xMSanalyzer

Version: 2.0.6.1

Website

https://sourceforge.net/projects/xmsanalyzer/

Description

Designed to improve feature detection of LC-MS data, running in conjunction with XCMS or apLCMS. As the scanning intervals with Fourier transform mass spectrometers is relatively constant, the optimum number of points to define a peak can vary over the course of a run. To deal with this, xMSanalyzer selects the number of points that is most reproducible for each peak, allowing for the extraction of low intensity peaks and those found in only a few samples. Sample quality is then evaluated using mean pairwise Pearson correlation coefficient between sample replicates. Quantitative feature reproducibility across sample replicates can then be evaluated using percent intensity difference (PID) or coefficient of variation (CoV). There is also the option of merging features detected using different parameter settings. Features can be matched across samples based on their m/z and their retention time. Features that are present in only single/few biological replicates but across multiple technical replicates can also be detected. It annotate metabolites using the METLIN and KEGG databases.

Functionality

• Preprocessing

Instrument Data Type

• MS/LC-MS

Approaches

• Untargeted

Computer Skills

Advanced

Software Type

R Package

Interface

Command line interface

Operating System (OS)

• Unix/Linux
• Mac OS
• Windows

Language

R

Dependencies

Rcpp, mzR, R2HTML, XML, limma, xcms, snow, rgl, gplots, foreach, RCurl, doSNOW, apLCMS

Input Formats - Open

mzData, mzML, mzXML, netCDF

Input Formats - Proprietary

N/A

Published

2013

Last Updated

2015

License

GPL-2

Paper

http://www.ncbi.nlm.nih.gov/pubmed/23323971

PMID

23323971