Abstract
Collision cross-section (CCS) measurements obtained from ion mobility spectrometry-mass spectrometry (IMS-MS) analyses often provide useful information concerning a protein’s size and shape and can be complemented by modeling procedures. However, there have been some concerns about the extent to which certain proteins maintain a native-like conformation during the gas-phase analysis, especially proteins with dynamic or extended regions. Here we have measured the CCSs of a range of biomolecules including non-globular proteins and RNAs of different sequence, size, and stability. Using traveling wave IMS-MS, we show that for the proteins studied, the measured CCS deviates significantly from predicted CCS values based upon currently available structures. The results presented indicate that these proteins collapse to different extents varying on their elongated structures upon transition into the gas-phase. Comparing two RNAs of similar mass but different solution structures, we show that these biomolecules may also be susceptible to gas-phase compaction. Together, the results suggest that caution is needed when predicting structural models based on CCS data for RNAs as well as proteins with non-globular folds.Graphical ᅟ
Highlights
The advent of electrospray ionisation (ESI) transformed the field of mass spectrometry (MS) by providing the ability to routinely analyze large proteins and noncovalently bound biomolecular complexes
Similar behavior of monoclonal antibodies has been reported by others [27, 28], and Pacholarz et al carried out in vacuo Molecular Dynamics (MD) simulations to interrogate the observed compaction of IgG molecules in the gas-phase, demonstrating that the protein likely collapsed around the hinge region in between the fragment antigen-binding (Fab) and the fragment crystallizable (Fc) regions [28]
Here we have presented a small number of protein examples from our 14 years’ experience with ESI-ion mobility spectrometry-mass spectrometry (IMS-MS) where we have found that the Collision cross-section (CCS) values measured underestimate the physical size of the solution structure and modeled data of the biomolecule under scrutiny
Summary
The advent of electrospray ionisation (ESI) transformed the field of mass spectrometry (MS) by providing the ability to routinely analyze large proteins and noncovalently bound biomolecular complexes. Ion mobility spectrometry (IMS) is a separation technique based on the gas-phase mobility of ions as they travel, under. Electronic supplementary material The online version of this article 1007/s13361-017-1689-9) contains supplementary material, which is available to authorized users. ESI-IMS-MS has been employed to study the 3D architecture and conformational properties of many proteins and noncovalently bound biomolecular complexes [4,5,6,7,8,9, 14,15,16,17,18,19,20,21,22]
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