This document discusses two mass spectrometry techniques for analyzing proteins and peptides - electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI). It provides an overview of how each technique works, including that ESI involves applying a high voltage to charge droplets containing sample which evaporate until single charged molecules enter the mass spectrometer, while MALDI involves mixing sample with an absorbing matrix that facilitates sublimation of ions into the gas phase with a laser. The document also compares advantages and disadvantages of each method, such as ESI being suitable for larger molecules and online coupling while MALDI provides quick, sensitive analysis of small amounts of sample. Examples of spectra from each technique analyzing can

1. Mass Spectrometry of Proteins
and Peptides
Electrospray Ionization(ESI) and
Matrix Assisted Laser Desorption
Ionization(MALDI)
by Matt Fisher

2. Outline
• Brief introduction to Proteomics
• How ESI and MALDI work
• Advantages/setbacks to each method
• ESI and MALDI in action

3. Proteomics
• “To really understand biological processes, we
need to understand how proteins function in and
around cells since they are the functioning
units.” - Hanno Steen, director of the Proteomics
Center at Children's Hospital Boston
• 30,000 genes code for 100,000 functional
proteins in humans
• Extreme cases of a single gene coding for 1,000
proteins!

4. Advances in Protein and Peptide
Analysis
• Such an enormous task requires every
conceivable technique to analyze proteins
• The 2002 Nobel Prize for Chemistry was shared
between John Fenn, and Koichi Tanaka for their
development of ESI and MALDI, respectively

5. Electrospray Ionization
Steps to Ionization
• Mix liquid sample with polar, volatile solvent
• Sample is put through a capillary with a fine tip on the
end
• A high voltage(~2000 V) is applied to the tip of the
capillary, charging the proteins and peptides in the
solvent. (Multiply-charged species common in ESI)
• Mixture is pushed through to an evaporation chamber

6. Electrospray Ionization

7. Electrospray Ionization
Evaporation Chamber
• The mixture starts out in “large” droplets. The addition
of nitrogen gas and heat begins to evaporate the solvent
in the droplets
• The droplets get smaller and the charged molecules get
closer together and repel, splitting into smaller
droplets(Coulombic fission)
• The process continues until each droplet consists of a
single molecule that is charged
• Molecules then enter a mass analyzer such as a time of
flight(TOF) tube to measure m/z

8. Matrix Assisted Laser Desorption
Ionization (MALDI)
•Liquid sample first mixed with an excess of
matrix on a MALDI plate
• The liquid in the mixture evaporates in open air,
with some of the sample incorporated into fine
crystals of the matrix
• The matrix is a UV-absorbing species, usually of
low molecular weight

9. MALDI
• MALDI plate is put into a high vacuum chamber and the laser is fired in bursts at
crystals on the spots on the plate
• At the right wavelength the crystals are irradiated and sublime. Energy is transferred
to the analytes which are now in the gas phase
• These protonated ions are accelerated into a mass analyzer such as a TOF tube

10. Advantages/Disadvantages to ESI
Advantages Disadvantages
• High accuracy • Complicated spectra
• Large mass range • salts drown signal and take
• Can be coupled with liquid time to remove from the
chromatography to separate machine
samples further • A high intensity peak can
• Fast eclipse smaller intensity peaks
• Auto run with sampler or • Fine tuning work: flow rate,
direct injection solvent/sample ratios, etc to
• Soft ionization get the analytes to ionize

11. Advantages/Disadvantages to MALDI
Advantages Disadvantages
• Preferable for large molecules • Fine tuning: spotting plate,
• Quick, quick, quick! getting good crystals, adjusting
• Sensitive to small amounts of intensity of laser, finding
sample crystals on plate with sample
• Easy spectra • Low shot to shot
• Accurate reproducibility
• Not affected by salts • Short sample life
• Soft ionization

