FiD: a software for ab initio structural identification of product ions from tandem mass spectrometric data

Research output: Contribution to journalArticleScientificpeer-review

Researchers

Research units

  • VTT Technical Research Centre of Finland
  • University of Helsinki
  • Swiss Federal Institute of Technology Zurich
  • Nokia Corporation

Abstract

We present FiD (Fragment iDentificator), a software tool for the structural identification of product ions produced with tandem mass spectrometric measurement of low molecular weight organic compounds. Tandem mass spectrometry (MS/MS) has proven to be an indispensable tool in modern, cell-wide metabolomics and fluxomics studies. In such studies, the structural information of the MSn product ions is usually needed in the downstream analysis of the measurement data. The manual identification of the structures of MSn product ions is, however, a nontrivial task requiring expertise, and calls for computer assistance. Commercial software tools, such as Mass Frontier and ACD/MS Fragmenter, rely on fragmentation rule databases for the identification of MSn product ions. FiD, on the other hand, conducts a combinatorial search over all possible fragmentation paths and outputs a ranked list of alternative structures. This gives the user an advantage in situations where the MS/MS data of compounds with less well-known fragmentation mechanisms are processed. FiD software implements two fragmentation models, the single-step model that ignores intermediate fragmentation states and the multi-step model, which allows for complex fragmentation pathways. The software works for MS/MS data produced both in positive- and negative-ion modes. The software has an easy-to-use graphical interface with built-in visualization capabilities for structures of product ions and fragmentation pathways. In our experiments involving amino acids and sugar-phosphates, often found, e.g., in the central carbon metabolism of yeasts, FiD software correctly predicted the structures of product ions on average in 85% of the cases. The FiD software is free for academic use and is available for download from www.cs.helsinki.fi/group/sysfys/software/fragid. Copyright (c) 2008 John Wiley & Sons, Ltd.

Details

Original languageEnglish
Pages (from-to)3043-3052
Number of pages10
JournalRapid Communications in Mass Spectrometry
Volume22
Issue number19
Publication statusPublished - Oct 2008
MoE publication typeA1 Journal article-refereed

    Research areas

  • METABOLIC FLUX ANALYSIS, ALPHA-AMINO-ACIDS, FRAGMENTATION MECHANISM, COLLISIONAL ACTIVATION, TRIPLE-QUADRUPOLE, SPECTRA, DISSOCIATION, PREDICTION, FRAMEWORK, PROTEINS

ID: 9939035