Gas chromatography - mass spectrometry data processing made easy.

Evaluation of GC-MS data may be challenging due to the high complexity of data including overlapped, embedded, retention time shifted and low S/N ratio peaks. In this work, we demonstrate a new approach, PARAFAC2 based Deconvolution and Identification System (PARADISe), for processing raw GC-MS data. PARADISe is a computer platform independent freely available software incorporating a number of newly developed algorithms in a coherent framework. It offers a solution for analysts dealing with complex chromatographic data. It allows extraction of chemical/metabolite information directly from the raw data. Using PARADISe requires only few inputs from the analyst to process GC-MS data and subsequently converts raw netCDF data files into a compiled peak table. Furthermore, the method is generally robust towards minor variations in the input parameters. The method automatically performs peak identification based on deconvoluted mass spectra using integrated NIST search engine and generates an identification report. In this paper, we compare PARADISe with AMDIS and ChromaTOF in terms of peak quantification and show that PARADISe is more robust to user-defined settings and that these are easier (and much fewer) to set. PARADISe is based on non-proprietary scientifically evaluated approaches and we here show that PARADISe can handle more overlapping signals, lower signal-to-noise peaks and do so in a manner that requires only about an hours worth of work regardless of the number of samples. We also show that there are no non-detects in PARADISe, meaning that all compounds are detected in all samples.

Glucose Metabolism via the Entner-Doudoroff Pathway in Campylobacter: A Rare Trait that Enhances Survival and Promotes Biofilm Formation in Some Isolates.

Isolates of the zoonotic pathogen Campylobacter are generally considered to be unable to metabolize glucose due to lack of key glycolytic enzymes. However, the Entner-Doudoroff (ED) pathway has been identified in Campylobacter jejuni subsp. doylei and a few C. coli isolates. A systematic search for ED pathway genes in a wide range of Campylobacter isolates and in the C. jejuni/coli PubMLST database revealed that 1.7% of >6,000 genomes encoded a complete ED pathway, including both C. jejuni and C. coli from diverse clinical, environmental and animal sources. In rich media, glucose significantly enhanced stationary phase survival of a set of ED-positive C. coli isolates. Unexpectedly, glucose massively promoted floating biofilm formation in some of these ED-positive isolates. Metabolic profiling by gas chromatography-mass spectrometry revealed distinct responses to glucose in a low biofilm strain (CV1257) compared to a high biofilm strain (B13117), consistent with preferential diversion of hexose-6-phosphate to polysaccharide in B13117. We conclude that while the ED pathway is rare amongst Campylobacter isolates causing human disease (the majority of which would be of agricultural origin), some glucose-utilizing isolates exhibit specific fitness advantages, including stationary-phase survival and biofilm production, highlighting key physiological benefits of this pathway in addition to energy conservation.

An automated method for baseline correction, peak finding and peak grouping in chromatographic data.

An automated method (FastChrom) for baseline correction, peak detection and assignment (grouping) of similar peaks across samples has been developed. The method has been tested both on artificial data and a dataset obtained from gas chromatograph analysis of wine samples. As part of the automated approach, a new method for baseline estimation has been developed and compared with other methods. FastChrom has been shown to perform at least as well as conventional software. However, compared to other approaches, FastChrom finds more peaks in the chromatograms and not only those with retention times defined by the user. FastChrom is fast and easy to use and offers the possibility of applying a retention time index which facilitates the identification of peaks and the comparison between experiments.