1. Ion Mobility Mass Spectrometry: Fundamentals
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What is it?
Why use it?
Hannah Florance
Field Applications Specialist LCMS
LMN Spring Workshop
26 April 2019
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September 22, 2019

2. Drift (Time Resolved) Ion Mobility – A Brief History…
1905
Ion mobility theory
Paul Langevin
1965
McDaniel & Mason
Transport of Ions in Gases
Clemmer, Jarrold
Applications to clusters & biomolecules
1997
2006
Clemmer, Smith
Drift Tube – with Analytical Merit
2014
Agilent
IM-QTOF
Mason-Schamp
Equation 1950’s
Mass Spectrograph
Aston & Thomson
1919
Paul Langevin (pronounced “Lon jeux van”) originated ion mobility theory in early 1900’s and ion mobility and mass spectrograph were joined in 1919 with collaboration between Aston and Thomson. The first commercial version of ion mobility appeared with Waters SYNAPT Triwave in Agilent has now introduced a high performance uniform field mobility drift tube design at this year’s ASMS conference.
Langevin ion-mobility theories [länzh·van ¦ī‚än mō′bil·əd·ē ‚thē·ə·rēz] (electronics) Two theories developed to calculate the mobility of ions in gases;
1. assumes that atoms and ions interact through a hard-sphere collision and have a constant mean free path, while the
2. assumes that there is an attraction between atoms and ions arising from the polarization of the atom in the ion's field, in addition to hard-sphere repulsion for close distances of approach.
McGraw-Hill Dictionary of Scientific & Technical Terms, 6E, Copyright © 2003 by The McGraw-Hill Companies, Inc.
Transport Properties of Ions in Gases Even though the book was published after Earl McDaniel's death, it carries his name because it is a sequel to a series of books entitled "Collision Phenomena in Ionized Gases" published in 1965, "The Mobility and Diffusion of Ions in Gases" published in 1973; and "Atomic Collisions" published in 1989 that do carry his name. "Transport Properties of Ions in Gases" is the last book that Edward Mason wrote before he died. It summarizes all his thoughts, both published and unpublished. Because of the amount of work that Edward Mason did on the classical theory of atomic and molecular scattering in ion mobility spectrometry, this book is an invaluable resource for the field of ion mobility spectrometry.
Hoaglund, C. S.; Valentine, S. J.; Sporleder, C. R.; Reilly, J. P.; Clemmer, D. E.  Three-Dimensional Ion Mobility/TOFMS Analysis of Electrosprayed Biomolecules, Analytical Chemistry  1998, 70,
Hoaglund, C. S.; Valentine, S. J.; Clemmer, D. E.  An Ion Trap Interface for ESI-Ion Mobility Experiments, Analytical Chemistry  1997, 69,
Liu, Y.; Clemmer, D. E.  Characterizing Oligosaccharides Using Injected-Ion Mobility/Mass Spectrometry, Analytical Chemistry  1997, 69,
Clemmer, D. E.; Jarrold, M. F.  Ion Mobility Measurements and their Applications to Clusters and Biomolecules, J. Mass Spectrom.  1997, 32,
Valentine SJ, MD Plasencia, X Liu, M Krishnan, S Naylor, HR Udseth, RD Smith, and DE Clemmer. 2006. "Toward Plasma Proteome Profiling with Ion Mobility-Mass Spectrometry." Journal of Proteome Research 5(11):   doi: /pr060232i
Eiceman and Karpas book published in 2005
Wilkins and Trimpin book published in 2010
Eiceman and H.Hill are 2 of the editors for the Int. Journal for IMS which supports the Int. Society for IMS.
300
200
100
# Journal Publications/ year
Anal. Chem., 2015, 87 (3), pp 1422–1436
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3. Ion Mobility – Commercial and Custom Instrumentation
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Drift Tube (DTIM)
Travelling Wave (TWIMS)
Trapped (TIMS)
High-Field Asymmetric Waveform (FAIMS)
Differential or field asymmetric waveform IMS (FAIMS) [4, 23] exploits that K depends on E to separate species by the difference of mobility (∆K) at high and low E. In practice, a strong periodic electric field E(t), with the peak intensity called “dispersion field” (E D), is created in a gap between two electrodes using an asymmetric waveform (with the amplitude called “dispersion voltage,” DV) applied to one. Ions, carried through the gap by gas flow, oscillate and drift toward one of the electrodes where they are neutralized. A weak fixed “compensation field” (E C) superposed on E(t) may offset the drift for a species with certain K(E) function and permit it to pass the gap, while other ions remain unstable and are eliminated. Scanning E C reveals the spectrum of ions entering the gap.
