deprofile {RMassBank} | R Documentation

## De-profile a high-resolution MS scan in profile mode.

### Description

The `deprofile` functions convert profile-mode high-resolution input data to "centroid"-mode data amenable to i.e. centWave. This is done using full-width, half-height algorithm, spline algorithm or local maximum method.

### Usage

    deprofile.scan(scan, noise = NA, method = "deprofile.fwhm",
    					colnames = TRUE, ...)

    				deprofile(df, noise, method, ...)

    				deprofile.fwhm(df, noise = NA, cut = 0.5)

    				deprofile.localMax(df, noise = NA)

    				deprofile.spline(df, noise=NA, minPts = 5, step = 0.00001)

### Arguments

`df` | A dataframe with at least the columns `mz` and `int` to perform deprofiling on.
`noise` | The noise cutoff. A peak is not included if the maximum stick intensity of the peak is below the noise cutoff.
`method` | "deprofile.fwhm" for full-width half-maximum or "deprofile.localMax" for local maximum.
`...` | Arguments to the workhorse functions `deprofile.fwhm` etc.
`scan` | A matrix with 2 columns for m/z and intensity; from profile-mode high-resolution data. Corresponds to the spectra obtained with xcms::getScan or mzR::peaks.
`colnames` | For deprofile.scan: return matrix with column names (xcms-style, `TRUE`, default) or plain (mzR-style, `FALSE`).
`cut` | A parameter for `deprofile.fwhm` indicating where the peak flanks should be taken. Standard is 0.5 (as the algorithm name says, at half maximum.) Setting `cut = 0.75` would instead determine the peak width at 3/4 maximum, which might give a better accuracy for merged peaks, but could be less accurate if too few data points are present.
`minPts` | The minimal points count in a peak to build a spline; for peaks with less points the local maximum will be used instead. Note: The minimum value is 4!
`step` | The interpolation step for the calculated spline, which limits the maximum precision which can be achieved.

### Details

The `deprofile.fwhm` method is basically an R-semantic version of the "Exact Mass" m/z deprofiler from MZmine. It takes the center between the m/z values at half-maximum intensity for the exact peak mass. The logic is stolen verbatim from the Java MZmine algorithm, but it has been rewritten to use the fast R vector operations instead of loops wherever possible. It's slower than the Java implementation, but still decently fast IMO. Using matrices instead of the data frame would be more memory-efficient and also faster, probably.

The `deprofile.localMax` method uses local maxima and is probably the same used by e.g. Xcalibur. For well-formed peaks, "deprofile.fwhm" gives more accurate mass results; for some applications, `deprofile.localMax` might be better (e.g. for fine isotopic structure peaks which are not separated by a valley and also not at half maximum.) For MS2 peaks, which have no isotopes, `deprofile.fwhm` is probably the better choice generally.

`deprofile.spline` calculates the mass using a cubic spline, as the HiRes peak detection in OpenMS does.

The word "centroid" is used for convenience to denote not-profile-mode data. The data points are NOT mathematical centroids; we would like to have a better word for it.

The `noise` parameter was only included for completeness, I personally don't use it.

`deprofile.fwhm` and `deprofile.localMax` are the workhorses; `deprofile.scan` takes a 2-column scan as input. `deprofile` dispatches the call to the appropriate worker method.

### Value

`deprofile.scan`: a matrix with 2 columns for m/z and intensity

### Note

Known limitations: If the absolute leftmost stick or the absolute rightmost stick in a scan are maxima, they will be discarded! However, I don't think this will ever present a practical problem.

### Author(s)

Michael Stravs, Eawag <michael.stravs@eawag.ch>

### References

mzMine source code http://sourceforge.net/svn/?group_id=139835

### Examples

    ## Not run:
    mzrFile <- openMSfile("myfile.mzML")
    acqNo <- xraw@acquisitionNum[[50]]
    scan.mzML.profile <- mzR::peaks(mzrFile, acqNo)
    scan.mzML <- deprofile.scan(scan.mzML.profile)
    close(mzrFile)

    ## End(Not run)

[Package RMassBank version 3.0.0 Index]