Enabling Efficient and Confident Annotation of LC-MS Metabolomics Data through MS1 Spectrum and Time Prediction.

Liquid chromatography coupled to electrospray ionization-mass spectrometry (LC-ESI-MS) is a versatile and robust platform for metabolomic analysis. However, while ESI is a soft ionization technique, in-source phenomena including multimerization, nonproton cation adduction, and in-source fragmentation complicate interpretation of MS data. Here, we report chromatographic and mass spectrometric behavior of 904 authentic standards collected under conditions identical to a typical nontargeted profiling experiment. The data illustrate that the often high level of complexity in MS spectra is likely to result in misinterpretation during the annotation phase of the experiment and a large overestimation of the number of compounds detected. However, our analysis of this MS spectral library data indicates that in-source phenomena are not random but depend at least in part on chemical structure. These nonrandom patterns enabled predictions to be made as to which in-source signals are likely to be observed for a given compound. Using the authentic standard spectra as a training set, we modeled the in-source phenomena for all compounds in the Human Metabolome Database to generate a theoretical in-source spectrum and retention time library. A novel spectral similarity matching platform was developed to facilitate efficient spectral searching for nontargeted profiling applications. Taken together, this collection of experimental spectral data, predictive modeling, and informatic tools enables more efficient, reliable, and transparent metabolite annotation.

Relationships between gas exchange and carbon isotope discrimination of Sitka x interior spruce introgressive genotypes and ribosomal DNA markers.

Effects of hybridization on physiological performance were investigated in seven natural introgressive populations and one F(1) population of Sitka (Picea sitchensis (Bong.) Carr.) x interior spruce (P. glauca (Moench) Voss. x P. engelmannii Parry ex Engelm.). Each population was represented by a Sitka-interior spruce ribosomal DNA (Si rDNA) index that was calculated from the relative abundance of species-specific DNA polymorphisms. Gas exchange parameters were measured under well-watered conditions on current-year needle tissues, which were also analyzed for carbon isotope discrimination. Sitka spruce populations had higher gas exchange rates (net photosynthesis, stomatal conductance to water vapor), but lower carbon isotope discrimination values than interior spruce populations. The natural hybrid populations had intermediate values of these parameters consistent with their Si rDNA index. The F(1) population had gas exchange parameters resembling those of Sitka spruce populations, but its carbon isotope discrimination was skewed toward that of interior spruce populations. These results confirmed previous findings that physiological performance of introgressive hybrid spruce populations varied as their DNA constitution changed.