Supporting Information For:
Interpretation and Deconvolution of Nanodisc
Native Mass Spectra
Michael T. Marty,1 Hao Zhang,2,3 Weidong Cui,2 Michael L. Gross,2 and Stephen
G. Sligar*1,4
1
University of Illinois Urbana-Champaign, Department of Chemistry, Urbana, IL 61801
2
Washington University in St. Louis, Department of Chemistry, St. Louis, MO 63130
3
Washington University in St. Louis, Photosynthetic Antenna Research Center (PARC), St.
Louis, MO 63130
4
University of Illinois Urbana-Champaign, Department of Biochemistry, Urbana, IL 61801
*Address reprint requests to:
Stephen G. Sligar
116 Morrill Hall
505 S. Goodwin MC-119
Urbana, IL 61801
Email: s-sligar@uiuc.edu
Phone: 217-244-7395
Fax: 217-265-4073
Figure S1: Mass spectra (black traces) and fits (colored traces) for DMPC Nanodiscs at various
levels of ISCAD fragmentation energy. Each lower colored spectrum corresponds with the color
scheme used in Figure 2.
Figure S2: Mass spectra (black traces) and fits (colored traces) for DMPC Nanodiscs at various
levels of IRMPD laser durations. Each lower colored spectrum corresponds with the color
scheme used in Figure 2.
Figure S3: Mass spectrum (black trace, top) of DMPC Nanodiscs at 70 V ISCAD, as shown in
Figure 1 and Figure S1, fit with a simplified model of lipid and charge distribution (blue trace
bottom). The bottom distribution was obtained by fitting a Gaussian distribution of charge and a
Cauchy distribution in lipid count.
Supporting Discussion
Other Models for Nanodisc Deconvolution
As described in the text, we attempted to fit simpler models for the lipid count and charge
state distributions to the Nanodisc spectra. While none of the distributions fit the spectra as well
as the probability-based deconvolution, the best of these models was a Cauchy distribution in the
lipid count and a Gaussian distribution in charge. F-tests were performed on each of the spectra
shown in Figures S1 and S2, which demonstrated that the probability-based deconvolution had a
statistically better fit than the simplified model.
As a representative example, we will consider the spectrum of DMPC Nanodiscs at 70 V
ISCAD as shown in Figure 1a. The final fit from the probability-based deconvolution (PBD) is
provided in the top right (blue) panel of Figure S1 and the final fit from the Cauchy model (CM)
is provided in the Figure S3. The sum of squared errors (SSE) from each model were 𝑆𝑆𝐸𝑃𝐵𝐷 =
22060 and 𝑆𝑆𝐸𝐶𝑀 = 116755. The number of data points in the spectrum following linearization
and truncation of the spectrum to the relevant region was 2691. After removing the (𝑘, 𝑧) pairs
with a probability less than 1% of the maximum probability from any pair, 429 nonzero pairs
remained as part of the model. Thus, the number of degrees of freedom from the PBD was
𝑑𝑜𝑓𝑃𝐵𝐷 = 2691 − 429 = 2262. Because the CM had four parameters, mean and deviation in
charge and lipid count, 𝑑𝑜𝑓𝐶𝑀 = 2691 − 4 = 2687. Using the equation:
𝐹=
(𝑆𝑆𝐸𝐶𝑀 − 𝑆𝑆𝐸𝑃𝐵𝐷 )/𝑆𝑆𝐸𝑃𝐵𝐷
(𝑑𝑜𝑓𝐶𝑀 − 𝑑𝑜𝑓𝑃𝐵𝐷 )/𝑑𝑜𝑓𝑃𝐵𝐷
the F value was calculated as 12.47. The critical F value for a numerator of 𝑑𝑜𝑓𝐶𝑀 − 𝑑𝑜𝑓𝑃𝐵𝐷 and
a denominator of 𝑑𝑜𝑓𝑃𝐵𝐷 has a critical F value of 1.12. Because the calculated F value is larger
than the critical F value, the PBD model is significantly better than the CM model. Similar
results were obtained for the other spectra in Figures S1 and S2.