":"2782","DOI":"10.1016\/j.chroma.2010.02.025","article-title":"Separation of intact\nproteins on porous layer open tubular (PLOT) columns","volume":"1217","author":"Rogeberg","year":"2010","journal-title":"J. Chromatogr. A"},{"issue":"7","key":"2026072808073615800_cit58","doi-asserted-by":"publisher","first-page":"4711","DOI":"10.1021\/acs.analchem.9b05639","article-title":"Picoflow Liquid Chromatography-Mass\nSpectrometry for Ultrasensitive Bottom-Up Proteomics Using 2-mum-i.d.\nOpen Tubular Columns","volume":"92","author":"Xiang","year":"2020","journal-title":"Anal. Chem."},{"issue":"8","key":"2026072808073615800_cit59","doi-asserted-by":"publisher","first-page":"1896","DOI":"10.1038\/nprot.2007.261","article-title":"Protocol for\nmicro-purification,\nenrichment, pre-fractionation and storage of peptides for proteomics\nusing StageTips","volume":"2","author":"Rappsilber","year":"2007","journal-title":"Nat. Protoc."},{"issue":"8","key":"2026072808073615800_cit60","doi-asserted-by":"publisher","first-page":"730","DOI":"10.1038\/nmeth.2557","article-title":"The CRAPome:\na contaminant repository for affinity\npurification-mass spectrometry data","volume":"10","author":"Mellacheruvu","year":"2013","journal-title":"Nat. Methods"},{"key":"2026072808073615800_cit61","doi-asserted-by":"publisher","DOI":"10.1002\/rcm.9128","article-title":"INFERYS rescoring:\nBoosting peptide identifications\nand scoring confidence of database search results","volume":"39","author":"Zolg","year":"2021","journal-title":"Rapid Commun. Mass Spectrom."},{"issue":"7","key":"2026072808073615800_cit62","doi-asserted-by":"publisher","first-page":"1235","DOI":"10.1002\/pmic.201400313","article-title":"ProSight Lite: graphical software\nto analyze top-down mass spectrometry data","volume":"15","author":"Fellers","year":"2015","journal-title":"Proteomics"},{"issue":"22","key":"2026072808073615800_cit63","doi-asserted-by":"publisher","first-page":"3495","DOI":"10.1093\/bioinformatics\/btw398","article-title":"TopPIC: a software tool for top-down mass spectrometry-based\nproteoform identification and characterization","volume":"32","author":"Kou","year":"2016","journal-title":"Bioinformatics"},{"issue":"8","key":"2026072808073615800_cit64","doi-asserted-by":"publisher","first-page":"1194","DOI":"10.1016\/j.molp.2020.06.009","article-title":"TBtools: An Integrative\nToolkit Developed for Interactive\nAnalyses of Big Biological Data","volume":"13","author":"Chen","year":"2020","journal-title":"Mol. Plant"},{"issue":"10","key":"2026072808073615800_cit65","doi-asserted-by":"publisher","first-page":"2247","DOI":"10.1021\/ac991412x","article-title":"Design\nand implementation of a new electrodynamic ion\nfunnel","volume":"72","author":"Kim","year":"2000","journal-title":"Anal. Chem."},{"issue":"12","key":"2026072808073615800_cit66","doi-asserted-by":"publisher","first-page":"2759","DOI":"10.1074\/mcp.M900375-MCP200","article-title":"A Dual Pressure Linear Ion Trap Orbitrap\nInstrument with Very High Sequencing Speed","volume":"8","author":"Olsen","year":"2009","journal-title":"Mol. Cell. Proteomics"},{"issue":"2","key":"2026072808073615800_cit67","doi-asserted-by":"publisher","first-page":"463","DOI":"10.1021\/jasms.9b00061","article-title":"Evaluation of Lipid\nIn-Source Fragmentation\non Different Orbitrap-based Mass Spectrometers","volume":"31","author":"Criscuolo","year":"2020","journal-title":"J. Am. Soc. Mass Spectrom."