title: Predicting molecular formulas of fragment ions with isotope patterns in tandem mass spectra.
abstract: A number of different approaches have been proposed to predict elemental component formulas (or molecular formulas) of molecular ions in low and medium resolution mass spectra. Most of them rely on isotope patterns, enumerate all possible formulas for an ion, and exclude certain formulas violating chemical constraints. However, these methods cannot be well generalized to the component prediction of fragment ions in tandem mass spectra. In this paper, a new method, FFP (Fragment ion Formula Prediction), is presented to predict elemental component formulas of fragment ions. In the FFP method, the prediction of the best formulas is converted into the minimization of the distance between theoretical and observed isotope patterns. And, then, a novel local search model is proposed to generate a set of candidate formulas efficiently. After the search, FFP applies a new multiconstraint filtering to exclude as many invalid and improbable formulas as possible. FFP is experimentally compared with the previous enumeration methods, and shown to outperform them significantly. The results of this paper can help to improve the reliability of de novo in the identification of peptide sequences.
authors.affiliation: Institute of Computing Technology, Chinese Academy of Sciences, JDL, Room 701, Power Creative A, No. 1, Shangdi East Road, Haidian District, Beijing, 100080, PR China. jfzhang@jdl.ac.cn
authors.forename: Jingfen
authors.initials: J
authors.lastname: Zhang
authors.forename: Wen
authors.initials: W
authors.lastname: Gao
authors.forename: Jinjin
authors.initials: J
authors.lastname: Cai
authors.forename: Simin
authors.initials: S
authors.lastname: He
authors.forename: Rong
authors.initials: R
authors.lastname: Zeng
authors.forename: Runsheng
authors.initials: R
authors.lastname: Chen
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D003198:Computer Simulation; D007477:Ions / Q000737:chemistry; D013058:Mass Spectrometry / Q000379:methods*; D008956:Models, Chemical; D008958:Models, Molecular; D010363:Pattern Recognition, Automated / Q000379:methods; D010446:Peptide Fragments / Q000032:analysis* / Q000737:chemistry*; D010449:Peptide Mapping / Q000379:methods*; D011868:Radioisotopes / Q000032:analysis / Q000737:chemistry; D020539:Sequence Analysis, Protein / Q000379:methods*
chemical_list: D007477:Ions; D010446:Peptide Fragments; D011868:Radioisotopes