18. Since proteins and complexes can exhibit conformational variations, the reported CCS may vary depending on these
conformations [49].
19. The CCS of some proteins may not reflect their “native” conformations or those calculated from their crystal structures,
due to structural collapse in the gas phase. This phenomenon
commonly affects systems which are intrinsically flexible or
unstructured [50–52].
20. The TJM value reported by IMPACT is an approximation of
the true TJM value [43].
References
1. Alber F et al (2007) Determining the architectures of macromolecular assemblies. Nature
450:683–694.
https://doi.org/10.1038/
nature06404
2. Ahdash Z, Pyle E, Politis A (2016) Hybrid
mass spectrometry: towards characterization
of protein conformational states. Trends Biochem Sci 41:650–653. https://doi.org/10.
1016/j.tibs.2016.04.008
3. Bullock JMA, Sen N, Thalassinos K, Topf M
(2018) Modeling protein complexes using
restraints from crosslinking mass spectrometry.
Structure 26:1015–1024.e1012. https://doi.
org/10.1016/j.str.2018.04.016
4. Degiacomi MT, Schmidt C, Baldwin AJ, Benesch JLP (2017) Accommodating protein
dynamics in the modeling of chemical crosslinks.
Structure
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https://doi.org/10.1016/j.str.2017.08.015
5. Lasker K et al (2012) Molecular architecture of
the 26S proteasome holocomplex determined
by an integrative approach. Proc Natl Acad Sci
U S A 109:1380–1387. https://doi.org/10.
1073/pnas.1120559109
6. Politis A et al (2014) A mass spectrometrybased hybrid method for structural modelling
of protein complexes. Nat Methods
11:403–406
7. Hall Z, Politis A, Robinson CV (2012) Structural modeling of heteromeric protein complexes from disassembly pathways and ion
mobility-mass
spectrometry.
Structure
20:1596–1609. https://doi.org/10.1016/j.
str.2012.07.001
8. Hansen K et al (2018) A mass spectrometrybased modelling workflow for accurate prediction of IgG antibody conformations in the gas
phase. Angew Chem Int Ed Engl 57
(52):17194–17199
9. Politis A et al (2015) Topological models of
heteromeric protein assemblies from mass
spectrometry: application to the yeast eIF3:
eIF5 complex. Chem Biol 22:117–128.
https://doi.org/10.1016/j.chembiol.2014.
11.010
10. Russel D et al (2012) Putting the pieces
together: integrative modeling platform software for structure determination of macromolecular assemblies. PLoS Biol 10:e1001244.
https://doi.org/10.1371/journal.pbio.
1001244
11. Faull SV et al (2019) Structural basis of Cullin
2 RING E3 ligase regulation by the COP9
signalosome. Nat Commun 10:3814. https://
doi.org/10.1038/s41467-019-11772-y
12. Zhou M et al (2014) ATP binding reduces
conformational flexibility in a rotary ATPase—
Evidence from ion mobility mass spectrometry.
Nat Chem 6(3):208–215
13. Alber F et al (2007) The molecular architecture
of the nuclear pore complex. Nature
450:695–701.
https://doi.org/10.1038/
nature06405
14. Bechara C et al (2015) A subset of annular
lipids is linked to the flippase activity of an
ABC transporter. Nat Chem 7:255–262.
https://doi.org/10.1038/nchem.2172
15. Bechara C, Robinson CV (2015) Different
modes of lipid binding to membrane proteins
probed by mass spectrometry. J Am Chem Soc
137:5240–5247. https://doi.org/10.1021/
jacs.5b00420
16. Ahdash Z et al (2017) Mechanistic insight into
the assembly of the HerA-NurA helicase-nuclease DNA end resection complex. Nucleic Acids
Res 45:12025–12038. https://doi.org/10.
1093/nar/gkx890
17. Pagel K, Natan E, Hall Z, Fersht AR, Robinson
CV (2013) Intrinsically disordered p53 and its
complexes populate compact conformations in
the gas phase. Angew Chem Int Ed Engl
Mass Spectrometry-Based Protein Modelling
239
conformations [49].
