A method of aligning peak lists generated by gas chromatography high-resolution mass spectrometry

We report a method for the peak list alignment of gas chromatography high resolution time-of-flight mass spectrometry data. The alignment is performed in a z-score transformed retention time domain to standardize chromatographic peak distribution across samples. A mixture score is developed to assess the similarity between two peaks by simultaneously evaluating the mass spectral similarity and the closeness of retention time. An analysis of experimental data acquired under three different flow rates indicates that the proposed method is able to correctly align the heterogeneous data. The effectiveness of method is further validated by analyzing experimental data of multiple mixtures of metabolite extract from mouse liver with 28 spiked-in acids. All of the detected spiked-in acids were correctly aligned. A statistical test correctly detected the concentration differences of the spiked-in compounds between sample groups using the alignment table. The area under curve (AUC) value in the receiver operating characteristic (ROC) curve is larger than 0.85 in all three of the compared sample groups, indicating a high accuracy of peak alignment and supporting the potential application of the proposed method for metabolomics projects such as biomarker discovery.