Global Membrane Protein Interactome Analysis using In vivo Crosslinking and Mass Spectrometry-based Protein Correlation Profiling.

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Formaldehyde crosslinked protein complexes were extracted with high yield using denaturing buffers that maintained complex solubility during chromatographic separation. We show this efficiently detects both integral membrane and membrane-associated protein complexes,in addition to soluble complexes, allowing identification and analysis of complexes not accessible in native extracts. We compare the protein complexes detected by HPLC-MS protein correlation profiling in both native and formaldehyde crosslinked U2OS cell extracts. These proteome-wide data sets of both in vivo crosslinked and native protein complexes from U2OS cells are freely available via a searchable online database (www.peptracker.com/epd). Raw data are also available via ProteomeXchange (identifier PXD003754).", "claims": [{"id": "claim-method", "statement": "To create an elution profile for an individual protein group in each of the three biological replicates in each experiment type (either native, or PFA crosslinked), we used the MaxQuant label free quantitation (LFQ) algorithm (24).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27114452", "locator": "sections[16] \"Experimental Design and Statistical Rationale\" paragraph 2", "quote": "To create an elution profile for an individual protein group in each of the three biological replicates in each experiment type (either native, or PFA crosslinked), we used the MaxQuant label free quantitation (LFQ) algorithm (24)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "These proteome-wide data sets of both in vivo crosslinked and native protein complexes from U2OS cells are freely available via a searchable online database (www.peptracker.com/epd). 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