September 22, 2019
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4. Ion Mobility - Gas Phase Separation of Ions
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Common Uses
Portable (In the Field)
Drugs and Explosives
Explosive screening (Airports/ Military)
Atmospheric Pressure
Mass Spectrometer (Research)
Proteomics
Protein Conformations/ Structure
Pesticides and Clinical
Metabolomics/ Lipidomcs
Controlled Temperature and Pressure
Anal. Chem. 2014, 86, 2107
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5. Ion Mobility – Gas Phase Separation of Ions
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td (ms)
Arrival Time Distribution (ATD)
Size (mass)
Shape (structure)
Charge
Mobility through a carrier buffer gas
Illustration how the shape of the analyte ion influences the
differences in cross section measured in distinct buffer gases with
different sizes (i.e., interaction potentials).
The shape of an analyte ion can also affect its interaction
potential with the buffer gas and thus influence the
relative difference between momentum transfer cross sections
determined in different buffer gases in addition to temperature
and molecular weight of the analyte. For example, a rod-like
analyte ion interacts with the buffer gas through a larger surface
area than a sphere-like ion. Hence, a rod-like ion (such as
charge state 13+ of ubiquitin) is expected to experience a larger
change in cross section than a sphere-like ion (such as the
native state of ubiquitin) when the buffer gas is changed. A
similar buffer gas effect is anticipated for analyte ions with a
strong surface roughness and molecular cavities present in
many protein systems compared to an ion without cavities
Increasing Interaction with Buffer Gas
Increasing Surface Area
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6. Ion Mobility – Collisional Cross Section
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td (ms)
CCS
The ion travels through the ion mobility drift cell and the instrument measures the time in ms to reach the detector.
The space an ion fills as it turns it’s way through the cell gives the impression of occupying a spherical space.
If you slice it in half, the calculated area of that surface is the collisional cross section.
Ω (CCS) Å2
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7. Ion Mobility – What does it bring to the table?
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Orthogonal separation
Reduced noise
More features (?)
Structural Information
Multiple conformations (proteins/peptides/glycans)
Separate isomers
Distinguish between isobars
Angew. Chem. Int. Ed. 2017, 56, 8342 – 8349
Unique identifying characteristic
RT, m/z, CCS
Aid to metabolite classification
I’ve put a (?) by more features because we might lose a bit on sensitivity, but we can separate co-eluting analytes
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8. Current Opinion in Chemical Biology 2018, 42:51–59
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Let’s look a bit more closely at the theoretical model behind ion mobility. For the most part I used this paper as the guide
Current Opinion in Chemical Biology 2018, 42:51–59
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9. Basic Principles of DTIM
𝑞=𝑧.ⅇ
𝑁, gas number density
𝑇, gas temperature
𝑝, gas pressure
Basic Principles of DTIM
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What are we measuring?
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Mobility of ions, 𝐾
Dependent on:
Charge of ion, 𝒛
No. of Collisions made with the gas
direct current Electric Field, 𝑬
Resulting in:
ions migrating at
Constant Velocity, 𝜈 𝑑 =𝐾.𝐸
Mobility is a function of an ions interaction with a buffer gas.
Note here that the SHAPE of the molecule really dictates the number of collisions. Therefore, the drag (or friction) is dependent on the shape of the molecule.
The presence of the electric field causes the ions to accelerate through the drift cell. In order to counteract that, so that there’s time for the different shapes to separate, we need to strike a balance by invoking enough drag (supplied in the form of the buffer gas) to decelerate the ions.
Drag Force/
Fluid Friction
𝐹=𝑞.𝐸
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10. Stacked ring ion guide gives linear field
Basic Operational Principle of Ion Mobility For Conventional DC Uniform Field IMS VH
Ion Mobility Cell VL
Analyte
Ions
Detector
If we take a look at what happens when there is no drag, i.e. no gas we see the ions fly straight through the drift cell.
Gating
Optics
Electric Field
Stacked ring ion guide gives linear field
𝑣=𝐾 𝐸 ∝ 𝑒 𝐸 𝑃 𝑇 Ω
2015 ASMS
IM-QTOF workshop 06/03/15

11. 60 msec 0 msec Low Field Drift Cell VH VL Detector Analyte Ions Gating
Ion Mobility Cell VL
Analyte
Ions
Detector
This animation is a basic depiction of how the ion mobility separation occurs in the low field drift cell of the The larger the structure of the ion moving through the cell, the slower it moves through as it interacts with the drift gas that is present in the cell. The smaller ions move through more quickly, as there is less interaction with the gas molecules. There is also a dependency on charge state. The pressure in the drift cell is approximately 4 torr.
