Robust discrimination between closely related species of salmon based on DNA fragments.

Closely related species of Salmonidae, including Pacific and Atlantic salmon, can be distinguished from one another based on nucleotide sequences from the cytochrome c oxidase sub-unit 1 mitochondrial gene (COI), using ensembles of fragments aligned to genetic barcodes that serve as digital proxies for the relevant species. This is accomplished by exploiting both the nucleotide sequences and their quality scores recorded in a FASTQ file obtained via Next Generation (NextGen) Sequencing of mitochondrial DNA extracted from Coho salmon caught with hook and line in the Gulf of Alaska. The alignment is done using MUSCLE (Muscle 5.

Proteomics as a Metrological Tool to Evaluate Genome Annotation Accuracy Following De Novo Genome Assembly: A Case Study Using the Atlantic Bottlenose Dolphin ().

The last decade has witnessed dramatic improvements in whole-genome sequencing capabilities coupled to drastically decreased costs, leading to an inundation of high-quality de novo genomes. For this reason, the continued development of genome quality metrics is imperative. Using the 2016 Atlantic bottlenose dolphin NCBI RefSeq annotation and mass spectrometry-based proteomic analysis of six tissues, we confirmed 10,402 proteins from 4711 protein groups, constituting nearly one-third of the possible predicted proteins.

Multi-omics characterization of NIST seafood reference materials and alternative matrix preparations.

The National Institute of Standards and Technology (NIST) has prepared four seafood reference materials (RMs) for use in food safety and nutrition studies: wild-caught and aquacultured salmon (RM 8256 and RM 8257) and wild-caught and aquacultured shrimp (RM 8258 and RM 8259). These materials were characterized using genetic, metabolomic (H-NMR, nuclear magnetic resonance and LC-HRMS/MS, liquid chromatography high-resolution tandem mass spectrometry), lipidomic, and proteomic methods to explore their use as matrix-matched, multi-omic differential materials for method development towards identifying product source and/or as quality control in untargeted omics studies. The results from experimental replicates were reproducible for each reference material and analytical method, with the most abundant features reported.

Investigating the feasibility of ICP-MS/MS for differentiating NIST salmon reference materials through determination of Sr and S isotope ratios.

Inductively coupled plasma tandem mass spectrometry (ICP-MS/MS) was investigated for possible use in food fraud studies through the measurement of strontium and sulfur isotope ratios. Oxygen mass shift mode was applied to shift Sr/Sr and S/S isotope ratios to their respective oxides, SrO/SrO and SO/SO, effecting a gas-phase chemical separation of the elements from Rb and Kr (for Sr) and molecular N and O species, along with P- and S-hydrides (for S). A total least squares regression approach was employed to generate the isotope ratio data from time-resolved analyses, and method uncertainties and accuracies were determined.

Spiking and homogenization of biological matrices for production of reference materials using cryogenic processes.

Biological reference materials (RMs) are essential for quality assurance, traceability of measurement results and for method validation. When addressing new measurement questions or emerging regulatory issues, rigorous large-scale CRM production may not be time efficient or economically practical using current production methods. By amending a relatively small matrix batch with a compound(s) of interest at the homogenization step, the National Institute of Standards and Technology (NIST) can create a custom material on an "as-needed" basis and circumvent the time delay inherent in large-batch production, thereby generating a fit-for-purpose, rapid-response RM.