High-sensitivity Orbitrap mass analysis of intact macromolecular assemblies. R. J. Rose, E. Damoc, E. Denisov, A. Makarov, A. J. R.

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1 High-sensitivity Orbitrap mass analysis of intact macromolecular assemblies R. J. Rose, E. Damoc, E. Denisov, A. Makarov, A. J. R. Heck SUPPLEMENTARY INFORMATION HCD multipole C -trap Transport octapole Ion gate Bent flatapole Injection flatapole S- lens Orbitrap analyzer Sprayer Supplementary Figure 1. Schematic of the modified Exactive Plus instrument (ThermoFisher Scientific, Bremen, Germany) with HCD option.

2 Supplementary Figure 2. NanoESI spectra of aqueous 25 mg.ml -1 CsI. Singly charged clusters of CsI are detected up to 19,000 Th at a resolution over 15,000, demonstrating that the transmission and detection of these high m/z ions is possible on the modified Orbitrap mass analyzer.

3 RK_Uni_glyc #57-95 RT: AV: 39 NL: E6 T: FTMS + p NSI sid= Full ms [ ] m/z Supplementary Figure 3. Zoom-in of the native nanoesi spectra IgG antibody under nondenaturing conditions (22+ to 28+ charge states) sprayed from aqueous ammonium acetate. Each charge state is comprised of 4 baseline-resolved peaks originating from different glycan structures decorating the IgG heavy chains. Inset: enlargement of 25+ charge state, with resolution (R) for each peak indicated. Fine structure on the higher m/z peaks is indicative of further mass heterogeneity.

4 HK97 # RT: AV: 56 NL: 2.78E7 T: FTMS + p NSI Full ms @hcd [ ] / m/z Supplementary Figure 4. Zoom-in of the native mass spectrum of capsomers of the HK97 bacteriophage. Pentameric capsomers are shown as filled circles (25+ to 35+) and hexameric capsomers as empty diamonds (31+ to 38+). Note that the peak at m/z has contributions from both the pentamer (30+) and the hexamer (36+), with identical m/z values.

5 proteasome_xe_ # RT: AV: 189 NL: 9.88E3 T: FTMS + p NSI Full ms @hcd10.00 [ ] m/z Supplementary Figure 5. Zoom-in of the native mass spectrum of yeast 20S proteasome (56+ to 64+ charge states). Peaks are much broader than seen for GroEL at similar m/z values- this is indicative of overlapping peaks resulting from a mix of complexes with slightly different molecular weights.

6 71+ GroEL_Xe_ # RT: AV: 23 NL: 3.63E5 T: FTMS + p NSI Full ms @hcd [ ] m/z Supplementary Figure 6. Zoom-in of the native mass spectrum of (unbound) GroEL (66+ to 75+ charge states). The mass resolving power of these ion signals is >

7 Supplementary Figure 7. Single ion detection in individual scans. (A-C) three individual single scans are shown detecting individual ions of GroEL. Single ions appear in the intensity range x10 6 a.u. (indicated by the pink area), 4 to 6 times the noise level (up to approximately 9 x 10 5 a.u., indicated by the dark grey area). Signals with higher intensity correspond to more than one ion being detected simultaneously. The expected m/z values of GroEL peaks are indicated by the upper arrows. The spectrum in (D) shows the accumulated signal, i.e. mass spectrum, for GroEL summed over nearly 50,000 individual scans.

8 Supplementary Figure 8. Tandem mass spectrum using HCD activation of the 14-subunit GroEL precursor ions. This asymmetric charge/subunit dissociation pathway, as shown in the cartoon, is typical for gas-phase dissociation of non-covalently bound protein complexes by collisional activation. 13-subunit GroEL fragment ions are detected at m/z values up to and above 20,000 Th.

9 Supplementary Figure 9. Native nano-esi mass spectra of unbound GroEL (top) and GroEL incubated with ATP (middle) and ADP (bottom). 100 μm ATP or ADP was added to a 5 μm solution of GroEL. The m/z of the observed peaks increases in discrete units, relating to increases in molecular weight of single ATP or single ADP molecules, plus sodium counterparts. See also figure 3.

10 Supplementary Figure 10. Comparison of mass spectra of GroEL plus nucleotides obtained on QTof or Orbitrap mass analyzers. The 69+ charge state of GroEL unbound (a), or in the presence of ATP (b) or ADP (c) is shown. Spectra obtained on a modified Q-Tof are shown in black, and on the Exactive Plus in red. The distribution as observed by Tof is displaced to higher m/z values, likely indicative of present of adducts or residual solvent.