Cargando…

metID: an R package for automatable compound annotation for LC−MS-based data

SUMMARY: Accurate and efficient compound annotation is a long-standing challenge for LC–MS-based data (e.g. untargeted metabolomics and exposomics). Substantial efforts have been devoted to overcoming this obstacle, whereas current tools are limited by the sources of spectral information used (in-ho...

Descripción completa

Detalles Bibliográficos
Autores principales:	Shen, Xiaotao, Wu, Si, Liang, Liang, Chen, Songjie, Contrepois, Kévin, Zhu, Zheng-Jiang, Snyder, Michael
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2021
Materias:	Applications Notes
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8722759/ https://www.ncbi.nlm.nih.gov/pubmed/34432001 http://dx.doi.org/10.1093/bioinformatics/btab583

Ejemplares similares

ProbMetab: an R package for Bayesian probabilistic annotation of LC–MS-based metabolomics
por: Silva, Ricardo R., et al.
Publicado: (2014)

An R package to analyse LC/MS metabolomic data: MAIT (Metabolite Automatic Identification Toolkit)
por: Fernández-Albert, Francesc, et al.
Publicado: (2014)

peakPantheR, an R package for large-scale targeted extraction and integration of annotated metabolic features in LC–MS profiling datasets
por: Wolfer, Arnaud M, et al.
Publicado: (2021)

ipaPy2: Integrated Probabilistic Annotation (IPA) 2.0—an improved Bayesian-based method for the annotation of LC–MS/MS untargeted metabolomics data
por: Del Carratore, Francesco, et al.
Publicado: (2023)

aLFQ: an R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data
por: Rosenberger, George, et al.
Publicado: (2014)

MetMSLine: an automated and fully integrated pipeline for rapid processing of high-resolution LC–MS metabolomic datasets
por: Edmands, William M. B., et al.
Publicado: (2015)

MetExtract: a new software tool for the automated comprehensive extraction of metabolite-derived LC/MS signals in metabolomics research
por: Bueschl, Christoph, et al.
Publicado: (2012)

MetQy—an R package to query metabolic functions of genes and genomes
por: Martinez-Vernon, Andrea S, et al.
Publicado: (2018)

CANDI: an R package and Shiny app for annotating radiographs and evaluating computer-aided diagnosis
por: Badgeley, Marcus A, et al.
Publicado: (2019)

MUSCLE: automated multi-objective evolutionary optimization of targeted LC-MS/MS analysis
por: Bradbury, James, et al.
Publicado: (2015)

localpdb—a Python package to manage protein structures and their annotations
por: Ludwiczak, Jan, et al.
Publicado: (2022)

Estimation of measurement uncertainty for the quantification of protein by ID-LC–MS/MS
por: Beasley-Green, Ashley, et al.
Publicado: (2023)

MassCascade: Visual Programming for LC-MS Data Processing in Metabolomics
por: Beisken, Stephan, et al.
Publicado: (2014)

Homologue series detection and management in LC-MS data with homologueDiscoverer
por: Mildau, Kevin, et al.
Publicado: (2022)

ensembldb: an R package to create and use Ensembl-based annotation resources
por: Rainer, Johannes, et al.
Publicado: (2019)

Peak Pair Pruner: a post-processing software to MS-DIAL for peak pair validation and ratio quantification of isotopic labeling LC-MS(/MS) data
por: Smith, Ryan A, et al.
Publicado: (2023)

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

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

3DBIONOTES v2.0: a web server for the automatic annotation of macromolecular structures
por: Segura, Joan, et al.
Publicado: (2017)

AlphaMap: an open-source Python package for the visual annotation of proteomics data with sequence-specific knowledge
por: Voytik, Eugenia, et al.
Publicado: (2021)

Decombinator V4: an improved AIRR-C compliant-software package for T-cell receptor sequence annotation?
por: Peacock, Thomas, et al.
Publicado: (2020)

eMZed: an open source framework in Python for rapid and interactive development of LC/MS data analysis workflows
por: Kiefer, Patrick, et al.
Publicado: (2013)

mPies: a novel metaproteomics tool for the creation of relevant protein databases and automatized protein annotation
por: Werner, Johannes, et al.
Publicado: (2019)

automRm: An R Package for Fully Automatic LC-QQQ-MS Data Preprocessing Powered by Machine Learning
por: Eilertz, Daniel, et al.
Publicado: (2022)

MsQuality: an interoperable open-source package for the calculation of standardized quality metrics of mass spectrometry data
por: Naake, Thomas, et al.
Publicado: (2023)

iq: an R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics
por: Pham, Thang V, et al.
Publicado: (2020)

The GCTx format and cmap{Py, R, M, J} packages: resources for optimized storage and integrated traversal of annotated dense matrices
por: Enache, Oana M, et al.
Publicado: (2019)

Joint species distribution modelling with the r‐package Hmsc
por: Tikhonov, Gleb, et al.
Publicado: (2020)

ODP479 Equilibrium Dialysis ID-LC/MS/MS Procedure for Routine Measurement of Free Thyroxine in Serum
por: Zhang, Li, et al.
Publicado: (2022)

The geodiv r package: Tools for calculating gradient surface metrics
por: Smith, Annie C., et al.
Publicado: (2021)

An in silico MS/MS library for automatic annotation of novel FAHFA lipids
por: Ma, Yan, et al.
Publicado: (2015)

damidseq_pipeline: an automated pipeline for processing DamID sequencing datasets
por: Marshall, Owen J., et al.
Publicado: (2015)

ODP179 Development of Derivatization-free ID-LC/MS/MS Method for Simultaneous Measurement of Human Serum Monosaccharides
por: Tse, Chui, et al.
Publicado: (2022)

Development of an ID-LC–MS/MS method using targeted proteomics for quantifying cardiac troponin I in human serum
por: Asicioglu, Meltem, et al.
Publicado: (2023)

TidyMass an object-oriented reproducible analysis framework for LC–MS data
por: Shen, Xiaotao, et al.
Publicado: (2022)

mizer: an R package for multispecies, trait-based and community size spectrum ecological modelling
por: Scott, Finlay, et al.
Publicado: (2014)

libAnnotationSBML: a library for exploiting SBML annotations
por: Swainston, Neil, et al.
Publicado: (2009)

Enhanced functionalities for annotating and indexing clinical text with the NCBO Annotator+
por: Tchechmedjiev, Andon, et al.
Publicado: (2018)

Ion annotation-assisted analysis of LC-MS based metabolomic experiment
por: Varghese, Rency S, et al.
Publicado: (2012)

i2d: an R package for simulating data from images and the implications in biomedical research
por: Liang, Xiaoyu, et al.
Publicado: (2020)

Cannot write session to /tmp/vufind_sessions/sess_q9aabckdge5kp3v9mfk3j0d6dg