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MetabolomicsCreating a Reliable Mass Spectral–Retention Time Library for All Ion Fragmentation-Based Metabolomics

Accurate metabolite identification remains one of the primary challenges in a metabolomics study. A reliable chemical spectral library increases the confidence in annotation, and the availability of raw and annotated data in public databases facilitates the transfer of Liquid chromatography coupl...

2019-10-30 | MTBLS1040 | MetaboLights
MetabolomicsOptimizing Deconvolution of Chimeric Fragmentation Spectra to reveal molecular structures of complex biological mixtures

Direct infusion mass spectrometry (DI-MS) offers a rapid, high-throughput analysis and, compared to liquid chromatography MS (LC-MS), a different analytical window into the composition of complex biological samples. However, the lack of chromatographic separation in DI-MS results in highly comple...

MTBLS13066 | MetaboLights
MetabolomicsFragmentation patterns of methyloxime-trimethylsilyl derivatives of constitutive mono- and disaccharide isomers analyzed by gas chromatography/field ionization mass spectrometry
In saccharide analysis by gas chromatography/mass spectrometry (GC/MS), electron ionization (EI) is used almost exclusively, whereas other gentler methods of ionization are rarely used. Field ionization (FI) is recognized as a GC/MS ionization method that causes fewer fragment ions, but only few stu...
2015-12-27 | MTBLS215 | MetaboLights
MetabolomicsStreamlining LC-MS/MS Data Analysis in R with Open-Source *xcms* and *RforMassSpectrometry*: An End-to-End Workflow

Despite untargeted LC-MS/MS data being a powerful approach for large-scale metabolomics analysis, a significant challenge in the field lies in the reproducible and efficient analysis of such data, in particular. The power of R-based analysis workflows lies in their high customizability and adapta...

2024-08-26 | MTBLS8735 | MetaboLights
MetabolomicsWT 2.0: Unveiling the “dark matter” in the metabolome using all-ion stepwise fragmentation acquisition mode (ASFAM) and deep learning-based feature extraction

Current metabolomics methods often miss low-abundance compounds and yield incomplete or ambiguous MS2 spectra, resulting in the presence of “dark matter” within the metabolome. Here, we introduce WT 2.0, which employs an all-ion stepwise fragmentation acquisition mode (ASFAM) to acquire comprehe...

2025-09-23 | MTBLS13023 | MetaboLights
ProteomicsIn-source CID improves HCD-dependent fragmentation of ADP-ribosyl peptides
ADP-ribosylation is a posttranslational modification whose HCD products are dominated by complete or partial modification losses, complicating peptide sequencing and acceptor site localization efforts. We tested whether in-source CID performed on a quadrupole Orbitrap could convert ADPr to the small...
ORGANISM(S): Homo sapiens (Human) 
2024-12-05 | PXD055586 | Pride
Sid Proteomics Hcd Exploris480 Adp-ribosylation 
ProteomicsInfluence of in-source ion activation energies on artificial proteoform truncation
In order to elucidate the influence of in-source ion activation on artificial proteoform truncation, intact proteoforms from Escherichia coli lysate (enriched by proteoforms smaller than 20 kDa) were analyzed using LC-FAIMS-MS/MS with varying in-source ion activation energies.
ORGANISM(S): Escherichia coli 
2025-11-11 | PXD066719 | Pride
E. coli Proteoform Top-down-proteomics In-source fragmentation 
GenomicsDouble fragmentation ChIP-seq provides single nucleotide resolution Tcf4 binding characteristics
ChIP-seq has become the method of choice for studying functional DNA-protein interactions on a genome wide scale. The method is based on co-immunoprecipitation of DNA binding proteins with formaldehyde cross-linked DNA, followed by deep sequencing of immunoprecipitated chromatin fragments, allowing ...
ORGANISM(S): Homo sapiens 
2010-11-01 | E-GEOD-18481 | biostudies-arrayexpress
UnknownIn-source fragmentation and the sources of partially tryptic peptides in shotgun proteomics.
Not available
S-EPMC3584699 | biostudies-literature
UnknownSpontaneous In-Source Fragmentation Reaction Mechanism and Highly Sensitive Analysis of Dicofol by Electrospray Ionization Mass Spectrometry.
Not available
S-EPMC10180504 | biostudies-literature
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