This is an animation which illustrates the basic operational principle of ion mobility within conventional drift tube designs. Use your prompt to sequentially show the nitrogen buffer gas molecules moving within the flight tube. Then show the trap gate holding back the two compounds- one has more of a more dense ball shape and the other a more open fan shape. When the ion gate opens the ball shaped molecule has fewer gas collisions and arrives at the detector faster while the fan shaped molecule has more gas collisions and comes out later. A direct current (DC) electric field is used to drive ions from the trapping funnel into the drift cell and then into the rear funnel.
Note : Nitrogen is used as the main buffer gas and the drift cell operates at pressure of 4 Torr nitrogen =~ 17 cm mean free path.
4mm nitrogen =~ 17 cm mean free path
Gating
Optics t0
tdrift
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12. Basic Principles of DTIM
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Measuring mobility, K
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𝜈 𝑑 =𝐾.𝐸
𝜈 𝑑 = 𝐿 𝑡 𝑑
𝐸= Δ𝑉 𝐿
𝐾= 𝐿 2 𝑡 𝑑 .Δ𝑉 VH VL ΔV
Length, L
t=0
t=td
𝐾= 𝐿 𝑡 𝑑 Δ𝑉 𝐿 𝐾= 𝜈 𝑑 𝐸
We can measure certain parameters such as the length of the tube, , the time taken for the ions to travel along the tube and the change on voltage. Using these 3 parameters we can calculate the velocity and electric field and thus, K.
However, it’s not that simple. We need to look at the influence of the gas and the friction/ drag it has on the mobility.
September 22, 2019
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13. Basic Principles of DTIM
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Reduced Mobility to correct for collision frequency
9/22/2019
Influential Parameters
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Standard Conditions
𝑁0 = x 1025 m−3
𝑇0 = K
𝑝0 = 760 Torr
Temperature and Pressure
𝑞=𝑧.ⅇ
𝑁, gas number density
𝑇, gas temperature
𝑝, gas pressure
We use standard conditions to correct for the collision frequency. Known as Reduce Mobility
𝐾 0 =𝐾 𝑁 𝑁 0 =𝐾 𝑝𝑇0 𝑝 0 𝑇
𝑁= 𝑛 𝑉 = 𝑝 𝑅𝑇
where
(perfect gas)
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14. Basic Principles of DTIM
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Influential Parameters
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𝐾 0 = 𝐿 2 𝑡 𝑑 .Δ𝑉 . 𝑝𝑇0 𝑝 0 𝑇 𝐾
Reaching the detector ΔV
Length, L
t=0 td
+t0 tA
tA = t0 + td
rearrange for td
tA = t0 + 𝐿 2 𝐾 0 .Δ𝑉 . 𝑝𝑇0 𝑝 0 𝑇
We know what p and delta V are at the time of acquisition. This leaves the remaining unknown K0 and t0 to be calculated. By plotting p/deltaV against tA the y intercept is t0 and the slope, K0 (reciprocal of reduced mobility)
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15. Basic Principles of DTIM
y = c + mx
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Influential Parameters
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tA = t0 + 𝐿 2 𝐾 0 .Δ𝑉 . 𝑝𝑇0 𝑝 0 𝑇
Reaching the Detector ΔV
Length, L
t=0 td
+t0 tA tA
1 𝐾 0
Substitute our mobility equation with known, measured values. We now have two unknowns remaining, t0 and K0. rearrange our reduced mobility for our known drift time and we have a classic equation t0
𝑝 Δ𝑉
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16. Basic Principles of DTIM
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9/22/2019
Drift Time to Ω (Momentum Transfer Collision Integral)
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K  Kinetic Energy Need Boltzmann Constant (𝑘𝑏) Assume: Elastic Collisions – energy is conserved
Charge on ion
Elementary charge
𝐾= 3.𝑧ⅇ 16.𝑁 2𝜋 𝜇𝑘𝑏𝑇 𝛺
Mobility K can be related to the collision cross section using kinetic theory
Buffer gas density no.
Observed Temp, K
Boltzmann Constant
𝑚 𝑖𝑜𝑛 𝑚 𝑔𝑎𝑠 𝑚 𝑖𝑜𝑛 + 𝑚 𝑔𝑎𝑠
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17. Basic Principles of DTIM
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Calculating the Collisional Cross Section
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Elementary charge
Electric field
Mason Schamp Eqn Think about CCS as a momentum transfer cross section Keep electric field low Assumption that drift velocity, 𝜈 𝑑 is small compared to thermal velocity, 𝜈 𝑇
Temp, K
Ion charge state
Corrected drift time
where Ω is the momentum transfer collision integral (the
measured CCS value in this study),
u is the reduced mass of the ion–gas pair (m = mM/(m + M), where m and M are the ion and gas-particle masses), kB is the Boltzmann constant, and ze is the analyte charge.