},{"issue":"9","key":"2026072808073615800_cit68","doi-asserted-by":"publisher","first-page":"3255","DOI":"10.1021\/acs.jproteome.7b00244","article-title":"Optimizing High-Resolution Mass Spectrometry for the\nIdentification of Low-Abundance Post-Translational Modifications of\nIntact Proteins","volume":"16","author":"Kilpatrick","year":"2017","journal-title":"J. Proteome Res."},{"issue":"12","key":"2026072808073615800_cit69","doi-asserted-by":"publisher","first-page":"101465","DOI":"10.1016\/j.mcpro.2025.101465","article-title":"Properties,\nOrigin, and Consistency\nof Truncated Proteoforms Across Top-Down Proteomic Studies","volume":"24","author":"Kaulich","year":"2025","journal-title":"Mol. Cell. Proteomics"},{"issue":"1","key":"2026072808073615800_cit70","doi-asserted-by":"publisher","first-page":"202","DOI":"10.1021\/acs.jproteome.0c00351","article-title":"Optimization of a Top-Down Proteomics Platform for\nClosely Related Pathogenic Bacterial Discrimination","volume":"20","author":"Dupre","year":"2021","journal-title":"J. Proteome Res."},{"key":"2026072808073615800_cit71","doi-asserted-by":"publisher","first-page":"460462","DOI":"10.1016\/j.chroma.2019.460462","article-title":"A comprehensive investigation of\nthe peak capacity for the reversed-phase gradient liquid-chromatographic\nanalysis of intact proteins using a polymer-monolithic capillary column","volume":"1609","author":"Ferna\u0301ndez-Pumarega","year":"2020","journal-title":"J. Chromatogr. A"},{"issue":"12","key":"2026072808073615800_cit72","doi-asserted-by":"publisher","first-page":"2397","DOI":"10.1038\/s41592-024-02481-6","article-title":"Influence of different\nsample preparation approaches on proteoform identification by top-down\nproteomics","volume":"21","author":"Kaulich","year":"2024","journal-title":"Nat. Methods"},{"issue":"5","key":"2026072808073615800_cit73","doi-asserted-by":"publisher","first-page":"2780","DOI":"10.1021\/acs.jproteome.1c00049","article-title":"Enhancing Top-Down Proteomics of\nBrain Tissue with\nFAIMS","volume":"20","author":"Fulcher","year":"2021","journal-title":"J. Proteome Res."},{"issue":"7","key":"2026072808073615800_cit74","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1002169","article-title":"NatF Contributes to an Evolutionary Shift in Protein\nN-Terminal Acetylation and Is Important for Normal Chromosome Segregation","volume":"7","author":"Van Damme","year":"2011","journal-title":"PLoS Genet."},{"key":"2026072808073615800_cit75","doi-asserted-by":"publisher","first-page":"MSB201181","DOI":"10.1038\/msb.2011.81","article-title":"Deep proteome and transcriptome\nmapping of a human cancer cell line","volume":"7","author":"Nagaraj","year":"2011","journal-title":"Mol. Syst.\nBiol."}],"container-title":["Analytical Chemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.analchem.6c01310","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/ancham\/article-pdf\/98\/29\/21319\/65980212\/acs.analchem.6c01310.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/ancham\/article-pdf\/98\/29\/21319\/65980212\/acs.analchem.6c01310.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T12:21:34Z","timestamp":1785241294000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/ancham\/article\/98\/29\/21319\/5212207\/Top-Down-versus-Bottom-Up-Proteomics-in-Highly"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,16]]},"references-count":75,"journal-issue":{"issue":"29","published-online":{"date-parts":[[2026,7,16]]},"published-print":{"date-parts":[[2026,7,28]]}},"URL":"https:\/\/doi.org\/10.1021\/acs.analchem.6c01310","relation":{},"ISSN":["0003-2700","1520-6882"],"issn-type":[{"value":"0003-2700","type":"print"},{"value":"1520-6882","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,16]]}}}