I. Kosheleva, R. Henning, A. Menzel, and J. A. Ihalainen, Signal Amplification and Transduction in Phytochrome Photosensors, Nature, vol.509, pp.245-248, 2014.

J. M. Christie, L. Blackwood, J. Petersen, and S. Sullivan, Plant Flavoprotein Photoreceptors, Plant and Cell Physiology, vol.56, issue.3, pp.401-413, 2015.
DOI : 10.1093/pcp/pcu196

S. M. Harper, L. C. Neil, and K. H. Gardner, Structural Basis of a Phototropin Light Switch, Science, vol.301, issue.5639, pp.1541-1544, 2003.
DOI : 10.1126/science.1086810

T. J. Graber, R. Henning, M. Wulff, and G. Hummer, Watching a Signaling Protein Function in Real Time via 100-Ps Time-Resolved Laue Crystallography, Proc. Natl. Acad. Sci. U. S. A, vol.109, pp.19256-19261, 2012.

F. Pennacchietti, A. Losi, X. Xu, K. Zhao, W. Gärtner et al., Photochromic conversion in a red/green cyanobacteriochrome from Synechocystis PCC6803: quantum yields in solution and photoswitching dynamics in living E. coli cells, Photochromic Conversion in a Red/green Cyanobacteriochrome from Synechocystis PCC6803: Quantum Yields in Solution and Photoswitching Dynamics in Living E. Coli Cells, pp.229-237, 2015.
DOI : 10.1039/C4PP00337C

M. A. Robb and H. Grubmüller, Photoswitching of the Fluorescent Protein asFP595: Mechanism, Proton Pathways, and Absorption Spectra, Angew. Chem. Int. Ed, vol.46, pp.530-536, 2007.

I. Lindner, B. Knipp, S. E. Braslavsky, W. Gärtner, and K. Schaffner, A Novel Chromophore Selectively Modifies the Spectral Properties of One of the Two Stable States of the Plant Photoreceptor Phytochrome, Angewandte Chemie International Edition, vol.37, issue.13-14, pp.1843-1846, 1998.
DOI : 10.1002/(SICI)1521-3773(19980803)37:13/14<1843::AID-ANIE1843>3.0.CO;2-W

C. Renner, S. Alefelder, J. H. Bae, N. Budisa, R. Huber et al., Fluoroprolines as Tools for Protein Design and Engineering, Angewandte Chemie International Edition, vol.70, issue.5, pp.923-925, 2001.
DOI : 10.1002/1521-3773(20010302)40:5<923::AID-ANIE923>3.0.CO;2-#

M. Schönberger and D. Trauner, A Photochromic Agonist for ??-Opioid Receptors, Angewandte Chemie International Edition, vol.39, issue.12, pp.3264-3267, 2014.
DOI : 10.1002/anie.201309633

Y. Tsai, S. Essig, J. R. James, K. Lang, J. W. Chin et al., Selective, rapid and optically switchable regulation of protein function in live mammalian cells, Nature Chemistry, vol.265, issue.7, pp.554-561, 2015.
DOI : 10.1038/nchem.2253

S. Warnke, C. Baldauf, M. T. Bowers, K. Pagel, and G. Von-helden, Isomerization of Proline Peptide Bonds, Journal of the American Chemical Society, vol.136, issue.29, pp.10308-10314, 2014.
DOI : 10.1021/ja502994b

A. Masson, M. Z. Kamrath, M. A. Perez, M. S. Glover, U. Rothlisberger et al., Infrared Spectroscopy of Mobility-Selected H+-Gly-Pro-Gly-Gly (GPGG), Journal of The American Society for Mass Spectrometry, vol.136, issue.9, pp.1444-1454, 2015.
DOI : 10.1007/s13361-015-1172-4

N. J. Coughlan, B. D. Adamson, L. Gamon, K. Catani, and E. J. Bieske, Retinal shows its true colours: photoisomerization action spectra of mobility-selected isomers of the retinal protonated Schiff base, Phys. Chem. Chem. Phys., vol.50, issue.35, pp.22623-22631, 2015.
DOI : 10.1039/c5cp01567g

P. B. Markworth, B. D. Adamson, N. J. Coughlan, L. Goerigk, and E. J. Bieske, Photoisomerization action spectroscopy: flicking the protonated merocyanine???spiropyran switch in the gas phase, Phys. Chem. Chem. Phys., vol.139, issue.39, pp.25676-25688, 2015.
DOI : 10.1021/jp511975f

M. De-souza, V. R. Caetano, W. De-oliveira, H. P. Scarminio, I. S. Hioka et al., pKa Determinations of Xanthene Derivates in Aqueous Solutions by Multivariate Analysis Applied to UV?Vis Spectrophotometric Data, Spectrochim. Acta Part A Mol. Biomol. Spectrosc, vol.79, pp.889-897, 2011.

