Tandem mass spectrometry
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SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information Open
Mass spectrometry is a predominant experimental technique in metabolomics and related fields, but metabolite structural elucidation remains highly challenging. We report SIRIUS 4 (https://bio.informatik.uni-jena.de/sirius/), which provides…
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METLIN: A Technology Platform for Identifying Knowns and Unknowns Open
METLIN originated as a database to characterize known metabolites and has since expanded into a technology platform for the identification of known and unknown metabolites and other chemical entities. Through this effort it has become a co…
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Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics Open
The annotation of small molecules remains a major challenge in untargeted mass spectrometry-based metabolomics. We here critically discuss structured elucidation approaches and software that are designed to help during the annotation of un…
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A Cyclic Ion Mobility-Mass Spectrometry System Open
Improvements in the performance and availability of commercial instrumentation have made ion mobility-mass spectrometry (IM-MS) an increasingly popular approach for the structural analysis of ionic species as well as for separation of comp…
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Identification of small molecules using accurate mass MS/MS search Open
Tandem mass spectral library search (MS/MS) is the fastest way to correctly annotate MS/MS spectra from screening small molecules in fields such as environmental analysis, drug screening, lipid analysis, and metabolomics. The confidence in…
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A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients Open
State-of-the-art proteomics-grade mass spectrometers can measure peptide precursors and their fragments with ppm mass accuracy at sequencing speeds of tens of peptides per second with attomolar sensitivity. Here we describe a compact and r…
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Best practices and benchmarks for intact protein analysis for top-down mass spectrometry Open
One gene can give rise to many functionally distinct proteoforms, each of which has a characteristic molecular mass. Top-down mass spectrometry enables the analysis of intact proteins and proteoforms. Here members of the Consortium for Top…
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Streamlined Tandem Mass Tag (SL-TMT) Protocol: An Efficient Strategy for Quantitative (Phospho)proteome Profiling Using Tandem Mass Tag-Synchronous Precursor Selection-MS3 Open
Mass spectrometry (MS) coupled toisobaric labeling has developed rapidly into a powerful strategy for high-throughput protein quantification. Sample multiplexing and exceptional sensitivity allow for the quantification of tens of thousands…
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Identification and quantitation of lipid C=C location isomers: A shotgun lipidomics approach enabled by photochemical reaction Open
Significance Unsaturated lipids constitute a significant portion of total lipids in mammalian cells. They fulfill different biological roles and often exist in isomeric structures that differ only in the locations of carbon-carbon double (…
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Benchmarking common quantification strategies for large-scale phosphoproteomics Open
Comprehensive mass spectrometry (MS)-based proteomics is now feasible, but reproducible quantification remains challenging, especially for post-translational modifications such as phosphorylation. Here, we compare the most popular quantifi…
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Ultraviolet Photodissociation Mass Spectrometry for Analysis of Biological Molecules Open
The development of new ion-activation/dissociation methods continues to be one of the most active areas of mass spectrometry owing to the broad applications of tandem mass spectrometry in the identification and structural characterization …
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Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment Open
Molecular networking connects mass spectra of molecules based on the similarity of their fragmentation patterns. However, during ionization, molecules commonly form multiple ion species with different fragmentation behavior. As a result, t…
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TopPIC: a software tool for top-down mass spectrometry-based proteoform identification and characterization Open
Summary: Top-down mass spectrometry enables the observation of whole complex proteoforms in biological samples and provides crucial information complementary to bottom-up mass spectrometry. Because of the complexity of top-down mass spectr…
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CFM-ID 3.0: Significantly Improved ESI-MS/MS Prediction and Compound Identification Open
Metabolite identification for untargeted metabolomics is often hampered by the lack of experimentally collected reference spectra from tandem mass spectrometry (MS/MS). To circumvent this problem, Competitive Fragmentation Modeling-ID (CFM…
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Development, characterization and comparisons of targeted and non-targeted metabolomics methods Open
The potential of a metabolomics method to detect statistically significant perturbations in the metabolome of an organism is enhanced by excellent analytical precision, unequivocal identification, and broad metabolomic coverage. While the …
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Development of a High Coverage Pseudotargeted Lipidomics Method Based on Ultra-High Performance Liquid Chromatography–Mass Spectrometry Open
