{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/07/PXD063523/checksum.txt"],"Xml":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/07/PXD063523/R2_F2_intact_feature.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/07/PXD063523/R2_F1_intact_feature.xml","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/07/PXD063523/R2_F3_intact_feature.xml"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/07/PXD063523/R2_F3_MCF7.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/07/PXD063523/R2_F1_MCF7.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/07/PXD063523/R2_F2_MCF7.raw"]},"type":"primary"},"statusCodeValue":200,"statusCode":"OK"}],"scores":null,"additional":{"labhead_mail":["aeh@berkeley.edu"],"submitter":["Anna Fomitcheva Khartchenko"],"technology_type":["Mass Spectrometry","Top-down proteomics"],"disease":["Breast Cancer"],"software":["Not available"],"submitter_keywords":["Mcf7","Cytokeratin 8"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD063523"],"tissue":["Epithelial Cell"],"sample_protocol":["The samples were prepared using PEPPI-MS (Takemori et al J. Proteome Res. 2020) for fractionation. The fractions (6 μL) were analyzed by online capillary nanoLC-MS/MS  using a 25 cm reversed phase column fabricated in-house (50 µm inner diameter, packed with ReproSil-Gold C8-3 μm resin (Dr. Maisch GmbH)) that was equipped with a laser-pulled nanoelectrospray emitter tip. Peptides were eluted at a flow rate of 100 nL/min using a linear gradient of 2–40% buffer B in 140 min (buffer A: 0.05% Formic acid in water; buffer B: 0.05% Formic acid and 95% acetonitrile in water) in an Thermo Fisher Easy-nLC1200 nanoLC system. Peptides were ionized using a FLEX ion source (Thermo Fisher) using electrospray ionization into an Fusion Lumos Tribrid Orbitrap Mass Spectrometer (Thermo Fisher Scientific). Data was acquired in orbi-trap mode."],"repository":["Pride"],"modification":[""],"quantification_method":[""],"data_protocol":["Samples were processed using TopMSV (Choi et al J. Am. Soc. Mass Spectrom. 2021)."],"omics_type":["Proteomics"],"labhead":["Amy E. Herr"],"instrument_platform":[""],"labhead_affiliation":["Univerisy of California, Berkeley"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"publication":["Not available"],"submitter_mail":["afomkh@gmail.com"],"submitter_affiliation":["University of California, Berkeley"],"submitter_country":["United States"],"additional_accession":[]},"is_claimable":false,"name":"Top-down on MCF7 for CK8 identification","description":"This study aimed to identify the CK8 proteoforms present in MCF7 cells for comparison with alternative