A. Simon, F. Chirot, C. M. Choi, C. Clavier, M. Barbaire et al., Tandem ion mobility spectrometry coupled to laser excitation, Review of Scientific Instruments, vol.86, issue.9, pp.94101-94102, 2015.
DOI : 10.1063/1.4930604
URL : https://hal.archives-ouvertes.fr/hal-01229281

H. E. Revercomb and E. A. Mason, Theory of plasma chromatography/gaseous electrophoresis. Review, Analytical Chemistry, vol.47, issue.7, pp.970-983, 1975.
DOI : 10.1021/ac60357a043

D. A. Pearlman, D. A. Case, J. W. Caldwell, W. S. Ross, T. E. Cheatham et al., AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules, Computer Physics Communications, vol.91, issue.1-3, pp.1-41, 1995.
DOI : 10.1016/0010-4655(95)00041-D

J. Wang, P. Cieplak, and P. Kollman, How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?, Journal of Computational Chemistry, vol.18, issue.12, pp.1049-1074, 2000.
DOI : 10.1002/1096-987X(200009)21:12<1049::AID-JCC3>3.0.CO;2-F

J. Wang, R. M. Wolf, J. W. Caldwell, and P. Kollman, Development and testing of a general amber force field, Journal of Computational Chemistry, vol.17, issue.9, pp.1157-1174, 2004.
DOI : 10.1002/jcc.20035

J. Wang, W. Wang, and . Kollman, Development and testing of a general amber force field, Journal of Computational Chemistry, vol.17, issue.9, pp.1157-1174, 2005.
DOI : 10.1002/jcc.20035

Y. Sugita and Y. Okamoto, Replica-exchange molecular dynamics method for protein folding, Chemical Physics Letters, vol.314, issue.1-2, pp.141-151, 1999.
DOI : 10.1016/S0009-2614(99)01123-9

D. Van-der-spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark et al., GROMACS: Fast, flexible, and free, Journal of Computational Chemistry, vol.26, issue.16, pp.1701-1718, 2005.
DOI : 10.1002/jcc.20291

B. Hess, C. Kutzner, D. Van-der-spoel, E. Lindahl, and . Gromacs, GROMACS 4:?? Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation, Journal of Chemical Theory and Computation, vol.4, issue.3, pp.435-447, 2008.
DOI : 10.1021/ct700301q

A. Kulesza, S. Daly, L. Macaleese, R. Antoine, and P. Dugourd, peptides, The Journal of Chemical Physics, vol.143, issue.2, pp.25101-25102, 2015.
DOI : 10.1063/1.4926390
URL : https://hal.archives-ouvertes.fr/hal-01344520

A. Becke, Density???functional thermochemistry. III. The role of exact exchange, The Journal of Chemical Physics, vol.98, issue.7, pp.5648-5652, 1993.
DOI : 10.1063/1.464913

J. Perdew, K. Burke, and M. Ernzerhof, Generalized Gradient Approximation Made Simple, Physical Review Letters, vol.77, issue.18, pp.3865-3868, 1996.
DOI : 10.1103/PhysRevLett.77.3865

T. Yanai, D. P. Tew, and N. C. Handy, A new hybrid exchange???correlation functional using the Coulomb-attenuating method (CAM-B3LYP), Chemical Physics Letters, vol.393, issue.1-3, pp.51-57, 2004.
DOI : 10.1016/j.cplett.2004.06.011

S. Grimme, S. Ehrlich, and L. Goerigk, Effect of the damping function in dispersion corrected density functional theory, Journal of Computational Chemistry, vol.22, issue.7, pp.1456-1465, 2011.
DOI : 10.1002/jcc.21759

S. Grimme, J. Antony, S. Ehrlich, and H. Krieg, parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu, The Journal of Chemical Physics, vol.132, issue.15
DOI : 10.1063/1.3382344

F. Weigend and R. Ahlrichs, Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy, Physical Chemistry Chemical Physics, vol.110, issue.16, pp.3297-3305, 2005.
DOI : 10.1039/b508541a

A. A. Shvartsburg and M. F. Jarrold, An exact hard-spheres scattering model for the mobilities of polyatomic ions, Chemical Physics Letters, vol.261, issue.1-2, pp.86-91, 1996.
DOI : 10.1016/0009-2614(96)00941-4

H. Shi, N. Atlasevich, S. I. Merenbloom, and D. E. Clemmer, Solution Dependence of the Collisional Activation of Ubiquitin [M + 7H]7+ Ions, Journal of The American Society for Mass Spectrometry, vol.50, issue.186, 2000.
DOI : 10.1007/s13361-014-0834-y

J. Dilger, L. Musbat, M. Sheves, A. V. Bochenkova, D. E. Clemmer et al., Direct Measurement of the Isomerization Barrier of the Isolated Retinal Chromophore, Angewandte Chemie International Edition, vol.5, issue.16, pp.4748-4752, 2015.
DOI : 10.1002/anie.201411894

R. Antoine and P. Dugourd, Visible and ultraviolet spectroscopy of gas phase protein ions, Physical Chemistry Chemical Physics, vol.130, issue.462, pp.16494-16509, 2011.
DOI : 10.1021/jp205617x
URL : https://hal.archives-ouvertes.fr/hal-00676501

S. B. Corchnoy, T. E. Swartz, J. W. Lewis, I. Szundi, W. R. Briggs et al., Intramolecular Proton Transfers and Structural Changes during the Photocycle of the LOV2 Domain of Phototropin 1, Journal of Biological Chemistry, vol.278, issue.2, pp.724-731, 2003.
DOI : 10.1074/jbc.M209119200

K. C. Toh, E. A. Stojkovic, I. H. Van-stokkum, K. Moffat, and J. T. Kennis, Proton-transfer and hydrogen-bond interactions determine fluorescence quantum yield and photochemical efficiency of bacteriophytochrome, Proceedings of the National Academy of Sciences, vol.107, issue.20, pp.9170-9175, 2010.
DOI : 10.1073/pnas.0911535107

A. Makarov and A. J. Heck, Exploring an Orbitrap Analyzer for the Characterization of Intact Antibodies by Native Mass Spectrometry, Angew. Chem. Int. Ed, vol.51, pp.12992-12996, 2012.

J. Marcoux and C. Robinson, Twenty Years of Gas Phase Structural Biology, Structure, vol.21, issue.9, pp.1541-1550, 2013.
DOI : 10.1016/j.str.2013.08.002