Dissolved organic matter (DOM) cycling across the land-ocean continuum is highly complex, and our limited understanding of DOM molecular transformations hinders a full assessment of land-ocean connect...

Untargeted tandem mass spectrometry (MS/MS)-based metabolomics enable broad characterization of small molecules in complex samples, yet the majority of spectra in a typical experiment remain unannotated, limiting biological interpretation. Reference data-driven (RDD) metabolomics addresses this gap by contextualizing spectra through comparison to curated, metadata-annotated reference data sets, allowing inference of spectrum origins without requiring exact structural identification. Here, we present an open-source RDD metabolomics platform comprising a user-friendly web application and a Python software package that performs RDD analyses directly from molecular networking outputs generated by GNPS. The tools support visualization and statistical analysis of RDD results, including interactive bar plots, heat maps, principal component analysis, and Sankey diagrams. We illustrate the approach using a hierarchical reference data set of 3500 food items to derive dietary patterns from stool metabolomics data of omnivore and vegan participants. The analysis reveals clear dietary group separation, demonstrating how RDD metabolomics can extract biologically meaningful patterns from otherwise unannotated spectra. Thus, the RDD metabolomics platform removes technical barriers for the metabolomics community to adopting RDD analysis, with the functionality freely available at https://github.com/bittremieuxlab/gnps-rdd and https://gnps-rdd.bittremieuxlab.org/.

Here we present CleaveScope, a lightweight standalone software tool for rapid and flexible analysis of protease specificity using LC-MS/MS data. The program accepts XML output files from the Mascot se...

The graphical abstract summerizes the Investigation of the phytochemical profile and biological activities of the roots and flowers of D. tortuosa and D. triradiata. Plant materials were extracted us...

Exenatide and H-GLP-1 belong to the GLP-1 agonist class of potential therapeutic agents. A robust multienzyme peptide-mapping workflow combined with LC-HRMS/MS enables high-resolution sequence covera...

Background Recurrent implantation failure (RIF) is a significant clinical challenge in assisted reproduction, yet its underlying molecular mechanisms remain poorly understood. This study aimed to char...

Abstract. Seronegative rheumatoid arthritis (negRA) is difficult to diagnose due to the absence of rheumatoid factor and anticitrullinated peptide antibodi

Abstract. Diabetic kidney disease (DKD) is a complication of diabetes and the leading cause of kidney failure among diabetic patients. Unfortunately, it is

Cyanobacteria are highly taxonomically and ecologically diverse species that have survived for billions of years. Here, authors show key structural features have remained within their light harvesting...

Four famous freshwater fish in China are renowned for their high production among freshwater species and are much-prized as sought-after delicacies. H…

There is a growing need for rapid, low-cost analytical tools to screen water supplies for persistent contaminants. Due to their ubiquitous presence in the environment and their detrimental effects on ...

Purpose This study investigates metabolic profiles in follicular fluid of patients with endometriosis (EM), polycystic ovary syndrome (PCOS), tubal blockage (TB), and unexplained infertility (UEI), as...

In this study, we focused on the spatial distribution of metabolites in areca palm (Areca catechu L.) floral organs. Using spatial metabolomics, the composit...

Animal-derived foods intended for human consumption are susceptible to the accumulation of toxic substances, including pesticides. In Mexico and other countries, pork is one of the most consumed me...

This study demonstrates that breath analysis using PTR-TOF MS and machine learning accurately distinguishes early lung cancer from benign nodules in a large cohort, identifying key biomarkers like al...

Translational Psychiatry - Lipidomic signatures reveal biomarkers of mild cognitive impairment

Anorexia in dairy cows arises from diverse causes, including metabolic disorders with and without hypocalcemia. We analyzed the serum metabolites of 2 …

As an important endogenous pollutant, the release of hydrophyte-derived dissolved organic matter (HDOM) significantly increases in eutrophication of w…

Secondary organic aerosol (SOA) compounds derived from both anthropogenic and biogenic volatile organic compounds (VOCs) in a smog chamber have been c…

Cyclotriphosphazene (CTP) flame retardants are extensively utilized in lithium-ion batteries, and their release into the environment during battery pr…

Since food is a major route of exposure to chemical contaminants, this study aimed to develop and apply an innovative method to improve assessment of …

Native mass spectrometry (nMS) preserves non-covalent interactions, thereby maintaining native-like protein complex assemblies in the gas phase. Herei…

The dried rhizome of Acorus tatarinowii Schott (SCP) is a valued medicinal material in traditional Chinese medicine (TCM). However, its quality and ef…

Mass spectrometry imaging (MSI) is widely used in biomedical sciences, as well as in plant sciences or microbiological studies. However, it is much le…

Supercritical fluid chromatography is traditionally employed for nonpolar and moderately polar analytes, while the analysis of ionic compounds remains…