Mass Spectrometry of Proteins and Peptides Electrospray Ionization(ESI) and Matrix Assisted Laser Desorption Ionization(MALDI)

by Matt Fisher

Outline

•Brief introduction to Proteomics

•How ESI and MALDI work

•Advantages/setbacks to each method

•ESI and MALDI in action

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!

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

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

Electrospray Ionization

Electrospray IonizationEvaporation 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

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

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

Advantages/Disadvantages to ESIAdvantages

• High accuracy• Large mass range• Can be coupled with liquid

chromatography to separate samples further

• Fast• Auto run with sampler or

direct injection• Soft ionization

Disadvantages

• Complicated spectra• salts drown signal and

take time to remove from the machine

• A high intensity peak can eclipse smaller intensity peaks

• Fine tuning work: flow rate, solvent/sample ratios, etc to get the analytes to ionize

Advantages/Disadvantages to MALDIAdvantages

• Preferable for large molecules

• Quick, quick, quick!• Sensitive to small amounts

of sample• Easy spectra• Accurate • Not affected by salts• Soft ionization

Disadvantages

• Fine tuning: spotting plate, getting good crystals, adjusting intensity of laser, finding crystals on plate with sample

• Low shot to shot reproducibility

• Short sample life

0 5 10 15 20 25 Time [min]0

1

2

3

5x10Intens.

CPV_B_30min_41_01_2213.d: TIC +All MS

624.1

831.8

864.9943.5

979.3

+MS, 12.0-12.9min #(1013-1091)

0

50

100

150

200

250

300

Intens.

200 400 600 800 1000 1200 1400 1600 m/z

51835.7 53151.8 55110.057351.0 60727.7

62615.8

64567.2

65664.7

67369.869381.7

+MS, 12.0-12.9min #(1013-1091), Deconvoluted (maximum entropy)

0.0

0.2

0.4

0.6

0.8

1.0

4x10Intens.

50000 52000 54000 56000 58000 60000 62000 64000 66000 68000 m/z

ESI Spectra

CPV Bromelin_30min Max. Entropy Deconvolution

Intact protein(VP2): 64,567.2 Da

Digested protein(VP3): 62,315.8 Da

0 5 10 15 20 25 Time [min]0

1

2

3

5x10Intens.

CPV_B_120min_42_01_2217.d: TIC +All MS

624.1

831.8

864.9979.3

+MS, 12.0-12.6min #(1019-1073)

0

100

200

300

Intens.

200 400 600 800 1000 1200 1400 1600 m/z

51836.753151.7 54833.0

57344.5 59841.6

61510.5

62614.4

64567.6

65666.0

67372.1 69805.9

+MS, 12.0-12.6min #(1019-1073), Deconvoluted (maximum entropy)

0.00

0.25

0.50

0.75

1.00

1.25

4x10Intens.

50000 52000 54000 56000 58000 60000 62000 64000 66000 68000 m/z

ESI Spectra

CPV Bromelin_150 min Max Entropy Deconvolution

Intact protein(VP2): 64,567.6 Da

Digested protein(VP3): 62,614.4 Da

0 5 10 15 20 25 Time [min]0.0

0.5

1.0

1.5

2.0

2.5

5x10Intens.

CPV_B_23hrs_43_01_2221.d: TIC +All MS

624.1

831.8

864.8 979.3

1099.6

+MS, 12.0-12.6min #(1024-1070)

0

100

200

300

Intens.

200 400 600 800 1000 1200 1400 1600 m/z

51835.0 53148.6 54840.057353.8 59839.4

61504.5

62615.8

64568.8

65663.8

67375.269389.9

+MS, 12.0-12.6min #(1024-1070), Deconvoluted (maximum entropy)

0.00

0.25

0.50

0.75

1.00

1.25

4x10Intens.

50000 52000 54000 56000 58000 60000 62000 64000 66000 68000 m/z

ESI Spectra

CPV Bromelin_23 hr

Max. Entropy Deconvolution

Intact Protein(VP2): 64,568.8 Da

Digested Protein(VP3): 62,615.8 Da

2007_05_31

MALDI analysis of CPV reacted with Trypsin @ 45°C 5 min

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