LC-MS processing, deisotoping and annotating

Description

This tool performs deisotyping and annotating of LC-MS data.

Inputs

There are two input data formats, either mzML/mzXML or R data file for deisotyping and annotating analysis.

1. LC-MS data with mzML/mzXML format

The LC-MS data format is mzML or mzXML which can be converted from raw data by MSConvert of ProteoWizard. Each file represents one sample or replicate. Select multiple mzXML files for processing. The input data will be either positive or negative mode. They cannot be mixed up.

These mzML/mzXML files are converted by R package xcms into R data files. The algorithm for peak detection is fixed as matchedFilter and retention times alignment across samples with obiwarp method. The density method is employed for the peak grouping. The parameters for user to choose are:

• FWHM: specifying the full width at half maximum of matched filtration Gaussian model peak. Default value is 3.
• snthresh: defining the signal to noise cutoff to be used in the chromatographic peak detection step. Default value is 5.
• profmethod: Method to use for profile generation. Supported values are "bin", "binlin" (default), "binlinbase" and "intlin". "bin" is better for centroid data, "binlin" for profile data.
• minfrac: minimum fraction (fefault: 0.25) of samples necessary in at least one of the sample groups for it to be a valid group.,

2. R data file

Already processed data can be loaded as xcmsSet object R data file, produced by the R package xcms.

Parameters

See brief description on the setting of parameters for deisotyping and annotating above.

Outputs