XCMS

Version: 3.0.0

Website

http://bioconductor.org/packages/release/bioc/html/xcms.html

Description

XCMS is a bioconductor package that provides preprocessing for LC-MS (and GC-MS and DI-MS) data. The following pipeline is used for preprocessing: peak picking, peak grouping, retention time alignment, peak regrouping and filling in missing values. XCMS currently provides five peak detection algorithms: matchedFilter and centWave are established methods; Massifquant, MS1-methods and MSW-methods have been more recently released. These different methods are optimised for different experimental setups. CentWave uses continuous wavelet transformation to pick peaks in centroid format high resolution LC-MS data, matchFilter is peck detection of low resolution data, Massifquant uses a 2D kalman filter for high resolution LC-MS peak picking (isotope trace detection, using the TracMass algorithm), MS1-methods are used to ensure the detection of MS1 precursor peaks, when MS1 and MS2 data are gathered quasi simultaneously, MSW-methods are for peak detection of DI-MS data (it is a wrapper of peak picking algorithm from the “MassSpecWavelet” package). Three methods for peak grouping are provided: group.density (peaks are grouped across samples into overlapping m/z bins), group.mzClust (high resolution alignment) and group.nearest (a master peak list is created and corresponding peaks from all samples are assigned - inspired the mzMine grouping algorithm). For retention time correction the methods available are: loess and obiwarp (Ordered Bijective Interpolated Warping). There are two methods for filling in missing data: one for chromatographic spectra, one for DI-MS. This is done by integrating the values of a peak group. It is also possible to analysis LC-MS/MS data with XCMS.

Functionality

• Preprocessing

Instrument Data Type

• MS/LC-MS/LC-MS/MS
• MS/GC-MS

Approaches

• Untargeted

Computer Skills

Advanced

Software Type

R Package

Interface

Command line interface

Operating System (OS)

• Unix/Linux
• Mac OS
• Windows

Language

R, C++

Dependencies

mzR, BiocGenerics, ProtGenerics, Biobase

Input Formats - Open

mzData, mzML, mzXML, netCDF

Input Formats - Proprietary

N/A

Published

2005

Last Updated

2018

License

GPL (≥ 2) and file license

Paper

http://www.ncbi.nlm.nih.gov/pubmed/16448051

PMID

16448051