Introduction to MALDI-TOF

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Introduction to MALDI-TOF

• Jennifer Krone Ph.D.
• Senior Field Application Specialist

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Basic Components of a Mass Spectrometer
Vacuum Envelope
Ionization
Mass Sorting (filtering)
Detection
Ion Source
Ion Detector
Mass Analyzer
Forms ions (charged molecules)
Sort Ions by Mass (m/z)
Detect ions
Data System
Mass Spectrum
Relative Abundance
Sample Inlet
Sample/Matrix dried on MALDI Plate
2000
1000
m/z
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Mass Spectrometer Schematic
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Ion Sources make ions from sample molecules

• For biological applications, ion sources convert
  neutral molecules to ions by adding (taking away)
  one or more protons.
• Ions may be singly or multiply charged.
• Ions are easier to control in the mass
  spectrometer than neutral molecules.
• Ions are easier to detect than neutral molecules.
• In Voyager MALDI-TOF MS ions are formed in pulses
  at 3 20 cycles per second.

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Ion Sources Make IonsFrom Sample Molecules

• For biological applications, ion sources convert
  neutral molecules to ions by adding or taking
  away one or more protons.
• Ions may be singly or multiply charged.
• Ions are easier to control in the mass
  spectrometer than neutral molecules.
• Ions are easier to detect than neutral molecules.

M H energy MH
M2H2

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Primary Ionization Techniques for Biological
Molecules

• Electrospray Ionization (ESI)
• Includes high (ml) and low (nl) flow rate liquid
  transfer
• NanosprayTM Ion Source
• ElectrosprayTM Source
• Micro Ion SprayTM Source
• Turbo Ion Spray TM Source
• Matrix Assisted Laser Desorption Ionization
  (MALDI)
• Sample is dissolved with an energy transferring
  compound or matrix
• This is spotted on to a metal plate and allowed
  to crystallize
• When a laser is applied matrix crystals transfer
  energy facilitating ionization

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Electrospray Ionization (ESI)
Vacuum Interface
charged droplets form
High Voltage



Sample Flow


Nebulizer Gas
Ions released
Spray
Broad range of implementations based on flow
rate and polarity of compound class
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ESI Spectrum of Trypsinogen (MW 23983)
M 15 H
1599.8
M 16 H
M 14 H
1499.9
1714.1
Relative Abundance
M 13 H
1845.9
1411.9
1999.6
2181.6
m/z
Mass-to-charge ratio
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Matrix Assisted Laser Desorption Ionization
(MALDI)
Laser
Sample plate
hn
1. Sample (A) is mixed with excess matrix (M)
and dried on a MALDI plate. 2. Laser flash
ionizes matrix molecules. 3. Sample molecules
are ionized by proton transfer from matrix MH
A ? M AH.
Variable Ground Grid Grid
20 kV
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MALDI/TOF Mass Spectrum of IgG
MH
Relative Abundance
(M2H)2
(M3H)3
50000
100000
150000
200000
m/z
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Mass Analyzers Measure The Mass of Ions

• Operate under high vacuum (keeps ions from
  bumping into gas molecules)
• Actually measure mass-to-charge ratio of ions
  (m/z)
• Key specifications are resolution, mass accuracy,
  sensitivity and mass range.

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Another parameter to rememberIsotopes
Most elements have more than one stable
isotope. For example, most carbon atoms have a
mass of 12 Da, but in nature, 1.1 of C atoms
have an extra neutron, making their mass 13 Da.
Mass spectrum of peptide with 94 C-atoms (19
amino acid residues)
Monoisotopic mass
No 13C atoms (all 12C)
One 13C atom
Two 13C atoms
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Mass Analyzers Employed in Modern Proteomics

• Quadrupole (including multiple Quadrupoles)
• Unit resolution capabilities using frequencies
  to separate ions. Low mass accuracy and
  resolution. Limited mass range.
• Time of Flight (including multiple TOF)
• High resolution and accurate mass capabilities
  using time and distance to separate ions.
  Unlimited mass range.
• Ion Trap
• Unit and higher resolution capabilities using
  frequency to separate ions. Moderate mass
  accuracy, limited mass range.
• Fourier Transform (FT)
• High resolution and mass accuracy using frequency
  to separate ions.
• Hybrid
• Combination of different types of analyzers to
  achieve specific application requirements.

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Quadrupole Mass Analyzer
Uses a combination of Radio Frequency(RF) and
Direct Current(DC) voltages to operate as a mass
filter.

• Has four parallel metal rods.
• Lets one mass pass through at a time.
• Can scan through all masses or sit at one fixed
  mass.

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QTRAP Hybrid Mass Spectrometer
3D Trap Full Scan Sensitivity MS3 (or greater)
Q Trap
Tandem in SPACE TIME
Tandem in TIME
QqQ MRM Sensitivity Neutral Loss Precursor Scan
Full Scan Sensitivity MS3 MRM Sensitivity Neutral
Loss Precursor Scan Novel Scan Types
Tandem in SPACE
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MS/MS Tandem Mass Spectrometry Provides
information about the basic structure of the
compound
Applying two or more steps of mass analysis
separated in space or time (in the same
instrument) to select an analyte (ion) of
interest from a mixture and generate fragments
from it to give structural information.
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MS/MSTandem Mass Spectrum
Product ion spectrum of a compound m 1
Tandem Mass Spectrometers Triple Quadrupoles,
hybrid Quadrupole/trap, hybrid Quadrupole/TOF,
tandem time-of-flight
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Mass Spectrometers used in proteome research
Aebersold and Mann (2003) Nature 422, 198-207
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Voyager System Components
1. Sample matrix dried on target plate
4. Ions are accelerated by an electric field to
the same kinetic energy they separate
according to mass as they drift thru the
field-free region of the flight tube

