Editing DNA sequencing (section)

=== Sequencing with mass spectrometry ===
[[Mass spectrometry]] may be used to determine DNA sequences. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry, or [[Matrix-assisted laser desorption/ionization|MALDI-TOF MS]], has specifically been investigated as an alternative method to gel electrophoresis for visualizing DNA fragments. With this method, DNA fragments generated by chain-termination sequencing reactions are compared by mass rather than by size. The mass of each nucleotide is different from the others and this difference is detectable by mass spectrometry. Single-nucleotide mutations in a fragment can be more easily detected with MS than by gel electrophoresis alone. MALDI-TOF MS can more easily detect differences between RNA fragments, so researchers may indirectly sequence DNA with MS-based methods by converting it to RNA first.<ref>{{cite journal | vauthors = Edwards JR, Ruparel H, Ju J | title = Mass-spectrometry DNA sequencing | journal = Mutation Research | volume = 573 | issue = 1–2 | pages = 3–12 | year = 2005 | pmid = 15829234 | doi = 10.1016/j.mrfmmm.2004.07.021 | bibcode = 2005MRFMM.573....3E }}</ref>

The higher resolution of DNA fragments permitted by MS-based methods is of special interest to researchers in forensic science, as they may wish to find [[single-nucleotide polymorphisms]] in human DNA samples to identify individuals. These samples may be highly degraded so forensic researchers often prefer [[mitochondrial DNA]] for its higher stability and applications for lineage studies. MS-based sequencing methods have been used to compare the sequences of human mitochondrial DNA from samples in a [[Federal Bureau of Investigation]] database<ref>{{cite journal | vauthors = Hall TA, Budowle B, Jiang Y, Blyn L, Eshoo M, Sannes-Lowery KA, Sampath R, Drader JJ, Hannis JC, Harrell P, Samant V, White N, Ecker DJ, Hofstadler SA | title = Base composition analysis of human mitochondrial DNA using electrospray ionization mass spectrometry: A novel tool for the identification and differentiation of humans | journal = Analytical Biochemistry | volume = 344 | issue = 1 | pages = 53–69 | year = 2005 | pmid = 16054106 | doi = 10.1016/j.ab.2005.05.028 }}</ref> and from bones found in mass graves of World War I soldiers.<ref>{{cite journal | vauthors = Howard R, Encheva V, Thomson J, Bache K, Chan YT, Cowen S, Debenham P, Dixon A, Krause JU, Krishan E, Moore D, Moore V, Ojo M, Rodrigues S, Stokes P, Walker J, Zimmermann W, Barallon R | title = Comparative analysis of human mitochondrial DNA from World War I bone samples by DNA sequencing and ESI-TOF mass spectrometry | journal = Forensic Science International: Genetics | volume = 7 | issue = 1 | pages = 1–9 | date = 15 June 2011 | pmid = 21683667 | doi = 10.1016/j.fsigen.2011.05.009 | doi-access = free }}</ref>

Early chain-termination and TOF MS methods demonstrated read lengths of up to 100 base pairs.<ref>{{cite journal | vauthors = Monforte JA, Becker CH | title = High-throughput DNA analysis by time-of-flight mass spectrometry | journal = Nature Medicine | volume = 3 | issue = 3 | pages = 360–62 | date = 1 March 1997 | pmid = 9055869 | doi = 10.1038/nm0397-360 | s2cid = 28386145 }}</ref> Researchers have been unable to exceed this average read size; like chain-termination sequencing alone, MS-based DNA sequencing may not be suitable for large ''de novo'' sequencing projects. Even so, a recent study did use the short sequence reads and mass spectroscopy to compare single-nucleotide polymorphisms in pathogenic ''[[Streptococcus]]'' strains.<ref>{{cite journal | vauthors = Beres SB, Carroll RK, Shea PR, Sitkiewicz I, Martinez-Gutierrez JC, Low DE, McGeer A, Willey BM, Green K, Tyrrell GJ, Goldman TD, Feldgarden M, Birren BW, Fofanov Y, Boos J, Wheaton WD, Honisch C, Musser JM | title = Molecular complexity of successive bacterial epidemics deconvoluted by comparative pathogenomics | journal = Proceedings of the National Academy of Sciences | volume = 107 | issue = 9 | pages = 4371–76 | date = 8 February 2010 | pmid = 20142485 | pmc = 2840111 | doi = 10.1073/pnas.0911295107 | bibcode = 2010PNAS..107.4371B | doi-access = free }}</ref>