Abstract
| I. | Introduction | 389 |
| | A. A Brief History of DNA Analysis by Mass Spectrometry | 389 |
| | B. What Exactly Are SNPs | 390 |
| | C. Why Use MALDI for DNA Analysis? | 391 |
| II. | Methods for Allele‐Discrimination | 391 |
| | A. Hybridization | 391 |
| | B. Oligonucleotide Ligation | 394 |
| | C. Cleavage | 394 |
| | D. Primer Extension | 395 |
| | 1. Purification Procedures and Sample Preparation | 395 |
| | 2. The PinPoint Assay | 396 |
| | 3. The PROBE Assay | 398 |
| | 4. The VSET Assay | 398 |
| | 5. The GenoLINK and GenoSNIP Assay | 400 |
| | 6. The GOOD Assay | 400 |
| | E. High‐Throughput SNP Genotyping by Mass Spectrometry | 401 |
| | F. Other Applications | 403 |
| | 1. Quantitation | 403 |
| | 2. Haplotyping | 404 |
| | 3. Epigenotyping | 404 |
| | 4. Analysis of Larger DNA Segments/Complete PCR Products | 405 |
| III. | Strategies for the Discovery of Unknown Mutations | 406 |
| | A. Sequencing by Mass Spectrometry | 406 |
| | B. Transcription into RNA | 407 |
| | C. Base‐Specific Fragmentation of Amplified DNA | 408 |
| IV. | ESI for DNA Analysis | 409 |
| | A. Whole PCR Products | 409 |
| | B. Liquid Chromatography‐ESI | 409 |
| | C. Cleavage | 410 |
| | D. The Survivor Assay | 410 |
| V. | Use of Other Kinds of Mass Spectrometers for DNA Analysis | 410 |
| VI. | Conclusions | 411 |
| | Acknowledgments | 411 |
| | Abbreviations | 411 |
| | References | 412 |
In the last decade, the demand for high‐throughput DNA analysis methods has dramatically increased, mainly due to the advent of the human genome sequencing project that is now nearing completion. Even though mass spectrometry did not contribute to that project, it is clear that it will have an important role in the post‐genome sequencing era, in genomics and proteomics. In genomics, mainly matrix‐assisted laser desorption/ionization (MALDI) mass spectrometry will contribute to large‐scale single nucleotide polymorphism (SNP) genotyping projects. Here, the development and history of DNA analysis by mass spectrometry is reviewed and put into the context with the requirements of genomics. All major contributions to the field and their status and limitations are described in detail. © 2003 Wiley Periodicals, Inc., Mass Spec Rev 21:388–418, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mas.1009