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Automating data analysis for hydrogen/deuterium exchange mass spectrometry using data-independent acquisition methodology

ABSTRACT: We developed an HX-MS2 strategy that supports the acquisition of CID-generated fragment ions alongside their peptide precursors. The approach enables true auto-validation of HX data by mining the rich set of deuterated fragments, using the extra dimension of data to simultaneously confirm the peptide ID and authenticate (even correct) MS1-based deuteration calculations. The high redundancy provided by the fragments generates an opportunity to determine the confidence of deuterium calculations using a combinatorial strategy. The approach requires DIA-based acquisition methods that are available on most MS platforms, making the switch to HX-MS2 straightforward. Considerable time is saved through auto-validation and more importantly, more complex samples can now be characterized and at higher throughput, as illustrated in a drug binding analysis of the ultralarge kinase DNA-PKcs, isolated directly from mammalian cells.

INSTRUMENT(S): Orbitrap Eclipse, TripleTOF 6600, Q Exactive Plus

ORGANISM(S): Homo Sapiens (human) Oryctolagus Cuniculus (rabbit)

SUBMITTER: Frantisek Filandr

LAB HEAD: David C.

PROVIDER: PXD045012 | Pride | 2023-09-08

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	2022-04-01-PolQ-Fragmentation-Bins-File.csv	Csv
	20220307_134748_POlQ-mapping-Rep1_30.wiff	Wiff
	20220307_134748_POlQ-mapping-Rep1_30.wiff.scan	Wiff
	20220307_143418_POlQ-mapping-Rep2_30.wiff	Wiff
	20220307_143418_POlQ-mapping-Rep2_30.wiff.scan	Wiff

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