Lipid coverage is crucial in comprehensive lipidomics studies challenged by high diversity in lipid structures and wide dynamic range in lipid levels. Current state-of-the-art lipidomics technologies are mostly based on mass spectrometry (…
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Identification and Quantification of Proteoforms by Mass Spectrometry Open
A proteoform is a defined form of a protein derived from a given gene with a specific amino acid sequence and localized post‐translational modifications. In top‐down proteomic analyses, proteoforms are identified and quantified through mas…
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Electron-Transfer/Higher-Energy Collision Dissociation (EThcD)-Enabled Intact Glycopeptide/Glycoproteome Characterization Open
Protein glycosylation, one of the most heterogeneous post-translational modifications, can play a major role in cellular signal transduction and disease progression. Traditional mass spectrometry (MS)-based large-scale glycoprotein sequenc…
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Pinpointing Double Bond and <i>sn</i>-Positions in Glycerophospholipids via Hybrid 193 nm Ultraviolet Photodissociation (UVPD) Mass Spectrometry Open
Complete structural characterization of complex lipids, such as glycerophospholipids, by tandem mass spectrometry (MS/MS) continues to present a major challenge. Conventional activation methods do not generate fragmentation patterns that p…
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High-Throughput Single Cell Proteomics Enabled by Multiplex Isobaric Labeling in a Nanodroplet Sample Preparation Platform Open
Effective extension of mass spectrometry-based proteomics to single cells remains challenging. Herein we combined microfluidic nanodroplet technology with tandem mass tag (TMT) isobaric labeling to significantly improve analysis throughput…
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Precise, fast and comprehensive analysis of intact glycopeptides and modified glycans with pGlyco3 Open
Great advances have been made in mass spectrometric data interpretation for intact glycopeptide analysis. However, accurate identification of intact glycopeptides and modified saccharide units at the site-specific level and with fast speed…
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Accelerator Mass Spectrometry Open
A type of mass spectrometry in which ions in the sample are accelerated to very high kinetic energies, thus allowing for the separation of rare isotopes from more abundant isotopes.
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EpiProfile 2.0: A Computational Platform for Processing Epi-Proteomics Mass Spectrometry Data Open
Epigenetics has become a fundamental scientific discipline with various implications for biology and medicine. Epigenetic marks, mostly DNA methylation and histone post-translational modifications (PTMs), play important roles in chromatin …
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MSstatsTMT: Statistical Detection of Differentially Abundant Proteins in Experiments with Isobaric Labeling and Multiple Mixtures Open
Tandem mass tag (TMT) is a multiplexing technology widely-used in proteomic research. It enables relative quantification of proteins from multiple biological samples in a single MS run with high efficiency and high throughput. However, exp…
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Determination of Polyphenols Using Liquid Chromatography–Tandem Mass Spectrometry Technique (LC–MS/MS): A Review Open
In recent years, the consumption of polyphenols has been increasing, largely due to its beneficial effects on health. They are present in a wide variety of foods, but their extraction and characterization are complicated since they are mos…
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Parallelized Acquisition of Orbitrap and Astral Analyzers Enables High-Throughput Quantitative Analysis Open
The growing trend toward high-throughput proteomics demands rapid liquid chromatography-mass spectrometry (LC-MS) cycles that limit the available time to gather the large numbers of MS/MS fragmentation spectra required for identification. …
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Adding a new separation dimension to MS and LC–MS: What is the utility of ion mobility spectrometry? Open
Ion mobility spectrometry is an analytical technique known for more than 100 years, which entails separating ions in the gas phase based on their size, shape, and charge. While ion mobility spectrometry alone can be useful for some applica…
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Tentative Characterization of Polyphenolic Compounds in the Male Flowers of Phoenix dactylifera by Liquid Chromatography Coupled with Mass Spectrometry and DFT Open
Phoenix dacylifera is an ancient palm species rich in (poly)phenols. These phenolic compounds were tentatively identified by using liquid chromatography coupled with ion spray mass spectrometry in tandem mode (LC/MS/MS) with negative ion d…
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Glycan Analysis by Ion Mobility–Mass Spectrometry Open
Carbohydrates form one of the major classes of biological macromolecules in living organisms. To investigate their properties and function, an in‐depth knowledge of their underlying structure is essential. However, the inherent structural …
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Rapid quantification of underivatized amino acids in plasma by hydrophilic interaction liquid chromatography (HILIC) coupled with tandem mass‐spectrometry Open
Background Amino acidopathies are a class of inborn errors of metabolism (IEM) that can be diagnosed by analysis of amino acids (AA) in plasma. Current strategies for AA analysis include cation exchange HPLC with post‐column ninhydrin deri…