20 - 25 kV
Flight tube
2. Target is introduced into high vacuum
chamber
High vacuum
High voltage
5. Ions strike the detector at different
times depending on the mass/charge ratio
3. Sample is irradiated with laser, clock starts
to measure time-of-flight
Pulsed laser


.
6. A data system controls instrument
parameters, acquires signal vs. time, and
processes the data
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Mass analyzers measure the mass of ions

• Operate under high vacuum (keeps ions from
  bumping into gas molecules), typically 10-7
  10-8 torr
• Actually measure mass-to-charge ratio of ions
  (m/z)
• Several kinds exist for bioanalysis, quadrupole
  and time-of-flight (TOF) are most used.
• Ions are detected by devices that convert the
  arrival of ions into emitted electrons or photons
  and amplify this signal, e.g., Microchannel
  Plates, Photomultipliers.

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MALDI Matrix Assisted Laser Desorption
Ionization
Sample plate
hn

• Sample (M) is mixed with excess matrix (X) and
  dried on a MALDI plate.
• The plate is loaded onto the sample stage in the
  Ion Source

to Mass Analyzer
Sample Matrix
Ground Grid
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MALDI Matrix Assisted Laser Desorption
Ionization
Laser
hn

• Laser flash produces matrix neutrals (X), matrix
  ions (XH), (X-H)- , and sample neutrals (M).
• 3. Sample molecules are ionized by proton
  transfer from matrix ions
• XH M ? X MH.
• X-H- M ? X M-H-

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MALDI Matrix Assisted Laser Desorption
Ionization
hn

• Ion Extraction High voltage is applied
  to the sample plate, accelerating ions out of the
  Ion Source into the Flight Tube.

MH
20 kV
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Time-of-Flight Mass Analyzer
Flight Tube
Ion Source
20-25 kV
Detector


Principle If ions are accelerated with the same
potential at a fixed point and a fixed initial
time and are allowed to drift, the ions will
separate according to their mass to charge ratios.
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Time-of-Flight Mass Analyzer
Flight Tube
Ion Source
Detector

The ions enter the flight tube with the lighter
ions travelling faster than the heavier ions to
the detector
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Time-of-Flight Mass Analyzer
Flight Tube
Ion Source
Detector

The lighter ions strike the detector before the
heavier ions. This time of flight (TOF) can be
converted to mass
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Ions are detected with a Microchannel Plate
-1000 V
-100 V
D 6-25 u
Primary Ion from Flight Tube
L
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Ions are detected with a Microchannel Plate
-1000 V
-100 V
D 6-25 u
L
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Ions are detected with a Microchannel Plate
-1000 V
-100 V
D 6-25 u
e-
L
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Ions are detected with a Microchannel Plate
-1000 V
-100 V
D 6-25 u
e-
e-
e-
e-
L
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Ions are detected with a Microchannel Plate
-1000 V
-100 V
D 6-25 u
e-
e-
e-
e-
L
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Ions are detected with a Microchannel Plate
-1000 V
-100 V
D 6-25 u
e-
e-
e-
e-
103 Amplification
L
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High Current Detector schematic Used in Linear
Mode
Fast scintillator
Microchannel plate
Lens
Photomultiplier tube
Signal out to Digitizer
Ion in Flight Tube
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What is a Reflector TOF analyzer?
Reflector Detector
Flight Tube
Ion Source

Reflector (Ion Mirror)
The reflector acts as an ion mirror, extending
the flight length without increasing the
instrument size. The reflector also compensates
for the initial energy spread of ions having the
same mass. The result is improved resolution.
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Voyager Data System Options
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Calibration of the mass scale
The mass-to-charge ratio of an ion is
proportional to the square of its time of flight
in the analyzer (drift time).
t Drift time L Drift length m Mass K Kinet
ic energy of ion z Number of charges on ion
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Important performance factors

Mass accuracy How accurate is the mass
measurement? Resolution How well separated are
the peaks from each other? Sensitivity How
small an amount can be detected / analyzed?
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Higher Resolution means better Mass Accuracy
15 ppm error
24 ppm error
55 ppm error
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Voyager Product Line

• Voyager-DE Biospectrometry Workstation
• Benchtop linear with Delayed Extraction
• Voyager-DE PRO Biospectrometry Workstation
• Benchtop with reflector for increased performance
• Voyager-DE STR Biospectrometry Workstation
• Floor standing with reflector for ultimate
  performance and flexibility

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Voyager DE MALDI-TOF Applications
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Features of MALDI-TOF MS

• Soft ionization - biomolecules remain intact
• Broad mass range - analyze a wide variety
  
  of biomolecules (40
  Da to gt 400 KDa)
• Mixtures are OK - little need for purification
• High sensitivity
• Data is easy to interpret
• Buffers and salts have small effect
• Fast
• Easy to use and maintain

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US Technical Support

• 800-899-5858

Mass Spec 508-383-7779 Michelle Chen, Jing
DeNore e-mail tsupport_at_appliedbiosystems.com
Tech Support Fax [phone] or
508-383-7855 Front Desk 508-383-7700 Sales/Servi
ce 800-831-6844, option 1 (Foster City,
CA) Website www.appliedbiosystems.com