Dataset Information

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

ABSTRACT: 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.

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Cell Culture, Embryonic Stem Cell

SUBMITTER: Rupert Mayer

LAB HEAD: Karl Mechtler

PROVIDER: PXD037985 | Pride | 2024-02-13

REPOSITORIES: pride

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Dataset's files

Source:

			Action	DRS
	20211105_E2_RSLC2_Schmuecker_Berger_GMI_ID520_onbead_dig_10per_control_Untagged_rep1.raw	Raw
	20211105_E2_RSLC2_Schmuecker_Berger_GMI_ID520_onbead_dig_10per_control_Untagged_rep2.raw	Raw
	20211105_E2_RSLC2_Schmuecker_Berger_GMI_ID520_onbead_dig_10per_control_Untagged_rep3.raw	Raw
	20211105_E2_RSLC2_Schmuecker_Berger_GMI_ID520_onbead_dig_10per_sample_Smarca5_Flag_rep1.raw	Raw
	20211105_E2_RSLC2_Schmuecker_Berger_GMI_ID520_onbead_dig_10per_sample_Smarca5_Flag_rep2.raw	Raw

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Publications

Micropillar arrays, wide window acquisition and AI-based data analysis improve comprehensiveness in multiple proteomic applications.

Matzinger Manuel M Schmücker Anna A Yelagandula Ramesh R Stejskal Karel K Krššáková Gabriela G Berger Frédéric F Mechtler Karl K Mayer Rupert L RL

Nature communications 20240203 1

Comprehensive proteomic analysis is essential to elucidate molecular pathways and protein functions. Despite tremendous progress in proteomics, current studies still suffer from limited proteomic coverage and dynamic range. Here, we utilize micropillar array columns (µPACs) together with wide-window acquisition and the AI-based CHIMERYS search engine to achieve excellent proteomic comprehensiveness for bulk proteomics, affinity purification mass spectrometry and single cell proteomics. Our data ...[more]

PMID: 38310095

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