Librarian: A quality control tool to analyse sequencing library compositions [version 2; peer review: 1 approved, 2 approved with reservations]

Background Robust analysis of DNA sequencing data needs to include a set of quality control steps to ensure that technical bias is kept to a minimum. A metric easily obtained is the frequency of each of the nucleobases for each position across all sequencing reads. Here, we explore the differences in nucleobase compositions of various library types produced by standard experimental methodologies. Methods We obtained the compositions of nearly 3000 publicly available datasets and subjected them to Uniform Manifold Approximation and Projection (UMAP) dimensionality reduction for a two-dimensional representation of their composition characteristics. Results We find that most library types result in a specific composition profile. We use this to give an estimate of how strongly the composition of a test library resembles the profiles of previously published libraries, and how likely the test sample is to be of a particular type. We introduce Librarian, a user-friendly web application and command line tool which enables checking base compositions of test libraries against known library types. Conclusions Library preparation methods strongly influence the per position nucleobase content. By comparing test libraries to a database of previously published library types we can make predictions regarding the library preparation method. Librarian is a user-friendly tool to access this information for quality assurance purposes as discrepancies can flag potential irregularities very early on

BioPAN: a web-based tool to explore mammalian lipidome metabolic pathways on LIPID MAPS.

Lipidomics increasingly describes the quantification using mass spectrometry of all lipids present in a biological sample.  As the power of lipidomics protocols increase, thousands of lipid molecular species from multiple categories can now be profiled in a single experiment.  Observed changes due to biological differences often encompass large numbers of structurally-related lipids, with these being regulated by enzymes from well-known metabolic pathways.  As lipidomics datasets increase in complexity, the interpretation of their results becomes more challenging.  BioPAN addresses this by enabling the researcher to visualise quantitative lipidomics data in the context of known biosynthetic pathways.  BioPAN provides a list of genes, which could be involved in the activation or suppression of enzymes catalysing lipid metabolism in mammalian tissues

LIPID MAPS: Update to databases and tools for the lipidomics community

LIPID MAPS (LIPID Metabolites and Pathways Strategy), www.lipidmaps.org, provides a systematic and standardized approach to organizing lipid structural and biochemical data. Founded 20 years ago, the LIPID MAPS nomenclature and classification has become the accepted community standard. LIPID MAPS provides databases for cataloging and identifying lipids at varying levels of characterization in addition to numerous software tools and educational resources, and became an ELIXIR-UK data resource in 2020. This paper describes the expansion of existing databases in LIPID MAPS, including richer metadata with literature provenance, taxonomic data and improved interoperability to facilitate FAIR compliance. A joint project funded by ELIXIR-UK, in collaboration with WikiPathways, curates and hosts pathway data, and annotates lipids in the context of their biochemical pathways. Updated features of the search infrastructure are described along with implementation of programmatic access via API and SPARQL. New lipid-specific databases have been developed and provision of lipidomics tools to the community has been updated. Training and engagement have been expanded with webinars, podcasts and an online training school

LipidFinder 2.0: advanced informatics pipeline for lipidomics discovery applications

We present LipidFinder 2.0, incorporating four new modules that apply artefact filters, remove lipid and contaminant stacks, in-source fragments and salt clusters, and a new isotope deletion method which is significantly more sensitive than available open-access alternatives. We also incorporate a novel false discovery rate (FDR) method, utilizing a target-decoy strategy, which allows users to assess data quality. A renewed lipid profiling method is introduced which searches three different databases from LIPID MAPS and returns bulk lipid structures only, and a lipid category scatter plot with color blind friendly pallet. An API interface with XCMS Online is made available on LipidFinder’s online version. We show using real data that LipidFinder 2.0 provides a significant improvement over non-lipid metabolite filtering and lipid profiling, compared to available tools

Data analysis strategies for the characterization of chemical contaminant mixtures. Fish as a case study

