Automated annotation of untargeted all-ion fragmentation LCMS metabolomics data with MetaboAnnotatoR

G Graca, Y Cai, CHE Lau, PA Vorkas… - Analytical …, 2022 - ACS Publications
… , the pseudo-MS/MS and pseudo-MS (MS1 spectrum containing all … E and MS/MS spectra
to confidence levels 2 and 3 as … This enables the direct application of the workflow to features …

Advanced analytical and informatic strategies for metabolite annotation in untargeted metabolomics

Y Cai, Z Zhou, ZJ Zhu - TrAC Trends in Analytical Chemistry, 2023 - Elsevier
metabolomics, which include tandem mass spectral match … MS/MS spectra in untargeted
metabolomics data based on … in-silico MS/MS spectral match enabling confident annotation of …

Enhancing metabolome coverage in data-dependent LCMS/MS analysis through an integrated feature extraction strategy

Y Hu, B Cai, T Huan - Analytical chemistry, 2019 - ACS Publications
spectra for both MS1 and auto MS/MS were collected using a … a metabolomics data set
generated through LCMS analysis … features have good MS/MS spectra for confident metabolite …

[HTML][HTML] A modular and expandable ecosystem for metabolomics data annotation in R

J Rainer, A Vicini, L Salzer, J Stanstrup, JM Badia… - Metabolites, 2022 - mdpi.com
across all annotation functions (spectra similarity calculations but also MS 1 annotations) …
a rich toolbox that enables building customized and reproducible annotation workflows in R. …

… for nontargeted Metabolomic annotation and quantitation using a high-resolution spectral-stitching Nanoelectrospray direct-infusion mass spectrometry with data …

L Wang, W Lv, X Sun, F Zheng, T Xu, X Liu… - Analytical …, 2021 - ACS Publications
… and MS/MS information to increase the annotation confidence of DI… Here, metabolites for
which MS1 or MS2 spectra had no … annotating and quantitating metabolomic data acquired by a …

Comprehensive investigation of pathway enrichment methods for functional interpretation of LCMS global metabolomics data

Y Lu, Z Pang, J Xia - Briefings in Bioinformatics, 2023 - academic.oup.com
… and offers an efficient computational package to enable pathway … To narrow the gap between
raw LCMS spectra and … of metabolic features can be annotated with high confidence [19]. …

[HTML][HTML] MetaPro: a web-based metabolomics application for LC-MS data batch inspection and library curation

S An, R Wang, M Lu, C Zhang, H Liu, J Wang, C Xie… - Metabolomics, 2023 - Springer
spectral curation towards high-throughput metabolomics data. It … A reliable spectral library
can increase the confidence level … , which helps them check all the MSI needed information. …

[HTML][HTML] High-confidence structural annotation of metabolites absent from spectral libraries

MA Hoffmann, LF Nothias, M Ludwig… - Nature …, 2022 - nature.com
… quickly growing public metabolomics data. We demonstrate … recalibrated every five injections
in MS1 and MS/MS mode. … Using a linear classifier enables explainable machine learning; …

De Novo Cleaning of Chimeric MS/MS Spectra for LC-MS/MS-Based Metabolomics

T Zhao, S Xing, H Yu, T Huan - Analytical Chemistry, 2023 - ACS Publications
… , only the spectra with the highest MS1 precursor intensity were used … 33% of the MS/MS
spectra have confident precursor peak … , we tested it on metabolomics data sets generated with …

Integrative open workflow for confident annotation and molecular networking of metabolomics MSE/DIA data

…, K de Jesus Nicácio, MS Ferreira… - Briefings in …, 2024 - academic.oup.com
… of our metabolomics data, careful and rigorous data processing … MS 1 monoisotopic masses
enabled manual examination of MS E spectra using MZmine 3, leading to level 2 confidence