Interpretation and Deconvolution of Nanodisc Native Mass Spectra

Abstract

Nanodiscs are a promising system for studying gas-phase and solution complexes of membrane proteins and lipids. We previously demonstrated that native electrospray ionization allows mass spectral analysis of intact Nanodisc complexes at single lipid resolution. This report details an improved theoretical framework for interpreting and deconvoluting native mass spectra of Nanodisc lipoprotein complexes. In addition to the intrinsic lipid count and charge distributions, Nanodisc mass spectra are significantly shaped by constructive overlap of adjacent charge states at integer multiples of the lipid mass. We describe the mathematical basis for this effect and develop a probability-based algorithm to deconvolute the underlying mass and charge distributions. The probability-based deconvolution algorithm is applied to a series of dimyristoylphosphatidylcholine Nanodisc native mass spectra and used to provide a quantitative picture of the lipid loss in gas-phase fragmentation.

Interpretation of solution scattering data from lipid nanodiscs

“…However, even at the optimal mixing ratio, there is a finite size distribution for the nanodiscs (Denisov et al, 2004;Marty et al, 2014). Here, we characterized the size distribution of the MSP1E3D1:DMPC nanodiscs at the nominally optimal composition using X-ray scattering.…”

Combining tandem mass spectrometry with ion mobility separation to determine the architecture of polydisperse proteins

“…To verify that this tandem-MS approach provided good coverage of the oligomers comprising the ensemble, we performed a deconvolution of the native mass spectrum (Fig. 5A), using a probability-based approach [46]. This suggested an oligomeric distribution spanning from 4 to 26 subunits (Fig.…”

“…CCS values were obtained from the experimental arrival-time data using established methods [43,44], employing as calibrants the native protein complexes avidin, alcohol dehydrogenase and glutamate dehydrogenase, which give good coverage of the mobility range analysed [45]. All data were initially analysed using Masslynx software (Waters Corp., Wilmslow, UK), and the distribution of oligomeric states populated by HSP16.9 was estimated using a probability-based deconvolution algorithm operating on the MS dimension of the data [46].…”

Advances in the use of nanoscale bilayers to study membrane protein structure and function

“…For instance, using nanodiscs containing the intestinal glycolipid ganglioside GM1, the heat-labile enterotoxin B was identified as a specific binding partner from lysates of pathogenic Escherichia coli (Borch, Roepstorff, & Moller-Jensen, 2011). Recent progress using native electrospray MS to analyze intact nanodisc complexes in the gas phase highlight the possibility of future studies that focus on subunit identity, stoichiometry, and interactions of nanodisc-bound MPs that are fully assembled (Marty et al, 2012;Marty, Zhang, Cui, Gross, & Sligar, 2014).…”