Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/07/PXD063523/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/07/PXD063523/R2_F2_intact_feature.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/07/PXD063523/R2_F1_intact_feature.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/07/PXD063523/R2_F3_intact_feature.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/07/PXD063523/R2_F3_MCF7.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/07/PXD063523/R2_F1_MCF7.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/07/PXD063523/R2_F2_MCF7.rawprimaryOK200aeh@berkeley.eduAnna Fomitcheva KhartchenkoMass SpectrometryTop-down proteomicsBreast CancerNot availableMcf7Cytokeratin 8https://www.ebi.ac.uk/pride/archive/projects/PXD063523Epithelial CellThe 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.PrideSamples were processed using TopMSV (Choi et al J. Am. Soc. Mass Spectrom. 2021).ProteomicsAmy E. HerrUniverisy of California, BerkeleyPARTIALHomo Sapiens (human)Not availableafomkh@gmail.comUniversity of California, BerkeleyUnited StatesfalseTop-down on MCF7 for CK8 identificationThis study aimed to identify the CK8 proteoforms present in MCF7 cells for comparison with alternative technique.2025-07-232025-05-01PXD063523NEWT:6945NEWT:3555NEWT:241368NEWT:2NEWT:157546NEWT:190802NEWT:35554NEWT:150475NEWT:9417NEWT:347515NEWT:1216979NEWT:307972NEWT:544496NEWT:5180NEWT:256737NEWT:115104NEWT:1081927NEWT:67825NEWT:13076NEWT:1249668NEWT:376741NEWT:317NEWT:1736309NEWT:7227NEWT:7469NEWT:885318NEWT:876138NEWT:4081NEWT:554NEWT:98334NEWT:237561NEWT:10036NEWT:7574NEWT:1351NEWT:7215NEWT:272563NEWT:507601NCBITaxon:79857NCBITaxon:6157NEWT:95648NEWT:746360NEWT:6239NEWT:1589NEWT:470150NEWT:135622NEWT:216257NEWT:6915NEWT:9986NEWT:101510NEWT:4054NEWT:3880NEWT:8782NEWT:1000589NEWT:1902NEWT:85962NEWT:160488NEWT:28104NEWT:317447NEWT:7955NCBITaxon:2NEWT:985076NEWT:7959NEWT:2261NEWT:4565NEWT:1264690NEWT:6192NEWT:28532NCBITaxon:38727NEWT:34305NEWT:59729NCBITaxon:183674NEWT:224308NEWT:626528NEWT:139927NEWT:4558NEWT:209285NEWT:216595NEWT:243230NEWT:8355NEWT:931281NEWT:7029NEWT:1283300NEWT:334747NCBITaxon:79824NCBITaxon:4563NEWT:5755NEWT:3218NEWT:5759NEWT:1736231NEWT:436486NEWT:6287NEWT:2242NEWT:300641NEWT:4784NEWT:727NEWT:9796NEWT:725NEWT:360106NEWT:260707NEWT:287NEWT:10117NEWT:10239NEWT:10116NEWT:1280NEWT:1836NEWT:1735272NEWT:83334NEWT:83332NEWT:29760NEWT:703612NEWT:260705NEWT:80863NEWT:2697049NEWT:1148NEWT:11676NEWT:55571NEWT:100226NCBITaxon:6073NEWT:4530NEWT:4896NEWT:6279NEWT:7370NEWT:6282NEWT:1134506NEWT:575584NEWT:1773NEWT:38783NEWT:8727NEWT:1895NEWT:1182590NEWT:8726NEWT:10090NEWT:935293NEWT:749200NEWT:4120NEWT:5693NEWT:8724NEWT:51511NEWT:92867NEWT:8723NEWT:990346NEWT:5334NEWT:145953NEWT:257309NEWT:230741NEWT:284812NCBITaxon:10359NCBITaxon:1313NEWT:43330NEWT:242619NEWT:44544NEWT:373995NEWT:544404NEWT:3702NEWT:129249NEWT:8839NEWT:4232NEWT:990119NEWT:4113NEWT:837NEWT:11298NEWT:171101NEWT:196627NEWT:408172NEWT:5691NEWT:408170NEWT:493760NEWT:260710NEWT:627025NEWT:400772NEWT:1097677NEWT:3708NEWT:106592NEWT:9913NEWT:1432138NEWT:10312NEWT:4100NEWT:1076NEWT:6763NEWT:803NEWT:8030NEWT:29722NEWT:380394NEWT:1692259NEWT:1639NEWT:188229NEWT:3818NEWT:480NEWT:4909NEWT:67767NEWT:135588NEWT:1843183NEWT:95486NEWT:58002NEWT:9103NEWT:4577NEWT:5664NEWT:2157NEWT:146479NEWT:10306NEWT:1911079NEWT:8022NEWT:145943NEWT:3635NEWT:5811NEWT:235443NEWT:1480154NEWT:1274414NEWT:3197NEWT:9615NEWT:10299NEWT:860688NEWT:884019NEWT:169963NEWT:36329NEWT:9606NEWT:367830NEWT:157295NEWT:410289NEWT:373153NEWT:915099NEWT:74940NEWT:1450511NEWT:470NEWT:84023NEWT:9838NCBITaxon:9615NEWT:1193501NEWT:3055NEWT:6326NEWT:6689NEWT:2762NEWT:5476NEWT:1174673NEWT:562NEWT:1274432NEWT:1274426NEWT:1423NEWT:4932NEWT:70448NEWT:9825NEWT:1274423NEWT:3603NEWT:698936NEWT:2759NEWT:3847NEWT:39946NEWT:9823NEWT:9940NEWT:573NEWT:9031NEWT:1274420NEWT:70910000-0002-4846-3923