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 0000-0001-9568-0245https://orcid.org/0000-0001-9568-0245  ORCID identifier (Luis Daniel Cruz-Zaragoza)

 0009-0009-7280-2102https://orcid.org/0009-0009-7280-2102  ORCID identifier (Drishan Dahal)

 0009-0008-3572-0223https://orcid.org/0009-0008-3572-0223  ORCID identifier (Angela Boshnakovska)

 0000-0001-7574-0829https://orcid.org/0000-0001-7574-0829  ORCID identifier (Aiturgan Zheenbekova)

 0000-0002-5548-3308https://orcid.org/0000-0002-5548-3308  ORCID identifier (Mehmet Yilmaz)

 0000-0001-6880-4839https://orcid.org/0000-0001-6880-4839  ORCID identifier (Marcel Morgenstern)

 0000-0003-3316-9999https://orcid.org/0000-0003-3316-9999  ORCID identifier (Julian Bender)

 0009-0006-4329-9876https://orcid.org/0009-0006-4329-9876  ORCID identifier (Anusha Valpadashi)

 0009-0004-7275-0094https://orcid.org/0009-0004-7275-0094  ORCID identifier (Kristine Ann Henningfeld)

 0000-0001-8908-4295https://orcid.org/0000-0001-8908-4295  ORCID identifier (Silke Oeljeklaus)

 0000-0002-1647-7538https://orcid.org/0000-0002-1647-7538  ORCID identifier (Laura Sophie Kremer)

 0009-0001-8641-2000https://orcid.org/0009-0001-8641-2000  ORCID identifier (Oliver Urbach)

 0000-0002-8901-0242https://orcid.org/0000-0002-8901-0242  ORCID identifier (Sven Dennerlein)

 0000-0002-6740-2755https://orcid.org/0000-0002-6740-2755  ORCID identifier (Michael Lidschreiber)

 0000-0002-8028-3121https://orcid.org/0000-0002-8028-3121  ORCID identifier (Stefan Jakobs)

 0000-0001-5096-1975https://orcid.org/0000-0001-5096-1975  ORCID identifier (Bettina Warscheid)

 0000-0001-5661-5272https://orcid.org/0000-0001-5661-5272  ORCID identifier (Peter Rehling)

 PXD061846http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD061846  Pride proteome dataset (PXD061846)

 PXD061876http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD061876  Pride proteome dataset (PXD061876)

 PXD061877http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD061877  Pride proteome dataset (PXD061877)

 77https://rdp.sfb1565.uni-goettingen.de/literature/publications/77  Published Data Registry entry (CRC 1565)

 1/614https://mbexc.uni-goettingen.de/archive/1/614  Research Data Archive (supplemental material)

 01s1h3j07https://ror.org/01s1h3j07  ROR identifier (01s1h3j07, Fraunhofer Institute for Translational Medicine and Pharmacology)

 03av75f26https://ror.org/03av75f26  ROR identifier (03av75f26, Max Planck Institute for Multidisciplinary Sciences)

 05xy1nn52https://ror.org/05xy1nn52  ROR identifier (05xy1nn52, Multiscale Bioimaging)

 021ft0n22https://ror.org/021ft0n22  ROR identifier (021ft0n22, University Medical Center Göttingen)

 00fbnyb24https://ror.org/00fbnyb24  ROR identifier (00fbnyb24, University of Würzburg)

 CVCL_0140https://scicrunch.org/resolver/CVCL_0140  SciCrunch identifier (RRID:CVCL_0140, AML12)

 CVCL_0063https://scicrunch.org/resolver/CVCL_0063  SciCrunch identifier (RRID:CVCL_0063, HEK293T)

 SCR_006442https://scicrunch.org/resolver/SCR_006442  SciCrunch identifier (RRID:SCR_006442, Bioconductor)

 SCR_016884https://scicrunch.org/resolver/SCR_016884  SciCrunch identifier (RRID:SCR_016884, clusterProfiler)

 SCR_015687https://scicrunch.org/resolver/SCR_015687  SciCrunch identifier (RRID:SCR_015687, DESeq2)

 SCR_014601https://scicrunch.org/resolver/SCR_014601  SciCrunch identifier (RRID:SCR_014601, ggplot2)

 SCR_002798https://scicrunch.org/resolver/SCR_002798  SciCrunch identifier (RRID:SCR_002798, GraphPad Prism)

 SCR_003070https://scicrunch.org/resolver/SCR_003070  SciCrunch identifier (RRID:SCR_003070, ImageJ)

 SCR_014246https://scicrunch.org/resolver/SCR_014246  SciCrunch identifier (RRID:SCR_014246, ImageQuant)

 SCR_010943https://scicrunch.org/resolver/SCR_010943  SciCrunch identifier (RRID:SCR_010943, LIMMA)

 SCR_014485https://scicrunch.org/resolver/SCR_014485  SciCrunch identifier (RRID:SCR_014485, MaxQuant)

 SCR_003420https://scicrunch.org/resolver/SCR_003420  SciCrunch identifier (RRID:SCR_003420, nSolver)

 SCR_015753https://scicrunch.org/resolver/SCR_015753  SciCrunch identifier (RRID:SCR_015753, Perseus)

 SCR_008394https://scicrunch.org/resolver/SCR_008394  SciCrunch identifier (RRID:SCR_008394, Python)

 SCR_013046https://scicrunch.org/resolver/SCR_013046  SciCrunch identifier (RRID:SCR_013046, RankProd)

 SCR_000432https://scicrunch.org/resolver/SCR_000432  SciCrunch identifier (RRID:SCR_000432, RStudio)

 SCR_019186https://scicrunch.org/resolver/SCR_019186  SciCrunch identifier (RRID:SCR_019186, tidyverse)

 SCR_002380https://scicrunch.org/resolver/SCR_002380  SciCrunch identifier (RRID:SCR_002380, UniProt)

 SCR_026112https://scicrunch.org/resolver/SCR_026112  SciCrunch identifier (RRID:SCR_026112, UpSetR)

 SCR_001459https://scicrunch.org/resolver/SCR_001459  SciCrunch identifier (RRID:SCR_001459, vsn)

 science....sm.pdfhttps://www.science.org/doi/suppl/10.1126/science.adr3498/suppl_file/science.adr3498_sm.pdf  Supplemental material

 goeseek.gwdguser.de/studies/237https://goeseek.gwdguser.de/studies/237  Supplemental material (goeseek study)

 science....ar.pdfhttps://www.science.org/doi/suppl/10.1126/science.adr3498/suppl_file/science.adr3498_mdar.pdf  Supplemental material (MDAR reproducibility checklist)

 science....s5.ziphttps://www.science.org/doi/suppl/10.1126/science.adr3498/suppl_file/science.adr3498_tables_s1_to_s5.zip  Supplemental material (table)

 10.5281/zenodo.15241939https://doi.org/10.5281/zenodo.15241939  Zenodo identifier (10.5281/zenodo.15241939, code)

 10.5281/zenodo.15260712https://doi.org/10.5281/zenodo.15260712  Zenodo identifier (10.5281/zenodo.15260712, code)