Literature DB >> 31953810

Metabolomics Data Processing Using XCMS.

Xavier Domingo-Almenara1, Gary Siuzdak2,3.   

Abstract

XCMS is one of the most used software for liquid chromatography-mass spectrometry (LC-MS) data processing and it exists both as an R package and as a cloud-based platform known as XCMS Online. In this chapter, we first overview the nature of LC-MS data to contextualize the need for data processing software. Next, we describe the algorithms used by XCMS and the role that the different user-defined parameters play in the data processing. Finally, we describe the extended capabilities of XCMS Online.

Entities:  

Keywords:  Data processing; Liquid chromatography; Mass spectrometry; Metabolomics; XCMS

Mesh：

Year:  2020        PMID： 31953810     DOI： 10.1007/978-1-0716-0239-3_2

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  11 in total

1.  C. elegans as a model for inter-individual variation in metabolism.

Authors:  Olga Ponomarova; Yong-Uk Lee; Gaotian Zhang; Bennett W Fox; Gabrielle E Giese; Melissa Walker; Nicole M Roberto; Huimin Na; Pedro R Rodrigues; Brian J Curtis; Aiden R Kolodziej; Timothy A Crombie; Stefan Zdraljevic; L Safak Yilmaz; Erik C Andersen; Frank C Schroeder; Albertha J M Walhout
Journal:  Nature       Date:  2022-07-06       Impact factor: 69.504

2.  From LC-MS/MS metabolomics profiling of Kanchanara Guggulu to molecular docking and dynamics simulation of quercetin pentaacetate with aldose reductase.

Authors:  Santosh Kumar Behera; Prashant Kumar Modi; Gayathree Karthikkeyan; Sameera Krishna Pervaje; Ravishankar Pervaje; Rajesh Raju; Thottethodi Subrahmanya Keshava Prasad; Yashwanth Subbannayya
Journal:  Bioinformation       Date:  2021-11-30

3.  High-Throughput Non-targeted Chemical Structure Identification Using Gas-Phase Infrared Spectra.

Authors:  Erandika Karunaratne; Dennis W Hill; Philipp Pracht; José A Gascón; Stefan Grimme; David F Grant
Journal:  Anal Chem       Date:  2021-07-21       Impact factor: 8.008

4.  Towards Predicting Gut Microbial Metabolism: Integration of Flux Balance Analysis and Untargeted Metabolomics.

Authors:  Ellen Kuang; Matthew Marney; Daniel Cuevas; Robert A Edwards; Erica M Forsberg
Journal:  Metabolites       Date:  2020-04-17

5.  Data preprocessing workflow for exhaled breath analysis by GC/MS using open sources.

Authors:  Rosa Alba Sola Martínez; José María Pastor Hernández; Gema Lozano Terol; Julia Gallego-Jara; Luis García-Marcos; Manuel Cánovas Díaz; Teresa de Diego Puente
Journal:  Sci Rep       Date:  2020-12-15       Impact factor: 4.379

6.  Porcine gut microbiota in mediating host metabolic adaptation to cold stress.

Authors:  Yu Zhang; Lan Sun; Run Zhu; Shiyu Zhang; Shuo Liu; Yan Wang; Yinbao Wu; Sicheng Xing; Xindi Liao; Jiandui Mi
Journal:  NPJ Biofilms Microbiomes       Date:  2022-04-05       Impact factor: 8.462

7.  mTORC1 and mTORC2 Complexes Regulate the Untargeted Metabolomics and Amino Acid Metabolites Profile through Mitochondrial Bioenergetic Functions in Pancreatic Beta Cells.

Authors:  Ghada A Soliman; Rinat R Abzalimov; Ye He
Journal:  Nutrients       Date:  2022-07-22       Impact factor: 6.706

8.  Chemical Constituents and Molecular Mechanism of the Yellow Phenotype of Yellow Mushroom (Floccularia luteovirens).

Authors:  Xiaolong Gan; Xuemei Bao; Baolong Liu; Yun Li; Dong Cao; Hg Zhang; Yuan Zong
Journal:  J Fungi (Basel)       Date:  2022-03-18

Review 9.  Defining Blood Plasma and Serum Metabolome by GC-MS.

Authors:  Olga Kiseleva; Ilya Kurbatov; Ekaterina Ilgisonis; Ekaterina Poverennaya
Journal:  Metabolites       Date:  2021-12-24

10.  Age-Related Metabolic Pathways Changes in Dental Follicles: A Pilot Study.

Authors:  Victor Coutinho Bastos; Jéssica Gardone Vitório; Roberta Rayra Martins-Chaves; Flávia Leite-Lima; Yuri Abner Rocha Lebron; Victor Rezende Moreira; Filipe Fideles Duarte-Andrade; Thaís Dos Santos Fontes Pereira; Lucilaine Valéria de Souza Santos; Liséte Celina Lange; Adriana Nori de Macedo; Gisele André Baptista Canuto; Carolina Cavaliéri Gomes; Ricardo Santiago Gomez
Journal:  Front Oral Health       Date:  2021-06-18
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