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METAMS-LC/MS Pick, Align and Group (version 0.0.4)
.zip file containing the CDF, mzML or mzXML files of the new measurements
Choose a name to give for the specific settings in the parameters below
Which polarity mode was used for measuring of the ms sample
matchedFilter=Feature detection in the chromatographic time domain ; centWave=Feature detection for high resolution LC/MS data
full width at half maximum of matched filtration gaussian model peak. Only used to calculate the actual sigma
denominator for standard deviation (width) of matched filtration model peak (e.g. sigma = fwhm/2.3548)
maximum number of peaks per extracted ion chromatogram
signal to noise ratio cutoff
step size to use for profile generation
number of steps to merge prior to filtration
minimum difference in m/z for peaks with overlapping retention times
Minimum fraction of samples necessary in the alignment to make it a valid alignment/group
Minimum number of samples necessary in the alignment to make it a valid alignment/group. The lowest criteria between this and min.class.fraction will be used.
width of overlapping m/z slices to use for creating peak density chromatograms and grouping peaks across samples
bandwidth (standard deviation or half width at half maximum) of gaussian smoothing kernel to apply to the peak density chromatogram. Fill in two values separated by comma. First value is used for first grouping round, seccond value is used for last grouping/alignment round after retention time correction.
retention time correction method. 'peakgroups' is the default density based approach, 'obiwarp' is alignment data by Ordered Bijective Interpolated Warping
retention time correction method type/family
either 'loess' for non-linear alignment or 'linear' for linear alignment
ratio of missing samples to allow in retention time correction groups
ratio of extra peaks to allow in retention time correction correction groups
Fill missing peaks in peak groups/alignments that do not include peaks from every sample. This method produces intensity values for those missing samples by integrating raw data in peak group region.
percentage of FWHM width
correlation threshold (0..1)
General ppm error
Method selection for grouping peaks after correlation analysis into pseudospectra.
significant correlation threshold
Use correlation inside samples for peak grouping
Use isotopic relationship for peak grouping
Use correlation across samples for peak grouping
max. ion charge
max. number of expected isotopes
The ratio for the number of samples, which must satisfy the C12/C13 rule for isotope annotation
If no ruleset is provided, calculate ruleset with max. number n of [nM+x] clusterions

Runs metaMS process for LC/MS feature feature picking, aligning and grouping. This part of the metaMS process makes use of the XCMS and CAMERA tools and algorithms. CAMERA is used for automatic deconvolution/annotation of LC/ESI-MS data. The figure below shows the main parts of the metaMS process wrapped by this tool.

/repository/static/images/02534e21e01840b4/metaMS_pick_align_camera.png

From CAMERA documentation:

/repository/static/images/02534e21e01840b4/CAMERA_results.png

References

If you use this Galaxy tool in work leading to a scientific publication please cite the following papers:

Wehrens, R.; Weingart, G.; Mattivi, F. (2014). metaMS: an open-source pipeline for GC-MS-based untargeted metabolomics. Journal of chromatography B: biomedical sciences and applications, 996 (1): 109-116. doi: 10.1016/j.jchromb.2014.02.051 handle: http://hdl.handle.net/10449/24012

Wrapper by Pieter Lukasse.