PXD037985-1

PXD037985 is an original dataset announced via ProteomeXchange.

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

Revision	Datetime	Status	ChangeLog Entry
0	2022-11-07 08:44:16	ID requested
⏵ 1	2024-02-13 04:32:41	announced
2	2024-10-22 06:29:16	announced	2024-10-22: Updated project metadata.

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;

submitter keyword: Mus musculus, co-immunoprecipitation, micropillar array chromatography, SMARCA5,Orbitrap Exploris 480, UltiMate3000 RSLCnano, protein-protein interactions, trap-and-elute

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

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/02/PXD037985

PRIDE project URI

• PRIDE
  1. PXD037985
     1. Label: PRIDE project
     2. 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