Tailoring peptide conformational space with organic gas modifiers in TIMS-MS
Recently, we showed the advantages of Trapped Ion Mobility Spectrometry for the study of kinetic intermediates of biomolecules as a function of the starting solvent composition (e.g., organic content and pH) and collisional induced activation. In the present work, we further characterize the influence of the bath composition (e.g., organic content) on the conformational space of an intrinsically disordered, DNA binding peptide: AT-hook 3 (Lys-Arg-Pro-Arg-Gly-Arg-Pro-Arg-Lys-Trp). Results show the dependence of the charge state distribution and mobility profiles by doping the solution and the bath gas with organic modifiers (e.g., methanol and acetone). The high resolving power of the TIMS analyzer allowed the separation of multiple IMS band per charge state, and their relative abundances are described as a function of the experimental conditions. The use of gas modifiers resulted in larger inverse mobilities, with a direct correlation between the size of the modifier and the 1/K0 differences. Conformational isomer inter-conversion rates were observed as a function of the trapping time. Different from solution experiments, a larger variety of organic gas modifiers can be used to tailor the peptide conformational space, since peptide precipitation is not a problem.
KeywordsTrapped ion mobility mass spectrometry Intrinsically disordered protein HMGA2 ATHP
This work was supported by the National Science Foundation Division of Chemistry, under CAREER award CHE-1654274, with co-funding from the Division of Molecular and Cellular Biosciences to F.F.-L. The authors will also like to acknowledge the helpful discussions and technical support from Dr. Mark E. Ridgeway and Dr. Melvin A. Park from Bruker Daltonics Inc. during the development and installation of the custom-built TIMS-TOF MS instrument.
- 3.Benigni P, Marin R, Fernandez-Lima F (2015) Towards unsupervised polyaromatic hydrocarbons structural assignment from SA-TIMS –FTMS data. Int J Ion Mobil Spectrom:1–7. https://doi.org/10.1007/s12127-015-0175-y
- 14.Levin DS, Vouros P, Miller RA, Nazarov EG, Morris JC (2006) Characterization of gas-phase molecular interactions on differential mobility ion behavior utilizing an electrospray ionization-differential mobility-mass spectrometer system. Anal Chem 78(1):96–106. https://doi.org/10.1021/ac051217k CrossRefGoogle Scholar
- 16.Loo JA (1997) Studying noncovalent protein complexes by electrospray ionization mass spectrometry. Mass Spectrom Rev 16(1):1–23. https://doi.org/10.1002/(sici)1098-2787(1997)16:1<1::aid-mas1>3.0.co;2-l CrossRefGoogle Scholar
- 17.McDaniel EW, Mason EA (1973) Mobility and diffusion of ions in gases. Wiley series in plasma physics. John Wiley and Sons, Inc., New YorkGoogle Scholar
- 18.Meyer T, Gabelica V, Grubmüller H, Orozco M (2013) Proteins in the gas phase. Wiley Interdiscip Rev: Comput Mol Sci 3:408–425Google Scholar
- 23.Porta T, Varesio E, Hopfgartner G (2013) Gas-phase separation of drugs and metabolites using modifier-assisted differential ion mobility spectrometry hyphenated to liquid extraction surface analysis and mass spectrometry. Anal Chem 85(24):11771–11779. https://doi.org/10.1021/ac4020353 CrossRefGoogle Scholar
- 32.Schneider B, Covey T, Nazarov E (2013) DMS-MS separations with different transport gas modifiers vol 16. https://doi.org/10.1007/s12127-013-0130-8
- 36.Silveira JA, Fort KL, Kim D, Servage KA, Pierson NA, Clemmer DE, Russell DH (2013) From solution to the gas phase: stepwise dehydration and kinetic trapping of substance P reveals the origin of peptide conformations. J Am Chem Soc 135(51):19147–19153. https://doi.org/10.1021/ja4114193 CrossRefGoogle Scholar
- 39.Waraksa E, Gaik U, Namieśnik J, Sillanpää M, Dymerski T, Wójtowicz M, Puton J (2016) Dopants and gas modifiers in ion mobility spectrometry vol 82. https://doi.org/10.1016/j.trac.2016.06.009
- 40.Winston RL, Fitzgerald MC (1997) Mass spectrometry as a readout of protein structure and function. Mass Spectrom Rev 16(4):165–179. https://doi.org/10.1002/(sici)1098-2787(1997)16:4<165::aid-mas1>3.0.co;2-f CrossRefGoogle Scholar