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PXD037985-1

PXD037985 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleWide Window Acquisition and AI-based data analysis to reach deep proteome coverage for a wide sample range, including single cell proteomic inputs – Co-immunoprecipitation samples
DescriptionA comprehensive proteome map is essential to elucidate molecular pathways and protein functions. Although great improvements in sample preparation, instrumentation and data analysis already yielded impressive results, current studies suffer from a limited proteomic depth and dynamic range therefore lacking low abundant or highly hydrophobic proteins. Here, we combine and benchmark advanced micro pillar array columns (µPAC™) operated at nanoflow with Wide Window Acquisition (WWA) and the AI-based CHIMERYS™ search engine for data analysis to maximize chromatographic separation power, sensitivity and proteome coverage. Using this optimized workflow on immunoprecipitation samples of Smarca5/SNF2H, we found 32 additional interaction partners compared to the original workflow utilizing a packed bed column. These additional interaction partners include previously described interaction partners of Smarca5 like Baz2b as well as undescribed interactors including Arid1a, which is also involved in chromatin remodeling and has been described as key player in neurodevelopmental and malignant disorders.
HostingRepositoryPRIDE
AnnounceDate2024-02-13
AnnouncementXMLSubmission_2024-02-13_04:32:40.515.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterRupert Mayer
SpeciesList scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationListmethylthiolated residue; monohydroxylated residue
InstrumentOrbitrap Exploris 480
Dataset History
RevisionDatetimeStatusChangeLog Entry
02022-11-07 08:44:16ID requested
12024-02-13 04:32:41announced
Publication List
Matzinger M, Schm, ü, cker A, Yelagandula R, Stejskal K, Kr, š, š, á, kov, á G, Berger F, Mechtler K, Mayer RL, Micropillar arrays, wide window acquisition and AI-based data analysis improve comprehensiveness in multiple proteomic applications. Nat Commun, 15(1):1019(2024) [pubmed]
10.1038/s41467-024-45391-z;
Keyword List
submitter keyword: Mus musculus, co-immunoprecipitation, micropillar array chromatography, SMARCA5,Orbitrap Exploris 480, UltiMate3000 RSLCnano, protein-protein interactions, trap-and-elute
Contact List
Karl Mechtler
contact affiliationInstitute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.
contact emailkarl.mechtler@imp.ac.at
lab head
Rupert Mayer
contact affiliationInstitute of Molecular Pathology (IMP), Vienna BioCenter (VBC)
contact emailrupert.mayer@imp.ac.at
dataset submitter
Full Dataset Link List
Dataset FTP location
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