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J Biomol Tech. 2007 February; 18(1): 50.
PMCID: PMC2292024

P144-T Top Down Sequence Analysis of Intact Protein Species Using a Novel Travelling Wave Ion Mobility Device Coupled With a Time-of-Flight Mass Spectrometer


In this presentation we will demonstrate the utility of Ion Mobility Spectrometry in the top down sequencing of proteins. These data were acquired using a novel Quadrupole/TWIMS/oa-Tof mass spectrometer, operated with a nanoelectrospray ion source. The TWIMS is a stacked-ring ion guide, operated at elevated pressure, with opposite phases of an rf voltage applied to adjacent plates to provide radial ion confinement. A continual sequence of dc pulses is superimposed on the confining rf to provide ‘waves’ which propel ions through the gas. Protein species were ionised and the resulting ions separated based upon their ion mobility, or collision cross section, through the TWIMS device and subsequently mass analysed using the oa-TOF analyser.

We have investigated the use of the hybrid ion mobility/ time-of-flight system for the top down analysis of proteins and compared these data with the data that can be obtained without an IMS separation. We have fragmented different charge states of the same protein and, by the post analysis selection of different regions of m/z vs drift time plots, produced spectral information which contains fragment ions of similar charge states. These selected regions can reveal species that are hidden in the non mobility experiment and these specific charge state spectra can be subsequently deconvoluted to produce sequence information. Typical increases in sequence coverage of around 20–25% are observed with a mobility enabled acquisition compared to a non mobility experiment.

Articles from Journal of Biomolecular Techniques : JBT are provided here courtesy of The Association of Biomolecular Resource Facilities