Thousands of chemicals are potentially contaminating the environment and food resources, covering a wide spectrum of molecular structures, physico-chemical properties, sources, environmental behavior and toxic profiles. Beyond the description of the individual chemicals, characterizing contaminant mixtures in related matrices has become a major challenge in ecological and human health risk assessments. Continuous analytical developments, in the fields of targeted (TA) and non-targeted analysis (NTA), have resulted in ever larger sets of data on associated chemical profiles. More than ever, the implementation of advanced data analysis strategies is essential to elucidate profiles and extract new knowledge from these large data sets. Specifically focusing on the data analysis step, this review summarizes the recent progress in integrating data analysis tools into TA and NTA workflows to address the challenging characterization of chemical mixtures in environmental and food matrices. As fish matrices are relevant in both aquatic pollution and consumer exposure perspectives, fish was chosen as the main theme to illustrate this review, although the present document is equally relevant to other food and environmental matrices.The key features of TA and NTA data sets were reviewed to illustrate the challenges associated with their analysis. Advanced filtering strategies to mine NTA data sets are presented, with a particular focus on chemical filters and discriminant analysis. Further, the applications of supervised and unsupervised multivariate analysis methods to characterize exposure to chemical mixtures, and their associated challenges, is discussed

Factors determining the adherence to antimicrobial guidelines and the adoption of computerised decision support systems by physicians: A qualitative study in three European hospitals

Antimicrobial stewardship (AMS) programs aim to optimize antibiotic use and reduce inappropriate prescriptions through a panel of interventions. The implementation of clinical guidelines is a core strategy of AMS programs. Nevertheless, their dissemination and application remain low. Computerised decision support systems (CDSSs) offer new opportunities for semi-automated dissemination of guidelines. This qualitative study aimed at gaining an in-depth understanding of the determinants of adherence to antimicrobial prescribing guidelines and CDSSs adoption and is part of a larger project, the COMPASS trial, which aims to assess a CDSS for antimicrobial prescription. The final objective of this qualitative study is to 1) provide insights from end-users to assist in the design of the COMPASS CDSS, and to 2) help with the interpretation of the quantitative findings of the randomised controlled trial assessing the COMPASS CDSS, once data will be analysed

Ochratoxin A determination in swine muscle and liver from French conventional or organic farming production systems

International audienceConsumers generally considered organic products to be healthier and safer but data regarding the contamination of organic products are scarce. This study evaluated the impact of the farming system on the levels of ochratoxin A (OTA) in the tissues of French pigs (muscle and liver) reared following three different types of production (organic, Label Rouge and conventional). Because OTA is present at trace levels in animal products, a sensitive ultra-high performance liquid chromatography-tandem mass spectrometry method using stable isotope dilution assay was developed and validated. OTA was detected or quantified (LOQ of 0.10 mu g kg(-1)) in 67% (n = 47) of the 70 pig liver samples analysed, with concentrations ranging from < 0.10 to 3.65 mu g kg(-1). The maximum concentration was found in a sample from organic production but there were no significant differences in the content of OTA between farming systems. OTA was above the LOQ in four out of 25 samples of the pork muscles. A good agreement was found between OTA levels in muscle and liver (liver concentration = 2.9 x OTA muscle concentration, r = 0.981)

LIPID MAPS: update to databases and tools for the lipidomics community.

LIPID MAPS (LIPID Metabolites and Pathways Strategy), www.lipidmaps.org, provides a systematic and standardized approach to organizing lipid structural and biochemical data. Founded 20 years ago, the LIPID MAPS nomenclature and classification has become the accepted community standard. LIPID MAPS provides databases for cataloging and identifying lipids at varying levels of characterization in addition to numerous software tools and educational resources, and became an ELIXIR-UK data resource in 2020. This paper describes the expansion of existing databases in LIPID MAPS, including richer metadata with literature provenance, taxonomic data&nbsp;and improved interoperability to facilitate FAIR compliance. A joint project funded by ELIXIR-UK, in collaboration with WikiPathways, curates and hosts pathway data, and annotates lipids in the context of their biochemical pathways. Updated features of the search infrastructure are described along with implementation of programmatic access via API and SPARQL. New lipid-specific databases have been developed and provision of lipidomics tools to the community has been updated. Training and engagement have been expanded with webinars, podcasts and an online training school

Evaluating the performances of an operational absolute quantum gravimeter

International audienc