PXD037985 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Wide 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 |
Description | A 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. |
HostingRepository | PRIDE |
AnnounceDate | 2024-02-13 |
AnnouncementXML | Submission_2024-02-13_04:32:40.515.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Rupert Mayer |
SpeciesList | scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; |
ModificationList | methylthiolated residue; monohydroxylated residue |
Instrument | Orbitrap Exploris 480 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2022-11-07 08:44:16 | ID requested | |
⏵ 1 | 2024-02-13 04:32:41 | announced | |
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 affiliation | Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria. |
contact email | karl.mechtler@imp.ac.at |
lab head | |
Rupert Mayer |
contact affiliation | Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC) |
contact email | rupert.mayer@imp.ac.at |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD037985
- Label: PRIDE project
- Name: Wide 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