title: Computing fragmentation trees from tandem mass spectrometry data.
abstract: The structural elucidation of organic compounds in complex biofluids and tissues remains a significant analytical challenge. For mass spectrometry, the manual interpretation of collision-induced dissociation (CID) mass spectra is cumbersome and requires expert knowledge, as the fragmentation mechanisms of ions formed from small molecules are not completely understood. The automated identification of compounds is generally limited to searching in spectral libraries. Here, we present a method for interpreting the CID spectra of the organic compound's protonated ions by computing fragmentation trees that establish not only the molecular formula of the compound and all fragment ions but also the dependencies between fragment ions. This is an important step toward the automated identification of unknowns from the CID spectra of compounds that are not in any database.
authors.affiliation: Chair for Bioinformatics, Friedrich-Schiller-University Jena, Jena, Germany.
authors.forename: Florian
authors.initials: F
authors.lastname: Rasche
authors.forename: Ales
authors.initials: A
authors.lastname: Svatos
authors.forename: Ravi Kumar
authors.initials: RK
authors.lastname: Maddula
authors.forename: Christoph
authors.initials: C
authors.lastname: Böttcher
authors.forename: Sebastian
authors.initials: S
authors.lastname: Böcker
mesh_terms: D005103:Expert Systems; D009930:Organic Chemicals / Q000737:chemistry*; D012984:Software; D013223:Statistics as Topic / Q000379:methods*; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D009930:Organic Chemicals