A Modular and Expandable Ecosystem for Metabolomics Data Annotation in R.
R programming
annotation
metabolomics
reproducible research
small-compound databases
untargeted analysis
Journal
Metabolites
ISSN: 2218-1989
Titre abrégé: Metabolites
Pays: Switzerland
ID NLM: 101578790
Informations de publication
Date de publication:
11 Feb 2022
11 Feb 2022
Historique:
received:
12
01
2022
revised:
01
02
2022
accepted:
04
02
2022
entrez:
25
2
2022
pubmed:
26
2
2022
medline:
26
2
2022
Statut:
epublish
Résumé
Liquid chromatography-mass spectrometry (LC-MS)-based untargeted metabolomics experiments have become increasingly popular because of the wide range of metabolites that can be analyzed and the possibility to measure novel compounds. LC-MS instrumentation and analysis conditions can differ substantially among laboratories and experiments, thus resulting in non-standardized datasets demanding customized annotation workflows. We present an ecosystem of R packages, centered around the
Identifiants
pubmed: 35208247
pii: metabo12020173
doi: 10.3390/metabo12020173
pmc: PMC8878271
pii:
doi:
Types de publication
Journal Article
Langues
eng
Références
Anal Chem. 2017 Feb 21;89(4):2432-2439
pubmed: 28194963
Metabolomics. 2007 Sep;3(3):211-221
pubmed: 24039616
Nucleic Acids Res. 2016 Jan 4;44(D1):D1214-9
pubmed: 26467479
Metabolites. 2019 Mar 22;9(3):
pubmed: 30909447
J Cheminform. 2021 Jan 6;13(1):1
pubmed: 33407901
Metabolomics. 2021 May 11;17(5):49
pubmed: 33977389
J Am Soc Mass Spectrom. 1994 Sep;5(9):859-66
pubmed: 24222034
Nat Methods. 2020 Sep;17(9):905-908
pubmed: 32839597
Mol Cell Proteomics. 2014 Aug;13(8):2056-71
pubmed: 24623587
PLoS One. 2012;7(7):e39860
pubmed: 22815716
J Proteome Res. 2017 May 5;16(5):1924-1935
pubmed: 28367633
Anal Chem. 2020 Nov 3;92(21):14476-14483
pubmed: 33076659
Proc Natl Acad Sci U S A. 2015 Oct 13;112(41):12580-5
pubmed: 26392543
Nucleic Acids Res. 2021 Jan 8;49(D1):D1388-D1395
pubmed: 33151290
Anal Bioanal Chem. 2021 Dec 15;:
pubmed: 34907452
Electrophoresis. 2018 May;39(9-10):1222-1232
pubmed: 29292828
J Chromatogr B Analyt Technol Biomed Life Sci. 2008 Aug 15;871(2):182-90
pubmed: 18501684
J Chromatogr A. 2000 Oct 13;894(1-2):11-7
pubmed: 11100842
Nucleic Acids Res. 2018 Jan 4;46(D1):D608-D617
pubmed: 29140435
Nucleic Acids Res. 2022 Jan 7;50(D1):D622-D631
pubmed: 34986597
Bioinformatics. 2021 Aug 25;:
pubmed: 34432001
PLoS Comput Biol. 2013;9(7):e1003123
pubmed: 23861661
Anal Chem. 2021 Aug 24;93(33):11601-11611
pubmed: 34382770
Nucleic Acids Res. 2018 Jul 2;46(W1):W503-W509
pubmed: 29800320
Nat Biotechnol. 2021 Oct 14;:
pubmed: 34650271
Metabolites. 2019 Sep 23;9(10):
pubmed: 31548506
Proc Natl Acad Sci U S A. 2012 Jun 26;109(26):E1743-52
pubmed: 22586093
Anal Chem. 2019 Nov 5;91(21):13924-13932
pubmed: 31600070
J Mass Spectrom. 2010 Jul;45(7):703-14
pubmed: 20623627
Electrophoresis. 2001 Jan;22(1):77-87
pubmed: 11197183
Environ Sci Technol. 2014 Feb 18;48(4):2097-8
pubmed: 24476540