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Here we describe a detailed protocol for both data collection and interpretation with respect to ion mobility-mass spectrometry analysis of large protein assemblies. Ion mobility is a technique that can separate gaseous ions based on their size and shape. Specifically, within this protocol, we cover general approaches to data interpretation, methods of predicting whether specific model structures for a given protein assembly can be separated by ion mobility, and generalized strategies for data normalization and modeling. The protocol also covers basic instrument settings and best practices for both observation and detection of large noncovalent protein complexes by ion mobility-mass spectrometry.

Original publication




Journal article


Nat Protoc

Publication Date





1139 - 1152


Data Interpretation, Statistical, Ion Transport, Mass Spectrometry, Models, Molecular, Models, Statistical, Multiprotein Complexes