Native MS Analysis of Bacteriorhodopsin and an Empty Nanodisc by Orthogonal Acceleration Time-of-Flight, Orbitrap and Ion Cyclotron Resonance

Over the past two decades orthogonal acceleration time-of-flight has been the de facto analyzer of choice for solution and membrane soluble protein native mass spectrometry (MS) studies; this however is gradually changing. Here we compare three MS instruments, the Q-ToF, the Orbitrap and the FT-ICR to analyze, under native instrument and buffer conditions, the 7-transmembrane helical protein bacteriorhodopsin-octylglucoside micelle complex and the empty nanodisc (MSP1D1-Nd) using both MS and tandem-MS modes of operation. Bacteriorhodopsin can be released from the octylglucoside-micelle efficiently on all three instruments (MS-mode of operation) producing a narrow charge state distribution (z = 8+ to 10+) by either increasing the source lens or collision cell (or HCD) voltages. A lower center-of-mass collision energy (0.20–0.41 eV) is required for optimal bacteriorhodopsin liberation on the FT-ICR, in comparison to the Q-ToF and Orbitrap instruments (0.29–2.47 eV). The empty MSP1D1-Nd can be measured with relative ease on a three instruments, resulting in a highly complex spectrum of overlapping, polydisperse charge state; a consequence of varying levels of phospholipid incorporation. There is a measurable difference in MSP1D1-Nd charge state distribution (z = 15+ to 26+), average molecular weight (141.7 to 169.6 kDa) and phospholipid incorporation number (143 to 184) under low activation conditions. Utilizing tandem-MS, bacteriorhodopsin can be effectively liberated from the octylglucoside-micelle by collisional (Q-ToF and FT-ICR) or continuous IRMPD activation (FT-ICR). MSP1D1-Nd spectral complexity can also be significantly reduced by tandem-MS (Q-ToF and FT-ICR) followed by mild collisional or continuous IRMPD activation, resulting in a spectrum in which the charge state and phospholipid incorporation levels can easily be determined.