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Biochemistry 412 Biological Mass Spectrometry February 25 th , 2005. There are two major types of “soft ionization” methods of mass spectrometry for use in analyzing samples of biological origin: • Matrix-assisted laser desorption • Electrospray.

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Biochemistry 412 biological mass spectrometry february 25 th 2005

Biochemistry 412

Biological Mass Spectrometry

February 25th, 2005


Biochemistry 412 biological mass spectrometry february 25 th 2005

There are two major types of “soft ionization” methods

of mass spectrometry for use in analyzing

samples of biological origin:

• Matrix-assisted laser desorption

• Electrospray


Biochemistry 412 biological mass spectrometry february 25 th 2005

Matrix-Assisted Laser Desorption Ionization (MALDI) Mass Spectrometry

Mann et al (2001)

Annu. Rev. Biochem. 70, 437.


Biochemistry 412 biological mass spectrometry february 25 th 2005

Electrospray Ionization (ESI) Mass Spectrometry Spectrometry

Griffiths et al (2001)

Biochem. J.355, 545.


Biochemistry 412 biological mass spectrometry february 25 th 2005

Attractive Features of Mass Spectrometry Spectrometry

• High resolution (can measure mass differences of ~0.1 Da)

• High sensitivity (10-13 to 10-19[!] moles)

• Ability to work with complex samples (MALDI-MS)

• Ability to interface with other separation techniques (e.g., LC)

• “Reasonably” affordable


Biochemistry 412 biological mass spectrometry february 25 th 2005

Example of an ESI Mass Spectrum Spectrometry

Griffiths et al (2001)

Biochem. J.355, 545.

Note:

mass-charge ratio


Biochemistry 412 biological mass spectrometry february 25 th 2005

Now for some cool applications Spectrometry

of biological mass spectrometry..!!


Biochemistry 412 biological mass spectrometry february 25 th 2005

Single Nucleotide Polymorphism (SNP) Spectrometry

Genotyping by MS


Biochemistry 412 biological mass spectrometry february 25 th 2005

Solid-State DNA Genotyping Spectrometry

Note: extension reaction

done in thepresence of

one or more ddNTPs

Tang et al (1999)


Biochemistry 412 biological mass spectrometry february 25 th 2005

Tang et al (1999) Spectrometry


Biochemistry 412 biological mass spectrometry february 25 th 2005

Tang et al (1999) Spectrometry


Biochemistry 412 biological mass spectrometry february 25 th 2005

Generation of Distance Constraints for Spectrometry

Protein Structure Determination Using a

Combination of Protein Cross-Links and

Mass Spectrometry


Biochemistry 412 biological mass spectrometry february 25 th 2005

Young et al (2000) Spectrometry


Biochemistry 412 biological mass spectrometry february 25 th 2005

Young et al (2000) Spectrometry


Biochemistry 412 biological mass spectrometry february 25 th 2005

Young et al (2000) Spectrometry


Biochemistry 412 biological mass spectrometry february 25 th 2005

Hydrogen-Deuterium Exchange and SpectrometryMass Spectrometry to Probe

Protein Dynamics, Solvent-Accessibility,

and Protein-Protein Interactions


Biochemistry 412 biological mass spectrometry february 25 th 2005

Hamuro et al (2002) Spectrometry


Biochemistry 412 biological mass spectrometry february 25 th 2005

Hamuro et al (2002) Spectrometry


Biochemistry 412 biological mass spectrometry february 25 th 2005

Hydrogen - Deuterium Exchange and Protein Conformational Fluctuations

Hoofnagle et al (2003) Annu. Rev.

Biophys. Biomol. Struct.32, 1.


Biochemistry 412 biological mass spectrometry february 25 th 2005

Hydrogen - Deuterium Exchange: Schematic Experimental Design

Hoofnagle et al (2003) Annu. Rev.

Biophys. Biomol. Struct.32, 1.




Biochemistry 412 biological mass spectrometry february 25 th 2005

Fragment-Based Design

Drug Discovery





Biochemistry 412 biological mass spectrometry february 25 th 2005

The Monophore Binds in the Same Relative Orientation, Regardless of Attachment Site

Erlanson et al (2000)


Biochemistry 412 biological mass spectrometry february 25 th 2005

Erlanson et al (2000) Regardless of Attachment Site


Biochemistry 412 biological mass spectrometry february 25 th 2005

Pharmacology Using Regardless of Attachment Site

Imaging Mass Spectrometry


Biochemistry 412 biological mass spectrometry february 25 th 2005

Chaurand et al (2002) Regardless of Attachment Site