12. Intens.
x105
ESI Spectra 3
CPV 2
Bromelin_30min
Max. Entropy 1
Deconvolution
0
0 5 10 15 20 25 Time [min]
CPV_B_30min_41_01_2213.d: TIC +All MS
Intens. +MS, 12.0-12.9min #(1013-1091)
300 831.8
250
624.1 979.3
864.9
200 943.5
150
100
50
0
200 400 600 800 1000 1200 1400 1600 m/z
Intens. +MS, 12.0-12.9min #(1013-1091), Deconvoluted (maximum entropy)
x104
Intact protein(VP2): 64,567.2 Da
1.0 64567.2
0.8
Digested protein(VP3): 62,315.8 Da 62615.8
0.6
0.4
65664.7
0.2
67369.8
69381.7
51835.7 57351.0 60727.7
53151.8 55110.0
0.0
50000 52000 54000 56000 58000 60000 62000 64000 66000 68000 m/z

13. Intens.
x10 5
ESI Spectra
3
CPV 2
Bromelin_150
1
min Max
Entropy 0
Deconvolution
0 5 10 15 20 25 Time [min]
CPV_B_120min_42_01_2217.d: TIC +All MS
Intens. +MS, 12.0-12.6min #(1019-1073)
831.8
300 624.1
979.3
864.9
200
100
0
200 400 600 800 1000 1200 1400 1600 m/z
Intens. +MS, 12.0-12.6min #(1019-1073), Deconvoluted (maximum entropy)
x10 4
1.25
62614.4
Intact protein(VP2): 64,567.6 Da 64567.6
1.00
Digested protein(VP3): 62,614.4 Da
0.75
0.50
65666.0
0.25 61510.5
67372.1 69805.9
51836.7 57344.5 59841.6
53151.7 54833.0
0.00
50000 52000 54000 56000 58000 60000 62000 64000 66000 68000 m/z

14. ESI Spectra
Intens.
x10 5
2.5
CPV 2.0
Bromelin_23 hr 1.5
1.0
Max. Entropy 0.5
Deconvolution 0.0
0 5 10 15 20 25 Time [min]
CPV_B_23hrs_43_01_2221.d: T IC +All MS
Intens. +MS, 12.0-12.6min #(1024-1070)
831.8
300
624.1
864.8 979.3
200
1099.6
100
0
200 400 600 800 1000 1200 1400 1600 m/z
Intens. +MS, 12.0-12.6min #(1024-1070), Deconvoluted (maximum entropy)
x10 4
1.25
Intact Protein(VP2): 64,568.8 Da
62615.8
1.00
Digested Protein(VP3): 62,615.8 Da 64568.8
0.75
0.50
65663.8
0.25 61504.5
67375.2
69389.9
51835.0 57353.8 59839.4
53148.6 54840.0
0.00
50000 52000 54000 56000 58000 60000 62000 64000 66000 68000 m/z

15. 2007_05_31
MALDI analysis of
CPV reacted with
Trypsin @ 45°C 5
min

16. Sources
• C.Nelson, E.Minkkinen, M. Bergkvist, K.Hoelzer, M. Fisher, B. Bothner, and C.Parrish
(2008). “Detecting Small Changes and Additional Peptides in the Canine Parvovirus
Capsid Structure”. J. Virol. 82: 10397-10407
• http://www.magnet.fsu.edu/education/tutorials/tools/ionization_esi.html
• H. Steen, M. Mann (2004). “The Abc’s (and xyz’s) of Peptide Sequencing”. Nature Reviews
Molecular Cell Biology 5, 699-711
• http://www.childrenshospital.org/cfapps/research/data_admin/Site602/mainpageS602P0.html
• F.Witzmann, J. Li (2002). “Proteomics: Core Technologies and Applications in
Physiology”. American Journal of Physiology – Gastrointestinal and Liver Physiology.
10.1152
• http://www.innovadyne.com/Assets%20Doc/MALDI%20spots%20Biomek%20plate.jpg