technique.","dates":{"publication":"2025-07-23","submission":"2025-05-01"},"accession":"PXD063523","cross_references":{"TAXONOMY":["NEWT:6945","NEWT:3555","NEWT:241368","NEWT:2","NEWT:157546","NEWT:190802","NEWT:35554","NEWT:150475","NEWT:9417","NEWT:347515","NEWT:1216979","NEWT:307972","NEWT:544496","NEWT:5180","NEWT:256737","NEWT:115104","NEWT:1081927","NEWT:67825","NEWT:13076","NEWT:1249668","NEWT:376741","NEWT:317","NEWT:1736309","NEWT:7227","NEWT:7469","NEWT:885318","NEWT:876138","NEWT:4081","NEWT:554","NEWT:98334","NEWT:237561","NEWT:10036","NEWT:7574","NEWT:1351","NEWT:7215","NEWT:272563","NEWT:507601","NCBITaxon:79857","NCBITaxon:6157","NEWT:95648","NEWT:746360","NEWT:6239","NEWT:1589","NEWT:470150","NEWT:135622","NEWT:216257","NEWT:6915","NEWT:9986","NEWT:101510","NEWT:4054","NEWT:3880","NEWT:8782","NEWT:1000589","NEWT:1902","NEWT:85962","NEWT:160488","NEWT:28104","NEWT:317447","NEWT:7955","NCBITaxon:2","NEWT:985076","NEWT:7959","NEWT:2261","NEWT:4565","NEWT:1264690","NEWT:6192","NEWT:28532","NCBITaxon:38727","NEWT:34305","NEWT:59729","NCBITaxon:183674","NEWT:224308","NEWT:626528","NEWT:139927","NEWT:4558","NEWT:209285","NEWT:216595","NEWT:243230","NEWT:8355","NEWT:931281","NEWT:7029","NEWT:1283300","NEWT:334747","NCBITaxon:79824","NCBITaxon:4563","NEWT:5755","NEWT:3218","NEWT:5759","NEWT:1736231","NEWT:436486","NEWT:6287","NEWT:2242","NEWT:300641","NEWT:4784","NEWT:727","NEWT:9796","NEWT:725","NEWT:360106","NEWT:260707","NEWT:287","NEWT:10117","NEWT:10239","NEWT:10116","NEWT:1280","NEWT:1836","NEWT:1735272","NEWT:83334","NEWT:83332","NEWT:29760","NEWT:703612","NEWT:260705","NEWT:80863","NEWT:2697049","NEWT:1148","NEWT:11676","NEWT:55571","NEWT:100226","NCBITaxon:6073","NEWT:4530","NEWT:4896","NEWT:6279","NEWT:7370","NEWT:6282","NEWT:1134506","NEWT:575584","NEWT:1773","NEWT:38783","NEWT:8727","NEWT:1895","NEWT:1182590","NEWT:8726","NEWT:10090","NEWT:935293","NEWT:749200","NEWT:4120","NEWT:5693","NEWT:8724","NEWT:51511","NEWT:92867","NEWT:8723","NEWT:990346","NEWT:5334","NEWT:145953","NEWT:257309","NEWT:230741","NEWT:284812","NCBITaxon:10359","NCBITaxon:1313","NEWT:43330","NEWT:242619","NEWT:44544","NEWT:373995","NEWT:544404","NEWT:3702","NEWT:129249","NEWT:8839","NEWT:4232","NEWT:990119","NEWT:4113","NEWT:837","NEWT:11298","NEWT:171101","NEWT:196627","NEWT:408172","NEWT:5691","NEWT:408170","NEWT:493760","NEWT:260710","NEWT:627025","NEWT:400772","NEWT:1097677","NEWT:3708","NEWT:106592","NEWT:9913","NEWT:1432138","NEWT:10312","NEWT:4100","NEWT:1076","NEWT:6763","NEWT:803","NEWT:8030","NEWT:29722","NEWT:380394","NEWT:1692259","NEWT:1639","NEWT:188229","NEWT:3818","NEWT:480","NEWT:4909","NEWT:67767","NEWT:135588","NEWT:1843183","NEWT:95486","NEWT:58002","NEWT:9103","NEWT:4577","NEWT:5664","NEWT:2157","NEWT:146479","NEWT:10306","NEWT:1911079","NEWT:8022","NEWT:145943","NEWT:3635","NEWT:5811","NEWT:235443","NEWT:1480154","NEWT:1274414","NEWT:3197","NEWT:9615","NEWT:10299","NEWT:860688","NEWT:884019","NEWT:169963","NEWT:36329","NEWT:9606","NEWT:367830","NEWT:157295","NEWT:410289","NEWT:373153","NEWT:915099","NEWT:74940","NEWT:1450511","NEWT:470","NEWT:84023","NEWT:9838","NCBITaxon:9615","NEWT:1193501","NEWT:3055","NEWT:6326","NEWT:6689","NEWT:2762","NEWT:5476","NEWT:1174673","NEWT:562","NEWT:1274432","NEWT:1274426","NEWT:1423","NEWT:4932","NEWT:70448","NEWT:9825","NEWT:1274423","NEWT:3603","NEWT:698936","NEWT:2759","NEWT:3847","NEWT:39946","NEWT:9823","NEWT:9940","NEWT:573","NEWT:9031","NEWT:1274420","NEWT:7091"],"ORCID":["0000-0002-4846-3923"]}}