Measurement of collision cross section (CCS), a parameter
reflecting
an ion’s size and shape, alongside high-resolution mass analysis
extends the depth of molecular analysis by providing structural information
beyond molecular mass alone. Although these measurements are most
commonly undertaken using a dedicated ion mobility cell coupled to
a mass spectrometer, alternative methods have emerged to extract CCSs
directly by analysis of the decay rates of either time-domain transient
signals or the FWHM of frequency domain peaks in FT mass analyzers.
This information is also accessible from FTMS mass spectra obtained
in commonly used workflows directly without the explicit access to
transient or complex Fourier spectra. Previously, these experiments
required isolation of individual charge states of ions prior to CCS
analysis, limiting throughput. Here we advance Orbitrap CCS measurements
to more users and applications by determining CCSs from commonly available
mass spectra files as well as estimating CCS for multiple charge states
simultaneously and showcase these methods by the measurement of CCSs
of fragment ions produced from collisional activation of proteins.
Glycerophospholipids
(GPLs), one of the main components of bacterial
cell membranes, exhibit high levels of structural complexity that
are directly correlated with biophysical membrane properties such
as permeability and fluidity. This structural complexity arises from
the substantial variability in the individual GPL structural components
such as the acyl chain length and headgroup type and is further amplified
by the presence of modifications such as double bonds and cyclopropane
rings. Here we use liquid chromatography coupled to high-resolution
and high-mass-accuracy ultraviolet photodissociation mass spectrometry
for the most in-depth study of bacterial GPL modifications to date.
In doing so, we unravel a diverse array of unexplored GPL modifications,
ranging from acyl chain hydroxyl groups to novel headgroup structures.
Along with characterizing these modifications, we elucidate general
trends in bacterial GPL unsaturation elements and thus aim to decipher
some of the biochemical pathways of unsaturation incorporation in
bacterial GPLs. Finally, we discover aminoacyl-PGs not only in Gram-positive
bacteria but also in Gram-negative C. jejuni, advancing
our knowledge of the methods of surface charge modulation that Gram-negative
organisms may adopt for antibiotic resistance.
The structural diversity of phospholipids
plays a critical role
in cellular membrane dynamics, energy storage, and cellular signaling.
Despite its importance, the extent of this diversity has only recently
come into focus, largely owing to advances in separation science and
mass spectrometry methodology and instrumentation. Characterization
of glycerophospholipid (GP) isomers differing only in their acyl chain
configurations and locations of carbon–carbon double bonds
(CC) remains challenging due to the need for both effective
separation of isomers and advanced tandem mass spectrometry (MS/MS)
technologies capable of double-bond localization. Drift tube ion mobility
spectrometry (DTIMS) coupled with MS can provide both fast separation
and accurate determination of collision cross section (CCS) of molecules
but typically lacks the resolving power needed to separate phospholipid
isomers. Ultraviolet photodissociation (UVPD) can provide unambiguous
double-bond localization but is challenging to implement on the timescales
of modern commercial drift tube time-of-flight mass spectrometers.
Here, we present a novel method for coupling DTIMS with a UVPD-enabled
Orbitrap mass spectrometer using absorption mode Fourier transform
multiplexing that affords simultaneous localization of double bonds
and accurate CCS measurements even when isomers cannot be fully resolved
in the mobility dimension. This method is demonstrated on two- and
three-component mixtures and shown to provide CCS measurements that
differ from those obtained by individual analysis of each component
by less than 1%.
The direct correlation between proteoforms
and biological phenotype necessitates the exploration of mass spectrometry
(MS)-based methods more suitable for proteoform detection and characterization.
Here, we couple nano-hydrophobic interaction chromatography (nano-HIC)
to ultraviolet photodissociation MS (UVPD-MS) for separation and characterization
of intact proteins and proteoforms. High linearity, sensitivity, and
sequence coverage are obtained with this method for a variety of proteins.
Investigation of collisional cross sections of intact proteins during
nano-HIC indicates semifolded conformations in low charge states,
enabling a different dimension of separation in comparison to traditional,
fully denaturing reversed-phase separations. This method is demonstrated
for a mixture of intact proteins from Escherichia coli ribosomes; high sequence coverage is obtained for a variety of modified
and unmodified proteoforms.
The measurement of collision cross sections (CCS, σ) offers supplemental information about sizes and conformations of ions beyond mass analysis alone. We have previously shown that CCSs can be determined directly from the time-domain transient decay of ions in an Orbitrap mass analyzer as ions oscillate around the central electrode and collide with neutral gas, thus removing them from the ion packet. Herein, we develop the modified hard collision model, thus deviating from the prior FT-MS hard sphere model, to determine CCSs as a function of center-of-mass collision energy in the Orbitrap analyzer. With this model, we aim to increase the upper mass limit of CCS measurement for native-like proteins, characterized by low charge states and presumed to be in more compact conformations. We also combine CCS measurements with collision induced unfolding and tandem mass spectrometry experiments to monitor protein unfolding and disassembly of protein complexes and measure CCSs of ejected monomers from protein complexes.
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