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Tandem mass spectrometry provides a high-throughput framework for identifying and quantifying proteins in complex biological samples. In computational proteomics, predicting peptide MS/MS spectra is a critical task, enabling downstream…
Tandem Mass Spectrometry is a cornerstone technique for identifying unknown small molecules in fields such as metabolomics, natural product discovery and environmental analysis. However, certain aspects, such as the probabilistic…
Nuclear Magnetic Resonance (NMR) spectroscopy is the cornerstone of small-molecule structure elucidation. While deep learning has demonstrated significant potential in automating structure elucidation and spectral simulation, current…
Tandem mass spectra capture fragmentation patterns that provide key structural information about a molecule. Although mass spectrometry is applied in many areas, the vast majority of small molecules lack experimental reference spectra. For…
The identification and property prediction of chemical molecules is of central importance in the advancement of drug discovery and material science, where the tandem mass spectrometry technology gives valuable fragmentation cues in the form…
Mass spectrometry (MS) plays a critical role in molecular identification, significantly advancing scientific discovery. However, structure elucidation from MS data remains challenging due to the scarcity of annotated spectra. While…
Spectroscopic techniques are essential tools for determining the structure of molecules. Different spectroscopic techniques, such as Nuclear magnetic resonance (NMR), Infrared spectroscopy, and Mass Spectrometry, provide insight into the…
Mass spectrometry is the dominant technology in the field of proteomics, enabling high-throughput analysis of the protein content of complex biological samples. Due to the complexity of the instrumentation and resulting data, sophisticated…
Mass spectrometry is a widely used method to study molecules and processes in medicine, life sciences, chemistry, catalysis, and industrial product quality control, among many other applications. One of the main features of some mass…
Identifying molecules from mass spectrometry (MS) data remains a fundamental challenge due to the semantic gap between physical spectral peaks and underlying chemical structures. Existing deep learning approaches often treat spectral…
Accurately identifying metabolites i.e. small molecules from mass spectrometry data remains a core challenge in metabolomics, with broad applications in drug discovery, environmental analysis, and clinical research. We address the Molecule…
Small-molecule identification from tandem mass spectrometry (MS/MS) remains a bottleneck in untargeted settings where spectral libraries are incomplete. While deep learning offers a solution, current approaches typically fall into two…
Machine learning methods for identifying molecular structures from tandem mass spectra (MS/MS) have advanced rapidly, yet current approaches still exhibit significant error rates. In high-stakes applications such as clinical metabolomics…
A vast majority of mass spectrometry data remains uncharacterized, leaving much of its biological and chemical information untapped. Recent advances in machine learning have begun to address this gap, particularly for tasks such as spectral…
Molecular assembly offers a promising path to detect life beyond Earth, while minimizing assumptions based on terrestrial life. As mass spectrometers will be central to upcoming Solar System missions, predicting molecular assembly from…
The annotation (assigning structural chemical identities) of MS/MS spectra remains a significant challenge due to the enormous molecular diversity in biological samples and the limited scope of reference databases. Currently, the vast…
Metabolomics complements investigation of the genome, transcriptome, and proteome of an organism. Today, the vast majority of metabolites remain unknown, in particular for non-model organisms. Mass spectrometry is one of the predominant…
Shotgun proteomics is a high-throughput technology used to identify unknown proteins in a complex mixture. At the heart of this process is a prediction task, the spectrum identification problem, in which each fragmentation spectrum produced…
Mass spectrometry imaging (MSI) as an analytical tool for bio-molecular and bio-medical research targets, accurate compound localization and identification. In terms of dedicated instrumentation, this translates into the demand for more…
Liquid chromatography mass spectrometry (LC-MS)-based metabolomics and exposomics aim to measure detectable small molecules in biological samples. The results facilitate hypothesis-generating discovery of metabolic changes and disease…