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Analyzing Biological and
Organic Polymers by
MALDI-TOF
Jonathan A. Karty, Ph.D.
Topics Covered
Sample Requirements
Instrument Overview
General Instrument Use Instructions
Tips and Tricks
What is the Bruker Autoflex III?
Time-of-flight mass spectrometer
Ions of given same kinetic energy, heavy ions travel
slower than lighter ones
Two modes of operation
Linear
Reflectron
MALDI/LDI source
384 position target plate (~1 µL spot size)
355 nm Nd:YAG laser
Can analyze positive or negative ions (same spot)
Autoflex III Picture
Matrix-Assisted Laser Desorption/Ionization
(MALDI)
Analyte is mixed with UV-absorbing matrix
A drop of this liquid is dried on a target
Analyte incorporated into matrix crystals
Spot is irradiated by a laser pulse
~10,000:1 matrix:analyte ratio
Analyte does not need to absorb laser
Irradiated region sublimes, taking analyte with it
Matrix is often promoted to the excited state
Charges exchange between matrix and analyte in the
plume (very fast <100 nsec)
Ions are accelerated toward the detector
MALDI Diagram
Image from http://www.noble.org/Plantbio/MS/iontech.maldi.html
MALDI Advantages
Technique is relatively simple
Volatilize and ionize labile molecules
Imagine electron ionization on a protein
MALDI creates very simple mass spectra
Ions are usually (M+nH)n+ or (M-nH)nOnly 1-3 charge states are observed
MALDI ideal for time-of-flight analyzers
Usually 1 charge state for peptides < 3.5 kDa
Theoretically unlimited mass range (100 kDa done here)
MALDI is very rapid (<1 min/spot)
Low sample consumption (1 µL)
Wide array of matrices available for different analytes
Some Common MALDI Matrices
What Samples Can It Run?
Biopolymers
Organometallic complexes
Organometallic salts work great
Synthetic polymers
Peptides, proteins, DNA, RNA, oligosaccharides
Polymer need not be soluble in same solvent as
matrix
Molecules that photoionize upon irradiation by
355 nm laser
Porphyrins
Organometallic complexes
What Samples Can’t It Run?
“Dirty” samples
Significant concentration of involatiles
Alkali metal salts can be quite problematic
RNA/DNA analyses require extensive desalting
Molecules with significant vapor pressures
Glycerol, urea, most buffers, many detergents
Instrument is held at ~10-7 torr
Molecules that do not make stable ions in source
Lack charge acceptor/donor site
Cannot photoionize with Nd:YAG laser
MALDI Advantages
Relatively gentle ionization technique
Very high MW species can be ionized
Molecule need not be volatile
Very easy to get sub-picomole sensitivity
Spectra are easy to interpret
Positive or negative ions from same spot
Wide array of matrices available
MALDI Disadvantages
MALDI matrix cluster ions can obscure low
m/z (<600) range
Analyte must have very low vapor pressure
Coupling MALDI with chromatography can
be difficult
Analytes that absorb the laser can be
problematic
Fluorescein-labeled peptides
Instrument Diagram
355 nm Nd:YAG laser
Target
Reflectron
Linear
Detector
Lens
Extraction
Plate
Flight
Tube
Entrance
Reflector
Detector
Linear Mode
355 nm Nd:YAG laser
Target
Reflectron
Linear
Detector
Lens
Extraction
Plate
Flight
Tube
Entrance
Reflector
Detector
Linear mode is used for large
(>3.5 kDa) molecules or
exceedingly fragile species
(oligosaccharides). It is capable
of 4,000 resolving power @ 3.2
kDa (1,000 RP @ 12 kDa)
Reflectron Mode
355 nm Nd:YAG laser
Target
Reflectron
Linear
Detector
Lens
Extraction
Plate
Flight
Tube
Entrance
Reflector
Detector
Reflectron mode is used for
small species (<4 kDa) and is
capable of 11,000 resolving
power @ 3.2 kDa.
(ACTH 7-38+H)+
(Ubiq+2H)2+
(ACTH 18-37+H)+
MALDI Example
(Ins+H)+
(Ubiq+H)+
MALDI Example I Continued
Intens. [a.u.]
Intens. [a.u.]
MALDI-TOF Example 2
8476.61
16952.53
4000
6000
3000
16952.53
4000
2000
1000
2000
17056.51 17131.54
0
4802.98
16600
16800
17000
17200
1740
0
5000
7500
10000
12500
15000
17500
20000
22500
25000
27500
m/z
General Sample Guidelines
Purify analyte if possible
Use only volatile solvents/buffers
MeOH, H2O, acetone, CH3CN, THF, CH2Cl2, C6H6
TFA, HOAc, formic acid, NH3, etc.
Ionic strength < 20 mM (e.g. 0.1% v/v HOAc)
If you need a detergent, 20 mM noctylglucopyranoside can work
Analyte should be 5 – 100 µM in concentration
ZipTips can help purify dirty samples (C4 and C18
available in MSF)
No SDS, TWEEN, CHAPS, etc
Need at least 2 µL
Sample Prep Tricks
Ziptip to clean up dirty samples
C18 for peptides < 3 kDa
C4 for peptides/proteins > 3kDa
Elute directly into matrix for added sensitivity
ZipTip instructions on MSF website
If CCA liquid turns yellow, pH is too high
Spots from non-acidic CCA do not crystallize correctly
Add a little 1% v/v or 10% v/v TFA to lower pH
If sample needs base for solubility, try over-layer
method
Dissolve sample in NH3 or other volatile base
Place 1 uL of sample on target, let dry completely
Deposit 1 uL matrix over top of dried sample
Sample Prep Tricks 2
Non-aqueous over-layer
Make 1 uL spot of matrix on plate, let dry
Deposit small amount of sample in volatile
solvent (e.g. CHCl3, acetone, CH2Cl2)
You can even do internal calibration this way
Put
calibrants in matrix spot
For better mass accuracy, let voltages
stabilize 10-30 minutes before recording
data
Hands-on Training
Starts AFTER 11/7
Groups of no more than three
One hour or so to complete
No charge for first session
After training, students must demonstrate
competency by running their own samples
prior to being granted after-hours access