You may find an excellent description of the xcms alignment package here [PPT], however for people who have no experience with R (like me) and dislike the command line style (me too), here is a small helper script which can be used for all experiments. With a simple change of 4 lines the script runs then automatically without any further interaction needed. Parameters can be adjusted within the file. This is an R script. Copy and save it to example-macro-xcms-v1.R

				### ***********************************************************************

				### xcms v1.3.2

				### URL: http://metlin.scripps.edu/download/

				### LC/MS and GC/MS Data Analysis and Alignement from netCDF data

				### Author: Colin A. Smith <This email address is being protected from spambots. You need JavaScript enabled to view it.>;

				### ***********************************************************************
				

				### ***********************************************************************

				### The script assumes xcms is installed via Packages->Install->BioConducor

				### Copy this file into commandline or open via "Open script"

				### Set 4 variables in +++ section and run have fun

				### Example Script: Tobias Kind fiehnlab.ucdavis.edu 2006

				### ***********************************************************************

				

				myAlign <- function () {

				

				
				### +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

				### These are the 4 variables you have to set for your own datafiles anything else runs
				automatically

				### Set your working directory under Windows, where your netCDF files are stored

				### Organize samples in subdirectories according to their class names WT/GM, Sick/Healthy etc.

				### Important: use "/" not "\"

				myDir = "C:/chemistry/xcms/example/faahKO/inst/cdf"

				myClass1 = "KO"

				myClass2 = "WT"

				myResultDir = "myAlign"

				### +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

				

				### change working directory to your files, see +++ section

				setwd(myDir)

				

				### get working directory

				(WD <- getwd())

				

				### load the xcms package

				library(xcms)

				

				### you can get help typing the following command at the commandline

				# ?retcor

				

				### finds peaks in NetCDF

				xset <- xcmsSet()

				

				### print used files and memory usuage

				xset

				

				### Group peaks together across samples and show fancy graphics

				### you can remove the sleep timer (silent run) or set it to 0.001

				xset <- group(xset, sleep=.0001)

				

				### calculate retention time deviations for every time

				xset2 <- retcor(xset, family="s", plottype="m")

				

				### Group peaks together across samples, set bandwitdh, change important m/z parameters here

				### Syntax: group(object, bw = 30, minfrac = 0.5, minsamp= 1, mzwid = 0.25, max = 5, sleep = 0)

				xset2 <- group(xset2, bw =10)

				

				### identify peak groups and integrate samples

				xset3 <- fillPeaks(xset2)

				

				### print statistics

				xset3

				

				### create report and save the result in EXCEL file, print 20 important peaks as PNG

				reporttab <- diffreport(xset3, myClass1, myClass2, myResultDir, 20, metlin = 0.15)

				

				### print file names

				# dir(path = ".", pattern = NULL, all.files = FALSE, full.names = FALSE, recursive = FALSE)

				

				### output were done!

				print("Finished, open by yourself the file myAlign.tsv and pictures in myAlign_eic")

				}

				

				### gives CPU, system, TOTAL time in seconds

				system.time(myAlign())

				

				### Currently R has no dual or multicore functionality, only a parallel library(snow)

				### Benchmark on Dual Opteron 254 2.8 GHz with ARECA-1120 RAID5:

				### 55 seconds total for the original 12 samples of the faahKO testset

				### [1] 51.61 2.27 54.85 NA NA

				### ***********************************************************************

				### function finished

				### ***********************************************************************