Highly Accurate Chemical Formula Prediction Tool Utilizing High-Resolution Mass Spectra, MS/MS Fragmentation, Heuristic Rules, and Isotope Pattern Matching

• Published in: Analytical chemistry (Washington) Vol. 84; no. 10; pp. 4396 - 4403
• Main Authors: Pluskal, Tomáš, Uehara, Taisuke, Yanagida, Mitsuhiro
• Format: Journal Article
• Language: English
• Published: Washington, DC American Chemical Society 15.05.2012
• Subjects: Algorithms; Analytical chemistry; Carbon Isotopes - chemistry; Chemical compounds; Chemistry; Chromatography, High Pressure Liquid; computer software; data collection; Exact sciences and technology; Heuristic; ions; Isotopes; Lipids; Mass spectra; Mass Spectrometry; Metabolites; metabolomics; Peptides; prediction; Schizosaccharomyces - metabolism; Software; Spectrometers; Spectrometric and optical methods; Trace analysis; Performance evaluation; Metabolomics; High resolution; Peptides; Metabolite; Use; Prediction; Error; Lipids; Fragmentation pattern; Method; Algorithm; Fragmentation; Molecules; Accuracy; Detector; Mass spectrometry MS/MS; Software; Technique; Pattern analysis; Mass spectrometry; Tool
• ISSN: 0003-2700; 1520-6882; 1520-6882
• DOI: 10.1021/ac3000418

Mass spectrometry is commonly applied to qualitatively and quantitatively profile small molecules, such as peptides, metabolites, or lipids. Modern mass spectrometers provide accurate measurements of mass-to-charge ratios of ions, with errors as low as 1 ppm. Even such high mass accuracy, however, is not sufficient to determine the unique chemical formula of each ion, and additional algorithms are necessary. Here we present a universal software tool for predicting chemical formulas from high-resolution mass spectrometry data, developed within the MZmine 2 framework. The tool is based on the use of a combination of heuristic techniques, including MS/MS fragmentation analysis and isotope pattern matching. The performance of the tool was evaluated using a real metabolomic data set obtained with the Orbitrap MS detector. The true formula was correctly determined as the highest-ranking candidate for 79% of the tested compounds. The novel isotope pattern-scoring algorithm outperformed a previously published method in 64% of the tested Orbitrap spectra. The software described in this manuscript is freely available and its source code can be accessed within the MZmine 2 source code repository.