19. The CCS of some proteins may not reflect their “native” conformations or those calculated from their crystal structures,
due to structural collapse in the gas phase. This phenomenon
commonly affects systems which are intrinsically flexible or
unstructured [50–52].
20. The TJM value reported by IMPACT is an approximation of
the true TJM value [43].
References
1. Alber F et al (2007) Determining the architectures of macromolecular assemblies. Nature
450:683–694.
https://doi.org/10.1038/
nature06404
2. Ahdash Z, Pyle E, Politis A (2016) Hybrid
mass spectrometry: towards characterization
of protein conformational states. Trends Biochem Sci 41:650–653. https://doi.org/10.
1016/j.tibs.2016.04.008
3. Bullock JMA, Sen N, Thalassinos K, Topf M
(2018) Modeling protein complexes using
restraints from crosslinking mass spectrometry.
Structure 26:1015–1024.e1012. https://doi.
org/10.1016/j.str.2018.04.016
4. Degiacomi MT, Schmidt C, Baldwin AJ, Benesch JLP (2017) Accommodating protein
dynamics in the modeling of chemical crosslinks.
Structure
25:1751–1757.e1755.
https://doi.org/10.1016/j.str.2017.08.015
5. Lasker K et al (2012) Molecular architecture of
the 26S proteasome holocomplex determined
by an integrative approach. Proc Natl Acad Sci
U S A 109:1380–1387. https://doi.org/10.
1073/pnas.1120559109
6. Politis A et al (2014) A mass spectrometrybased hybrid method for structural modelling
of protein complexes. Nat Methods
11:403–406
7. Hall Z, Politis A, Robinson CV (2012) Structural modeling of heteromeric protein complexes from disassembly pathways and ion
mobility-mass
spectrometry.
Structure
20:1596–1609. https://doi.org/10.1016/j.
str.2012.07.001
8. Hansen K et al (2018) A mass spectrometrybased modelling workflow for accurate prediction of IgG antibody conformations in the gas
phase. Angew Chem Int Ed Engl 57
(52):17194–17199
9. Politis A et al (2015) Topological models of
heteromeric protein assemblies from mass
spectrometry: application to the yeast eIF3:
eIF5 complex. Chem Biol 22:117–128.
https://doi.org/10.1016/j.chembiol.2014.
11.010
10. Russel D et al (2012) Putting the pieces
together: integrative modeling platform software for structure determination of macromolecular assemblies. PLoS Biol 10:e1001244.
https://doi.org/10.1371/journal.pbio.
1001244
11. Faull SV et al (2019) Structural basis of Cullin
2 RING E3 ligase regulation by the COP9
signalosome. Nat Commun 10:3814. https://
doi.org/10.1038/s41467-019-11772-y
12. Zhou M et al (2014) ATP binding reduces
conformational flexibility in a rotary ATPase—
Evidence from ion mobility mass spectrometry.
Nat Chem 6(3):208–215
13. Alber F et al (2007) The molecular architecture
of the nuclear pore complex. Nature
450:695–701.
https://doi.org/10.1038/
nature06405
14. Bechara C et al (2015) A subset of annular
lipids is linked to the flippase activity of an
ABC transporter. Nat Chem 7:255–262.
https://doi.org/10.1038/nchem.2172
15. Bechara C, Robinson CV (2015) Different
modes of lipid binding to membrane proteins
probed by mass spectrometry. J Am Chem Soc
137:5240–5247. https://doi.org/10.1021/
jacs.5b00420
16. Ahdash Z et al (2017) Mechanistic insight into
the assembly of the HerA-NurA helicase-nuclease DNA end resection complex. Nucleic Acids
Res 45:12025–12038. https://doi.org/10.
1093/nar/gkx890
17. Pagel K, Natan E, Hall Z, Fersht AR, Robinson
CV (2013) Intrinsically disordered p53 and its
complexes populate compact conformations in
the gas phase. Angew Chem Int Ed Engl
Mass Spectrometry-Based Protein Modelling
239