XCMS Analyte Profiling Software

Category Metabolomics/Metabonomics>Metabolic Profiling/Analysis Systems/Tools

Abstract The XCMS and XCMS2 package reads and processes Liquid Chromatography-Mass Spectrometry (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 XCMS2 (see below...), allowing for automatic searching of targeted and data dependant tandem MS data file. This searching also includes the novel similarity search, search for structural motif in the tandem dataset.

XCMS2 is downloadable as part of the XCMS package.


XCMS is an LC/MS-based data analysis approach which incorporates novel nonlinear retention time alignment, matched filtration, peak detection, and peak matching.

Without using internal standards, the method dynamically identifies hundreds of endogenous metabolites for use as standards, calculating a nonlinear retention time correction profile for each sample.

Following retention time correction, the relative metabolite ion intensities are directly compared to identify changes in specific endogenous metabolites, such as potential biomarkers.

XCMS2 --

XCMS2 is an open source next generation metabolomics platform.

XCMS2 is an extension of XCMS, as it features the same reliable peak picking, alignment, statistical analysis of features but with the added capability of automatic searching of MS/MS spectra against the METLIN database.

Included in this platform is a “similarity search” functionality that analyzes MS/MS patterns for structural classification of unknown molecules.

XCMS2 has been developed to automatically search tandem mass spectrometry (MS/MS) data against high quality experimental MS/MS data from known metabolites contained in a reference library/database (METLIN) (as stated above...).

Scoring of hits is based on a “shared peak count” method (see below...) that identifies masses of fragment ions shared between the analytical and reference MS/MS spectra.

Another functional component of XCMS2 is the capability of providing structural information for unknown metabolites, which are Not in the METLIN database.

This “similarity search” algorithm (see below...) has been developed to detect possible structural motifs in the unknown metabolite which may produce characteristic fragment ions and neutral losses to related reference compounds contained in METLIN, even if the precursor masses are Not the same.

Shared Peak Count method --

The XCMS2 algorithm employs a modification of the “shared peak count” method, which takes the precursor mass from the MS scan and uses an indexed METLIN file for removal of any non-matching precursor mass.

After narrowing the search space by precursor mass, XCMS2 matches the collision energy of the MS/MS spectra. If there is No current matching collision energy in the experimental spectra, the algorithm will attempt to match with a higher collision energy spectrum.

Use of higher collision energy spectra gives the best performance. The software then performs comparative analysis between fragment data and a reference spectrum.

The match is made using a window of user specified error in parts per million (ppm) for each fragment mass. If the masses are outside the error window, then the algorithm moves onto the next fragment mass. This operation is performed using two different matrices, a similarity and distance matrix.

XCMS2 Similarity Search --

When the complete reference database with an unrestricted precursor mass is searched against, it was observed that along with an accurate hit on the correct compound many other compounds had a reasonable score. Upon further investigation, these compounds were found to be structurally related leading to the idea of a “similarity search”.

With further analysis of both the experimental and reference data, common structural elements can be identified, providing useful information for identification.

Using a scoring schema for compound comparison, the spectra are analyzed for similarity to the reference MS/MS spectrum, either by ‘neutral losses’ or ‘fragment ions’. Both the neutral loss search and fragment ion search work on the same basis as the scoring schema except the neutral loss search computes the difference in mass between each adjacent peak.

If there is a high degree of similarity, these compounds are reported in a table of results. While the amount or percentage of similarity is defined by the user, the manufacturers recommend using a similarity value of greater than 70%.

The results table contains important information on the compounds, including neutral losses and a fragment score, as well as the common structural motif identified.

The results table is a condensed version of the two (2) reported tables from the “similarity search” where the most significant hits are reported and figures have been added for clarity.

The first reported tables hold information on common structural motifs and collision energies that were used for the match. It was found that for a MS/MS search, using a collision energy that is greater or equal to the experimental value yields the strongest match. This phenomenon is believed to occur due to systematic variations in the concentrations of metabolites and intensities.

The second table provides a quick overview of the mass and gives a common collected substructure. This is obtained by a frequency counter which looks at all the common neutral losses and fragment ions separately, from the first table. The second table can be very useful for a comparison of the experimentally obtained spectrum to reported molecules.

Note: Different databases can also be used with XCMS2 by converting the database to the Metlin XML format and changing the address link to the new database.

Future developments of XCMS2 will include the use of basic structure-specific fragmentation rules and algorithms like the “similarity search” to facilitate structural elucidation of novel and yet unknown metabolite structures.

Recent development --

The Scripps Center for Metabolomics is pleased to announce “XCMS Online”, a new user-friendly variant of XCMS for processing metabolomics data without installation.

XCMS Online provides the same high-quality metabolomic analysis as the downloadable version but in a user-friendly, web-based format. XCMS Online allows users to easily upload LC/MS metabolomic data that can then be processed with a few simple mouse clicks.

Predefined parameter settings for different instruments (e.g. QTOF, Orbitrap, etc.) are available as well as options for customization.

Results can be viewed online in an interactive, customizable table showing statistics, chromatograms, and putative METLIN identities. All results and images are available for download as zip files.

You will need a user account to use the system however user accounts are free and only require a valid e-mail address to register.

Access the XCMS Online page.

System Requirements

Contact manufacturer.


Manufacturer Web Site XCMS Analyte Profiling Software

Price Contact manufacturer.

G6G Abstract Number 20665

G6G Manufacturer Number 104310