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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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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