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View article: MSnLib: efficient generation of open multi-stage fragmentation mass spectral libraries
MSnLib: efficient generation of open multi-stage fragmentation mass spectral libraries Open
Untargeted high-resolution mass spectrometry is a key tool in clinical metabolomics, natural product discovery and exposomics, with compound identification remaining the major bottleneck. Currently, the standard workflow applies spectral l…
View article: Enhancing tandem mass spectrometry-based metabolite annotation with online chemical labeling
Enhancing tandem mass spectrometry-based metabolite annotation with online chemical labeling Open
View article: Self-supervised learning of molecular representations from millions of tandem mass spectra using DreaMS
Self-supervised learning of molecular representations from millions of tandem mass spectra using DreaMS Open
Characterizing biological and environmental samples at a molecular level primarily uses tandem mass spectroscopy (MS/MS), yet the interpretation of tandem mass spectra from untargeted metabolomics experiments remains a challenge. Existing …
View article: Self-supervised learning of molecular representations from millions of tandem mass spectra using DreaMS
Self-supervised learning of molecular representations from millions of tandem mass spectra using DreaMS Open
Characterizing biological and environmental samples at a molecular level primarily uses tandem mass spectroscopy (MS/MS), yet the interpretation of tandem mass spectra from untargeted metabolomics experiments remains a challenge. Existing …
View article: Efficient generation of open multi-stage fragmentation mass spectral libraries
Efficient generation of open multi-stage fragmentation mass spectral libraries Open
Untargeted analysis based on high-resolution mass spectrometry is a key tool in clinical metabolomics, natural product discovery, and exposomics, with compound identification remaining the major bottleneck. Currently, MS2 fragmentation dat…
View article: Discovery of metabolites prevails amid in-source fragmentation
Discovery of metabolites prevails amid in-source fragmentation Open
View article: Emergence of molecular structures from repository-scale self-supervised learning on tandem mass spectra
Emergence of molecular structures from repository-scale self-supervised learning on tandem mass spectra Open
Tandem mass spectrometry (MS/MS) is the primary method for characterizing biological and environmental samples at a molecular level. Despite this, the interpretation of tandem mass spectra from untargeted metabolomics experiments remains a…
View article: Efficient generation of open multi-stage fragmentation mass spectral libraries
Efficient generation of open multi-stage fragmentation mass spectral libraries Open
Untargeted analysis based on high-resolution mass spectrometry is a key tool in clinical metabolomics, natural product discovery, and exposomics, with compound identification remaining the major bottleneck. Currently, MS2 fragmentation dat…
View article: Empirically establishing drug exposure records directly from untargeted metabolomics data
Empirically establishing drug exposure records directly from untargeted metabolomics data Open
Despite extensive efforts, extracting information on medication exposure from clinical records remains challenging. To complement this approach, we developed the tandem mass spectrometry (MS/MS) based GNPS Drug Library. This resource integ…
View article: Efficient generation of open multi-stage fragmentation mass spectral libraries
Efficient generation of open multi-stage fragmentation mass spectral libraries Open
Untargeted analysis based on high-resolution mass spectrometry is a key tool in clinical metabolomics, natural product discovery, and exposomics, with compound identification remaining the major bottleneck. Currently, MS2 fragmentation dat…
View article: Lessons learned in a decade: Medical‐toxicological view of tattooing
Lessons learned in a decade: Medical‐toxicological view of tattooing Open
Tattooing has been part of the human culture for thousands of years, yet only in the past decades has it entered the mainstream of the society. With the rise in popularity, tattoos also gained attention among researchers, with the aim to b…
View article: Emergence of molecular structures from repository-scale self-supervised learning on tandem mass spectra
Emergence of molecular structures from repository-scale self-supervised learning on tandem mass spectra Open
Tandem mass spectrometry (MS/MS) is the primary method for characterizing biological and environmental samples at a molecular level. Despite this, the interpretation of tandem mass spectra remains a challenge. Existing computational method…
View article: Reproducible mass spectrometry data processing and compound annotation in MZmine 3
Reproducible mass spectrometry data processing and compound annotation in MZmine 3 Open
Untargeted MS experiments produce complex, multi-dimensional data that are practically impossible to investigate manually. For this reason, computational pipelines are needed to extract relevant information from raw spectral data and conve…
View article: MassSpecGym: A benchmark for the discovery and identification of molecules
MassSpecGym: A benchmark for the discovery and identification of molecules Open
The discovery and identification of molecules in biological and environmental samples is crucial for advancing biomedical and chemical sciences. Tandem mass spectrometry (MS/MS) is the leading technique for high-throughput elucidation of m…
View article: Mass spectrometry data processing in MZmine 3: feature detection and annotation
Mass spectrometry data processing in MZmine 3: feature detection and annotation Open
Untargeted MS experiments produce complex, multi-dimensional data that are practically impossible to investigate manually. For this reason, computational pipelines are needed to extract relevant information from raw spectral data and conve…
View article: On-tissue dataset-dependent MALDI-TIMS-MS2 bioimaging
On-tissue dataset-dependent MALDI-TIMS-MS2 bioimaging Open
Trapped ion mobility spectrometry (TIMS) adds an additional separation dimension to mass spectrometry (MS) imaging, however, the lack of fragmentation spectra (MS 2 ) impedes confident compound annotation in spatial metabolomics. Here, we …
View article: On-tissue dataset-dependent MALDI-TIMS-MS2 bioimaging
On-tissue dataset-dependent MALDI-TIMS-MS2 bioimaging Open
Trapped ion mobility spectrometry (TIMS) adds an additional separation dimension to mass spectrometry (MS) imaging, however, the lack of fragmentation spectra (MS2) impedes confident compound annotation in spatial metabolomics. Here, we de…
View article: The Hitchhiker’s Guide to Statistical Analysis of Feature-based Molecular Networks from Non-Targeted Metabolomics Data
The Hitchhiker’s Guide to Statistical Analysis of Feature-based Molecular Networks from Non-Targeted Metabolomics Data Open
Feature-Based Molecular Networking (FBMN) is a popular analysis approach for LC-MS/MS-based non-targeted metabolomics data. While processing LC-MS/MS data through FBMN is fairly streamlined, downstream data handling and statistical interro…
View article: On-tissue dataset-dependent MALDI-TIMS-MS2 bioimaging
On-tissue dataset-dependent MALDI-TIMS-MS2 bioimaging Open
Trapped ion mobility spectrometry (TIMS) adds an additional separation dimension to mass spectrometry (MS) imaging, however, the lack of fragmentation spectra (MS2) impedes confident compound annotation in spatial metabolomics. Here, we de…
View article: On-tissue dataset-dependent MALDI-TIMS-MS2 bioimaging
On-tissue dataset-dependent MALDI-TIMS-MS2 bioimaging Open
Trapped ion mobility spectrometry (TIMS) adds an additional separation dimension to mass spectrometry (MS) imaging, however, the lack of fragmentation spectra (MS2) impedes confident compound annotation in spatial metabolomics. Here, we de…
View article: Integrative analysis of multimodal mass spectrometry data in MZmine 3
Integrative analysis of multimodal mass spectrometry data in MZmine 3 Open
to the linking with GNPS to facilitate molecular networking in MZmine