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 and xcms^2 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. A recent development of xcms is xcms^2, allowing for automatic searching of targeted and data dependant tandam MS data file. This searching also includes the novel similarity search, search for structural motif in the tandam dataset. XCMS^2 is downloadable as part of the xcms package >13.2.0.

XCMS is distrubited through bioconductor and can be download through the XCMS bioconductor page. To download the xcms version which is conmatible with your R version copy and paste the following code into an active R session.

For the cutting edge XCMS and unstable version have a look at Devel XCMS

Mailing List

We have 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
• XCMS² Howto

A PowerPoint presentation providing a visual demo/overview is also available. We have recently made a wiki that is also supporting xcms the link can be found at the xcms metlin wiki

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.

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]

H.P. Benton, D.M. Wong, S.A. Trager, G. Siuzdak. XCMS2: Processing Tandem Mass Spectrometry Data for Metabolite Identification and Structural Characterization.