XCMS Online

Version: 3.5.1

Website

https://xcmsonline.scripps.edu/landing_page.php?pgcontent=mainPage

Description

XCMS Online is an online implementation of XCMS, that include the entire data processing pipeline, from preprocessing to metabolite identification and statistical analysis. The processing pipeline is divided into three stages: data upload, parameter selection and result interpretation. Predefined parameter sets are available for different instrument setups or alternatively the user can set the parameters manually. For peak picking, grouping and retention time alignment, the algorithms implemented in XCMS are used. After a submitted job has been completed, plots of experimental results are displayed and the data are available for downloading. Retention time plots before and after alignment are displayed and a mirror plot (a plot showing dysregulated features) is used to visualise features with statistically significance differences in signal intensity between experimental conditions. Multidimensional scaling plots (MDS) and PCA plots are also included, both of which are performed on centred and scaled data (unit variance, log, pareto). Other visualisation provided includes EIC, box plots, cloud plots and Venn/Edwards diagrams. Putative Metabolite Annotation is performed using the METLIN database. Statistical analysis includes: Welch's t-test, Mann-Whitney test, paired t-test, Wilcoxon signed rank, one-way ANOVA with post-HOC, Kruskal-Wallis, repeated measures ANOVA and Friedman test. As with the other analysis, the user must input parameter settings (parametric or non-parametric and independent or dependent) and XCMS Online will automatically choose which statistical analysis to use. Features can be filtered by fold-change, ion intensity or p-value. metaXCMS is included, allowing for paired two-group analysis, multigroup analysis and meta-analysis. It also allows for pathway analysis and data integration of proteomics and transcriptomics data.

Functionality

• Workflow

Instrument Data Type

• MS/GC-MS
• MS/LC-MS

Approaches

• Untargeted

Computer Skills

Basic

Software Type

Web Based

Interface

Web User Interface

Operating System (OS)

• Unix/Linux
• Mac OS
• Windows

Language

R

Dependencies

3.5.1

Input Formats - Open

mzData, mzML, mzXML, netCDF

Input Formats - Proprietary

Agilent .d, AB SCIENX .wiff, Waters .raw, Thermo Fisher Scientific .raw, Bruker .d

Published

2012

Last Updated

2016

License

https://xcmsonline.scripps.edu/landing_page.php?pgcontent=termsOfUse

Paper

http://www.ncbi.nlm.nih.gov/pubmed/22533540

PMID

22533540