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Abstract Background Comprehensive two-dimensional gas chromatography coupled with mass spectrometry (GC × GC-MS) is a powerful technique which has gained increasing attention over the last two decades. The GC × GC-MS provides much increased separation capacity, chemical selectivity and sensitivity for complex sample analysis and brings more accurate information about compound retention times and mass spectra. Despite these advantages, the retention times of the resolved peaks on the two-dimensional gas chromatographic columns are always shifted due to experimental variations, introducing difficulty in the data processing for metabolomics analysis. Therefore, the retention time variation must be adjusted in order to compare multiple metabolic profiles obtained from different conditions. Results We developed novel peak alignment algorithms for both homogeneous (acquired under the identical experimental conditions) and heterogeneous (acquired under the different experimental conditions) GC × GC-MS data using modified Smith-Waterman local alignment algorithms along with mass spectral similarity. Compared with literature reported algorithms, the proposed algorithms eliminated the detection of landmark peaks and the usage of retention time transformation. Furthermore, an automated peak alignment software package was established by implementing a likelihood function for optimal peak alignment. Conclusions The proposed Smith-Waterman local alignment-based algorithms are capable of aligning both the homogeneous and heterogeneous data of multiple GC × GC-MS experiments without the transformation of retention times and the selection of landmark peaks. An optimal version of the SW-based algorithms was also established based on the associated likelihood function for the automatic peak alignment. The proposed alignment algorithms outperform the literature reported alignment method by analyzing the experiment data of a mixture of compound standards and a metabolite extract of mouse plasma with spiked-in compound standards.

A novel peak alignment algorithm using a distance and spectrum correlation optimization (DISCO) method has been developed for two-dimensional gas chromatography time-of-flight mass spectrometry (GCxGC/TOF-MS)based metabolomics. This algorithm uses the output of the instrument control software, ChromaTOF, as its input data. It detects and merges multiple peak entries of the same metabolite into one peak entry in each input peak fist. After a z-score transformation of metabolite retention times, DISCO selects landmark peaks from all samples based on beth two-dimensional retention times and mass spectrum similarity of fragment ions measured by Pearson's correlation coefficient. A local linear fitting method is employed in the original two-dimensional retention time space to correct retention time shifts. A progressive retention time map searching method is used to align metabolite peaks in all samples together based on optimization of the Euclidean distance and mass spectrum similarity. The effectiveness of the DISCO algorithm is demonstrated using data sets acquired under different experiment conditions and a spiked-in experiment. 10.1021/ac100064b

Inanalogy with benzene-derived molecular structures, we construct plasmonicmetamolecules by attaching Au nanospheres to specific sites on a hexagonalAu nanoplate. We employ a ligand exchange strategy that allows regioselectivecontrol of nanosphere attachment and study resulting structures usingcorrelated electron microscopy/optical spectroscopy at the single-metamoleculelevel. We find that plasmonic coupling within the resulting assemblyis strongly dependent on the structure of the metamolecule, in particularthe site of attachment of the nanosphere(s). We also uncover a synergyin the polarizing effect of multiple nanospheres attached to the nanoplate.Regioselective control of plasmonic properties demonstrated here enablesthe design of novel structure-dependent electromagnetic modes andapplications in three-dimensional spatial nanosensors. [ABSTRACT FROM AUTHOR]