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44. Ruotolo BT, Benesch JL, Sandercock AM,
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45. Benesch JL, Ruotolo BT (2011) Mass spectrometry: come of age for structural and dynamical biology. Curr Opin Struct Biol
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2011.08.002
46. Notredame C, Higgins DG, Heringa J (2000)
T-coffee: a novel method for fast and accurate
multiple sequence alignment. J Mol Biol
302:205–217.
https://doi.org/10.1006/
jmbi.2000.4042
47. Webb B, Sali A (2016) Comparative Protein
Structure Modeling Using MODELLER.
Curr Protoc Bioinformatics 54:5 6 1–5 6 37.
https://doi.org/10.1002/cpbi.3
48. Bleiholder C, Wyttenbach T, Bowers MT
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molecular collision cross sections (I). Method.
Int J Mass Spectrom 308:1–10. https://doi.
org/10.1016/j.ijms.2011.06.014
49. Faull PA et al (2009) Gas-phase metalloprotein
complexes interrogated by ion mobility-mass
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Int
J
Mass
Spectrom
283:140–148.
https://doi.org/10.1016/j.
ijms.2009.02.024
50. Devine PWA et al (2017) Investigating the
structural compaction of biomolecules upon
transition to the gas-phase using ESI-TWIMS-MS. J Am Soc Mass Spectr
28:1855–1862.
https://doi.org/10.1007/
s13361-017-1689-9
51. Porrini M et al (2017) Compaction of duplex
nucleic acids upon native electrospray mass
spectrometry. ACS Cent Sci 3:454–461.
https://doi.org/10.1021/acscentsci.
7b00084
52. Scott D, Layfield R, Oldham NJ (2015) Structural insights into interactions between ubiquitin specific protease 5 and its polyubiquitin
substrates by mass spectrometry and ion mobility spectrometry. Protein Sci 24:1257–1263.
https://doi.org/10.1002/pro.2692
Mass Spectrometry-Based Protein Modelling
241
https://doi.org/10.1007/
s00216-010-3556-4
39. Hebling CM et al (2010) Conformational analysis of membrane proteins in phospholipid
bilayer nanodiscs by hydrogen exchange mass
spectrometry. Anal Chem 82:5415–5419.
https://doi.org/10.1021/ac100962c
40. Eisinger ML, Dorrbaum AR, Michel H,
Padan E, Langer JD (2017) Ligand-induced
conformational dynamics of the Escherichia
coli Na(+)/H(+) antiporter NhaA revealed by
hydrogen/deuterium exchange mass spectrometry. Proc Natl Acad Sci U S A
114:11691–11696.
https://doi.org/10.
1073/pnas.1703422114
41. Martens C et al (2018) Direct protein-lipid
interactions shape the conformational landscape of secondary transporters. Nat Commun
9:415
42. Claesen J, Politis A (2019) POPPeT: a new
method to predict the protection factor of
backbone amide hydrogens. J Am Soc Mass
Spectrom 30(1):67–76. https://doi.org/10.
1007/s13361-018-2068-x
43. Marklund EG, Degiacomi MT, Robinson CV,
Baldwin AJ, Benesch JL (2015) Collision cross
sections for structural proteomics. Structure
23:791–799. https://doi.org/10.1016/j.str.
2015.02.010
44. Ruotolo BT, Benesch JL, Sandercock AM,
Hyung SJ, Robinson CV (2008) Ion
mobility-mass spectrometry analysis of large
protein complexes. Nat Protoc 3:1139–1152.
https://doi.org/10.1038/nprot.2008.78
45. Benesch JL, Ruotolo BT (2011) Mass spectrometry: come of age for structural and dynamical biology. Curr Opin Struct Biol
21:641–649. https://doi.org/10.1016/j.sbi.
2011.08.002
46. Notredame C, Higgins DG, Heringa J (2000)
T-coffee: a novel method for fast and accurate
multiple sequence alignment. J Mol Biol
302:205–217.
https://doi.org/10.1006/
jmbi.2000.4042
47. Webb B, Sali A (2016) Comparative Protein
Structure Modeling Using MODELLER.
Curr Protoc Bioinformatics 54:5 6 1–5 6 37.
https://doi.org/10.1002/cpbi.3
48. Bleiholder C, Wyttenbach T, Bowers MT
(2011) A novel projection approximation algorithm for the fast and accurate computation of
molecular collision cross sections (I). Method.
Int J Mass Spectrom 308:1–10. https://doi.
org/10.1016/j.ijms.2011.06.014
49. Faull PA et al (2009) Gas-phase metalloprotein
complexes interrogated by ion mobility-mass
spectrometry.
Int
J
Mass
Spectrom
283:140–148.
https://doi.org/10.1016/j.
ijms.2009.02.024
50. Devine PWA et al (2017) Investigating the
structural compaction of biomolecules upon
transition to the gas-phase using ESI-TWIMS-MS. J Am Soc Mass Spectr
28:1855–1862.
https://doi.org/10.1007/
s13361-017-1689-9
51. Porrini M et al (2017) Compaction of duplex
nucleic acids upon native electrospray mass
spectrometry. ACS Cent Sci 3:454–461.
https://doi.org/10.1021/acscentsci.
7b00084
52. Scott D, Layfield R, Oldham NJ (2015) Structural insights into interactions between ubiquitin specific protease 5 and its polyubiquitin
substrates by mass spectrometry and ion mobility spectrometry. Protein Sci 24:1257–1263.
https://doi.org/10.1002/pro.2692
Mass Spectrometry-Based Protein Modelling
241