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Eur. J. Mass Spectrom. 9, 445 - 457 (2003)
DOI: 10.1255/ejms.577

MASSIS: a mass spectrum simulation system. 2: Procedures and performance

HaiFeng Chen
ITODYS, CNRS UMR 7086, Université Paris 7, 1, rue Guy de la Brosse, 75005 Paris, France and Key Laboratory of Computer Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, PR China
BoTao Fan,* Michel Petitjean, Annick Panaye and Jean-Pierre Doucet
ITODYS, CNRS UMR 7086, Université Paris 7, 1, rue Guy de la Brosse, 75005 Paris, France. E-mail:
Feng Li, HaiRong Xia and ShenGang Yuan
Key Laboratory of Computer Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, PR China

ABSTRACT:
The use of the mass spectral simulation system, MASSIS, is reported and its performance has been evaluated. The search for substructures matching with fragments stored in four pivot databases was realised using the Ullmann algorithm. Special cleavage rules, such as the McLafferty rearrangement, the retro-DielsAlder reaction, elimination of a neutral small molecule and oxygen migration, are processed through shortest path and depth-first search algorithms. For a search in the database of small fragments, the key step is to determine the tautomeric fragments; then a match can be obtained using a subgraph isomorphism algorithm. A string match is used to determine peak intensity. If the limited environment of an atom is the same as that found in the database of relationships between fragment and intensity, this intensity value is assigned to the query atom. Performance in a set of tests is very important in evaluating the system performance. A comparison of peaks with an intensity greater than 5% (relative) shows that our system has a very high performance figure (> 90% ) for routine organic compounds.

Keywords: mass spectral simulation, fragment intensity determination, comparative study, databases, Ullmann algorithm, software

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