Boltzmann Constant
No. density of drift gas
Mass of ion
Drift gas pressure
Mass of drift gas
Drift tube length
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18. DTIM - Challenges Practical challenges: Theoretical challenges:
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9/22/2019
Practical challenges:
Increasing the resolution
longer tube
higher p
higher ΔV
alternative gas
Gas purity with no net gas flow
Measuring p inside the tube
Measuring T inside the tube
Determining the tube length L
Measuring the actual voltages
ΔV applied
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Theoretical challenges:
Widely used algorithms such as MobCal use He
Hard Spheres
MetCCS/ LipidCCS
Calc using chemical info
no structural information
Account for polarizability of gas
Trajectory method for other gases (N2)
Density Function Theory
Machine learning (input: chemical descriptors, not the structure)
• MetCCS: Zhou, Shen, Tu & Zhu, Anal. Chem. (2016) 88: 11084
• LipidCCS: Zhou, Tu, Xiong, Shen & Zhu, Anal. Chem. (2017) 89: 9559
Trajectory method (input: 3D structure from DFT calculation, and partial charges)
• Wu, Derrick, Nahin, Chen & Larriba-Andaluz, J. Chem. Phys. (2018) 148:
• Lee, Lee, Davidson, Bush & Kim, Analyst (2018) 143: 1786
• Ieritano, Crouse, Campbell & Hopkins, Analyst (2019) 144: 1660
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19. DTIM - Gases Nitrogen Helium Anal. Chem. 2014, 86, 2107−2116
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Nitrogen
Helium
Comparisons between helium and nitrogen-derived CCS values. (A) A scatter plot of class-specific subsets of CCS data measured in both
helium and nitrogen.
Anal. Chem. 2014, 86, 2107−2116
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20. Ubiquitin DTIM - Gases Native (N) state (charge states 6+ to 8+)
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Native (N) state
(charge states 6+ to 8+)
Unfolded A-state
(charge states 8+ to 11+)
PSA theoretical cross section
Ion mobility data in nitrogen and helium for ubiquitin. Experimental cross section data (triangles) for the native (N) state
(charge states 6+ to 8+) and the A-state (charge states 8+ to 11+) and
PSA theoretical cross section data (dots) in nitrogen (blue) and
helium (green).
Anal. Chem. 2015, 87, 7196−7203
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21. DTIM - Gases Agilent tune mix Alprenolol Ondansetron Clozapine N-oxide
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Analyst, 2015, 140, 6834–6844
Agilent tune mix
Alprenolol
Ondansetron
Clozapine N-oxide
Colchicine
Verapamil
Reserpine
CCS measurements for methoxyphosphazine and fluorophosphazine
compounds from the Agilent tune mix and the small molecules
(alprenolol, ondansetron, clozapine N-oxide, colchicine, verapamil
and reserpine) in different drift gases. The CCS values for a give ion in
different drift gases scale with the size of the drift gas atom or molecule
and the polarizability of the drift gas used.
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22. Drift Tube Ion Mobility Mass Spectrometer
Front Funnel
Trapping Funnel
Drift Tube
Rear Funnel
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23. Ion Mobility – Why use it?
Applications
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24. Ion Mobility – Collisional Cross Section
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Orthogonal separation
Reduced noise
Structural Information
Multiple conformations (proteins/peptides/glycans)
Separate isomers
Distinguish between isobars
Angew. Chem. Int. Ed. 2017, 56, 8342 – 8349
Unique identifying characteristic
RT, m/z, CCS
Aid to metabolite classification
What is the CCS giving us
September 22, 2019
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25. Time of Flight Mass Spectra
Orthogonal Separation
Mass Spectrum
Chromatogram
Ion Mobility
Signal Response
Separation
Full Time Scale
Peak Width
Chromatographic
Minutes
Seconds
Ion Mobility
~5-100 milliseconds
1-2 milliseconds
Time of Flight Mass Spectra
~150 microseconds
nanoseconds
The reason we can add ion mobility in line with our normal analysis is due to the extremely high rate of sampling in our QTOF. The key is being able to fully sample each peak within a signal. At the chromatographic time scale, peaks are a few seconds wide. In the ion mobility separation, the complete separation takes approximately 60 milliseconds, thus we can have dozens of samples of the peak coming out of the LC or GC. The ion mobility separated peaks are approximately 1-2 milliseconds wide. Our time of flight analyzer is sampling the entire mass range every 150 microseconds, allowing yet again many samples across the IM peak.
