ShiftedIonsFinder: A standalone Java tool for finding peaks with specified mass differences by comparing mass spectra of isotope-labeled and unlabeled data sets

Abstract

In mass spectrometry (MS)-based metabolite annotation, the prediction of theoretical elemental compositions from accurate mass is effective to support database search results or annotation for unknown metabolites. However, there are deviations (error) from the accurate mass such that accurate estimation of elemental composition may not be possible. A technique to label the biological sample with a stable isotope is effective to solve this problem, but the software for handling labeled MS data is limited. In this paper, we present a standalone Java graphical user interface (GUI) program tool—ShiftedIonsFinder—that helps find peaks having specified mass differences by comparing the mass spectra between two data sets. Using this tool, it is possible to select candidate labeled peaks by comparing a sample labeled with a stable isotope against an unlabeled sample. This tool also detects peaks with chemical modifications, such as glycosylation and acylation. Since the search results can be generated in Excel format, the user can easily perform further analyses or edit the list as needed. ShiftedIonsFinder (http://www.kazusa.or.jp/komics/software/ShiftedIonsFinder) is available free of charge at KOMICS.