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Identification and Characterization of DNA-Binding Proteins by Mass Spectrometry

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Book cover Analytics of Protein–DNA Interactions

Part of the book series: Advances in Biochemical Engineering/Biotechnology ((ABE,volume 104))

Abstract

Mass spectrometry is the most sensitive and specific analytical technique available for protein identification and quantification. Over the past 10 years, by the use of mass spectrometric techniques hundreds of previously unknown proteins have been identified as DNA-binding proteins that are involved in the regulation of gene expression, replication, or DNA repair. Beyond this task, the applications of mass spectrometry cover all aspects from sequence and modification analysis to protein structure, dynamics, and interactions. In particular, two new, complementary ionization techniques have made this possible: matrix-assisted laser desorption/ionization and electrospray ionization. Their combination with different mass-over-charge analyzers and ion fragmentation techniques, as well as specific enzymatic or chemical reactions and other analytical techniques, has led to the development of a broad repertoire of mass spectrometric methods that are now available for the identification and detailed characterization of DNA-binding proteins. These techniques, how they work, what their requirements and limitations are, and selected examples that document their performance are described and discussed in this chapter.

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Abbreviations

2-DE:

Two-dimensional gel electrophoresis

BIA:

Biomolecular interaction analysis

cAMP:

Cyclic adenosine monophosphate

CDIT:

Culture-derived isotope tags

CE:

Capillary electrophoresis

CHCA:

α-Cyano-4-hydroxycinnamic acid

CID:

Collision-induced dissociation

DHB:

2,5-Dihydroxybenzoic acid

Dnmt2:

DNA methyltransferase-2

ECD:

Electron capture dissociation

ESI:

Electrospray ionization

ETD:

Electron transfer dissociation

HX:

Hydrogen/deuterium exchange

ICAT:

Isotope-coded affinity tag

ICPL:

Isotope-coded protein tag

ICR:

Ion cyclotron resonance

IRMPD:

Infrared multiple photon dissociation

iTRAQ:

Isobaric tag for relative and absolute quantification

LC:

Liquid chromatography

m/z :

Mass-over-charge

MALDI:

Matrix-assisted laser desorption/ionization

MudPIT:

Multidimensional protein identification technology

PMF:

Peptide mass fingerprinting

PSD:

Post-source decay

PTM:

Posttranslational modification

RNAi:

RNA interference

SA:

Sinapic acid

SDS-PAGE:

Sodium dodecyl sulfate–polyacrylamide gel electrophoresis

SELDI:

Surface-enhanced laser desorption/ionization

SILAC:

Stable isotope labeling by amino acids in cell culture

SLE:

Systemic lupus erythematosus

SPR:

Surface plasmon resonance

TAP:

Tandem affinity purification

TEV:

Tobacco etch virus

TOF:

Time-of-flight

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Acknowledgments

The authors thank Dr. J. Gobom, Max Planck Institute for Molecular Genetics, for assistance in preparing the manuscript and scientific discussion. Funding of the Zukunftsfond of Berlin within the project 2D/3D-ProteinChips is acknowledged.

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  1. Department Lehrach, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195, Berlin, Germany

    Eckhard Nordhoff & Hans Lehrach

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  1. Eckhard Nordhoff
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Correspondence to Eckhard Nordhoff .

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Nordhoff, E., Lehrach, H. (2006). Identification and Characterization of DNA-Binding Proteins by Mass Spectrometry. In: Seitz, H. (eds) Analytics of Protein–DNA Interactions. Advances in Biochemical Engineering/Biotechnology, vol 104. Springer, Berlin, Heidelberg . https://doi.org/10.1007/10_2006_037

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