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26. Compound Classification using CCS
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Compoumd prediction – obtain a CCS for unknown – does it fall within a specfic region?
(A) A scatter plot of the CCS values measured in this study, separated by chemical class. (B) Best fit lines of the data, separated into class
and fit to a power-law function. Also shown are data inclusion bands representing ±5% deviation from the best fit line. The inset bar graph
represents the amount of data included within different sized inclusion bands.
Anal. Chem. 2014, 86, 2107−2116
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27. Applications - Isobars
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Two pesticides, differing in mass by less than 0.2 millidaltons, require overall separation power of approximately 2,000,000x to resolve them. Clear IMS drift separation of the two compounds (blue and red), which are separated by milliseconds in drift time. Even at a concentration difference of 10:1 between the two compounds, the drift resolution is sufficient to separate the two isobaric compounds without the use of UHPLC.
© Agilent Technologies, Inc., EN
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28. Applications - Isomers
© Agilent Technologies, Inc., EN
Applications - Isomers
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Citrate
(C6 H8 O7)
Isocitrate
(C6 H8 O7)
Citrate and isocitrate are isomers that are very similar in physical properties and structure. This presents challenges in their bio-analytical characterization.
September 22, 2019
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29. Applications – Lipid Classification
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456 Singly charged lipids
7 classes
2 categories
Ion mobility conformational lipid atlas for high confidence lipidomics
Katrina L. Leaptrot, Jody C. May, James N. Dodds & John A. McLean
Conformational space analysis of all 456 singly charged lipids surveyed in this work. Included are data from 7 classes from 2 lipid categories in positive and negative ionization mode. Markers for cations are indicated by a white border while those for anions are indicated by a black border. Error bars represent standard errors and are for each point within the scale of the marker. Specific lipid identifications, numerical measurement data, and number of measurements per data point (n = 8 or 16 repeat measurements for positive ionization mode data, n = 20, 21, or 28 repeat measurements for negative ionization mode data) are provided in Supplementary Data 1
Nature Communications,
Vol. 10, 985 (2019) 
Phosphatidylethanolamines
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30. Applications – Lipid Classification
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Ion mobility conformational lipid atlas for high confidence lipidomics
Katrina L. Leaptrot, Jody C. May, James N. Dodds & John A. McLean
Conformational space occupancy of lipids within a narrow range of mass. a Expanded region from Fig. 2 highlighting occupancy of each lipid class by mass and DTCCSN2. Note the largest DTCCSN2 difference for peaks of similar mass is between glycerophospholipids and sphingolipids. Markers for cations are indicated by a white border while those for anions are indicated by a black border. Error bars represent standard errors and are within the marker itself for each point. bPrimary structures of the five positively charged nominal mass isomeric lipid ions (809.6–810.7 Da, SM structure is for the feature of lesser cross section) highlighted in panel A. DTCCSN2 values are all statistically different and largest for sphingolipids. Note structural information is inferred from rules described by Voet, et al. with (i) lipids assembled as concatenations of C2 units making even-numbered chains prevalent, (ii) the first unsaturation site preferably located between C9 and C10, (iii) subsequent unsaturation sites occurring every third bond, and (iv) double bonds existing primarily in the cis- configuration44. Poly-unsaturated fatty acyl side chains are constructed from commonly encountered fatty acid structures with preference for ω-3 and ω-6 chains. Adducts are shown at likely basic sites. Additionally, sphingolipids contain a sphingosine backbone. Specific lipid identifications, numerical measurement data, and number of measurements per data point (n = 8 or 16 repeat measurements for positive ionization mode data, n = 20, 21, or 28 repeat measurements for negative ionization mode data) are provided in Supplementary Data 1
Nature Communications,
Vol. 10, 985 (2019) 
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31. Round-Up Ion Mobility – What is it? Ion Mobility – Why use it?
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9/22/2019
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Ion Mobility – What is it?
Measurement of mobility, K (m2 V-1 s-1)
Ions separated by size, shape and charge
Force of the electric field on the ion is balanced by the drag/ friction of the gas
Constant velocity, 𝜈 𝑑
CCS is dependent on the ion-gas pair
Temperature, Pressure
Polarizability
Mobility must relate to kinetic energy to calculate the CCS
Momentum Transfer Cross Section
Ion Mobility – Why use it?
Orthogonal Separation for Hyphenated MS techniques
Improved S/N
Increased numbers of metabolites
Separation isomers/ isobars
Provides an extra dimension of information for identifying known and unknown metabolites
Method for classifying compounds
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