Cargando…

TopNEXt: automatic DDA exclusion framework for multi-sample mass spectrometry experiments

MOTIVATION: Liquid Chromatography Tandem Mass Spectrometry experiments aim to produce high-quality fragmentation spectra, which can be used to annotate metabolites. However, current Data-Dependent Acquisition approaches may fail to collect spectra of sufficient quality and quantity for experimental...

Descripción completa

Detalles Bibliográficos
Autores principales:	McBride, Ross, Wandy, Joe, Weidt, Stefan, Rogers, Simon, Davies, Vinny, Daly, Rónán, Bryson, Kevin
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2023
Materias:	Original Paper
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10336026/ https://www.ncbi.nlm.nih.gov/pubmed/37364005 http://dx.doi.org/10.1093/bioinformatics/btad406

Ejemplares similares

In Silico Optimization of Mass Spectrometry Fragmentation Strategies in Metabolomics
por: Wandy, Joe, et al.
Publicado: (2019)

Simulated-to-real benchmarking of acquisition methods in untargeted metabolomics
por: Wandy, Joe, et al.
Publicado: (2023)

Rapid Development of Improved Data-Dependent Acquisition Strategies
por: Davies, Vinny, et al.
Publicado: (2021)

Incorporating peak grouping information for alignment of multiple liquid chromatography-mass spectrometry datasets
por: Wandy, Joe, et al.
Publicado: (2015)

Ms2lda.org: web-based topic modelling for substructure discovery in mass spectrometry
por: Wandy, Joe, et al.
Publicado: (2018)

GraphOmics: an interactive platform to explore and integrate multi-omics data
por: Wandy, Joe, et al.
Publicado: (2021)

ShinyKGode: an interactive application for ODE parameter inference using gradient matching
por: Wandy, Joe, et al.
Publicado: (2018)

Displacement of a DNA binding protein by Dda helicase
por: Byrd, Alicia K., et al.
Publicado: (2006)

A streamlined platform for analyzing tera-scale DDA and DIA mass spectrometry data enables highly sensitive immunopeptidomics
por: Xin, Lei, et al.
Publicado: (2022)

MetAssign: probabilistic annotation of metabolites from LC–MS data using a Bayesian clustering approach
por: Daly, Rónán, et al.
Publicado: (2014)

2D Dynamic Directional Amplification (DDA) in Phononic Metamaterials
por: Kalderon, Moris, et al.
Publicado: (2021)

voomDDA: discovery of diagnostic biomarkers and classification of RNA-seq data
por: Zararsiz, Gokmen, et al.
Publicado: (2017)

Predicting chromosomal compartments directly from the nucleotide sequence with DNA-DDA
por: Lainscsek, Xenia, et al.
Publicado: (2023)

Fast Proteome Identification and Quantification from Data-Dependent Acquisition–Tandem Mass Spectrometry (DDA MS/MS) Using Free Software Tools
por: Meyer, Jesse G.
Publicado: (2019)

PiMP my metabolome: an integrated, web-based tool for LC-MS metabolomics data
por: Gloaguen, Yoann, et al.
Publicado: (2017)

DDA-SKF: Predicting Drug–Disease Associations Using Similarity Kernel Fusion
por: Gao, Chu-Qiao, et al.
Publicado: (2022)

Ranking Metabolite Sets by Their Activity Levels
por: McLuskey, Karen, et al.
Publicado: (2021)

DDA: A Novel Network-Based Scoring Method to Identify Disease–Disease Associations
por: Suratanee, Apichat, et al.
Publicado: (2015)

MUC1 Specific Immune Responses Enhanced by Coadministration of Liposomal DDA/MPLA and Lipoglycopeptide
por: Du, Jing-Jing, et al.
Publicado: (2022)

DDA‐imaging with structural identification of lipid molecules on an Orbitrap Velos Pro mass spectrometer
por: Khalil, Saleh M., et al.
Publicado: (2022)

Misregulation of the LOB domain gene DDA1 suggests possible functions in auxin signalling and photomorphogenesis
por: Mangeon, Amanda, et al.
Publicado: (2011)

DDA3 associates with microtubule plus ends and orchestrates microtubule dynamics and directional cell migration
por: Zhang, Liangyu, et al.
Publicado: (2013)

ASB7 regulates spindle dynamics and genome integrity by targeting DDA3 for proteasomal degradation
por: Uematsu, Keiji, et al.
Publicado: (2016)

A fluorescently labelled quaternary ammonium compound (NBD-DDA) to study resistance mechanisms in bacteria
por: Nordholt, Niclas, et al.
Publicado: (2022)

Central exclusive production of top quarks
por: Potrebko, Andris
Publicado: (2018)

DDA suppresses angiogenesis and tumor growth of colorectal cancer in vivo through decreasing VEGFR2 signaling
por: Huang, Shiu-Wen, et al.
Publicado: (2016)

DDA1, a novel oncogene, promotes lung cancer progression through regulation of cell cycle
por: Cheng, Lin, et al.
Publicado: (2017)

Proteomic datasets of HeLa and SiHa cell lines acquired by DDA-PASEF and diaPASEF
por: Huang, Zelu, et al.
Publicado: (2022)

Self-Assembly of NaOL-DDA Mixtures in Aqueous Solution: A Molecular Dynamics Simulation Study
por: Wang, Li, et al.
Publicado: (2021)

Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions
por: Hjörleifsson Eldjárn, Grímur, et al.
Publicado: (2021)

Simultaneous binding to the tracking strand, displaced strand and the duplex of a DNA fork enhances unwinding by Dda helicase
por: Aarattuthodiyil, Suja, et al.
Publicado: (2014)

Structural insights into DDA1 function as a core component of the CRL4-DDB1 ubiquitin ligase
por: Shabek, Nitzan, et al.
Publicado: (2018)

MultiPro: DDA-PASEF and diaPASEF acquired cell line proteomic datasets with deliberate batch effects
por: Wang, He, et al.
Publicado: (2023)

ATLAS Distributed Computing on the way to the automatic site exclusion
por: Schovancova, J
Publicado: (2012)

Automatic motor activation in the executive control of action
por: McBride, Jennifer, et al.
Publicado: (2012)

Patient Acceptability of the Yorkshire Dialysis Decision Aid (YoDDA) Booklet: A Prospective Non-Randomized Comparison Study Across 6 Predialysis Services
por: Winterbottom, Anna E., et al.
Publicado: (2016)

c-Cbl Acts as an E3 Ligase Against DDA3 for Spindle Dynamics and Centriole Duplication during Mitosis
por: Gwon, Dasom, et al.
Publicado: (2019)

Search for exclusively produced top quark pairs at the LHC
por: Ribeiro Lopes, Beatriz
Publicado: (2020)

Top quark pair production in the exclusive processes at LHC
por: Gonçalves, Victor P., et al.
Publicado: (2020)

DDA3 recruits microtubule depolymerase Kif2a to spindle poles and controls spindle dynamics and mitotic chromosome movement
por: Jang, Chang-Young, et al.
Publicado: (2008)

Cannot write session to /tmp/vufind_sessions/sess_cris6vt5feuk0n6vubpsv22r64