The following are R packages we have produced for performing untargeted metabolite profiling with LC/MS. They are also used to preprocess data for this web site. Both packages are freely available under the GPL open-source license.

XCMS Analyte Profiling Software

The xcms package reads and processes LC/MS data stored in NetCDF (AIA/ANDI), mzXML, and mzData files. It includes numerous options for visualizing and interacting with that data. In addition, it includes functionality for peak picking, non-linear retention time alignment, and relative quantitation. It is capable of simultaneously preprocessing, analyzing, and visualizing the raw data from hundreds of samples.

XCMS is distrubited through bioconductor and can be download through the XCMS bioconductor page. Source packages and older versions can be downloaded here.

Also see list of changes and previous versions.

FAAH Knockout Dataset

The faahKO package contains a subset of the raw LC/MS data from Saghatelian 2004. It contains positive ionization mode data collected in centroid mode. There are samples from the spinal cords of 6 wild-type mice and 6 fatty acid amide hydrolase (FAAH) knockout mice.

Mailing List

We have just created a mailing list for users to post questions/problems related to xcms. Updates to xcms will also be announced on this list. To subscribe, please send an e-mail to majordomo@scripps.edu with the words "subscribe xcms" in the body of your message. After that, you will recieve instructions for confirming your subscription via e-mail. Archives of the mailing list are available on Google here.

Note: If you subcribe through Google, you will not be able to send messages to the list. If you wish to send messages, please subscribe using the instructions above.

Documentation

A number of PDF manuals are available for the software distributed here. They include tutorials and demonstrations of much of the major functionality.

• Installation Instructions for xcms
• LC/MS Preprocessing and Analysis with xcms

A PowerPoint presentation providing a visual demo/overview is also available.

Links

esi - An R package that supplements xcms with functions for annotating isotope/adduct peaks, reintegrating peaks, and assessing peak quality.

Publications

C.A. Smith, E.J. Want, G.C. Tong, R. Abagyan, and G. Siuzdak. XCMS: Processing Mass Spectrometry Data for Metabolite Profiling Using Nonlinear Peak Alignment, Matching, and Identification. Analytical Chemistry, 2006. [DOI]

C.A. Smith, E.J. Want, G.C. Tong, A. Saghatelian, B.F. Cravatt, R. Abagyan, and G. Siuzdak. Metlin XCMS: Global metabolite profiling incorporating LC/MS filtering, peak detection, and novel non-linear retention time alignment with open-source software. 53rd ASMS Conference on Mass Spectrometry, June 2005, San Antonio Texas. [PDF]