enviPickbatch: Batch peak picking for several .mzXML input files
In enviPick: Peak Picking for High Resolution Mass Spectrometry Data

Description Usage Arguments Details Value Author(s) See Also

Given a folder of .mzXML input files and subsequent processing, .csv peak tables with picked peaks are written to an output folder

enviPickbatch(folderin, folderout, MSlevel=c(1), dmzgap=15, dmzdens=4, 
ppm=TRUE, drtgap=500, drtsmall=20, drtdens=250, drtfill=10, drttotal=200, 
minpeak=4, recurs=10, weight=2, SB=3, SN=2, minint=1E5, maxint=1E7, 
ended=2, ion_mode=FALSE, progbar=FALSE)

`folderin`	Folder containing .mzXML input files
`folderout`	Destination folder for .csv peak tables
`MSlevel`	numeric 1 (MS) or 2 (MS-MS), `readMSdata`
`dmzgap`	m/z gap width for partitioning, `mzpart`
`dmzdens`	Maximum measurement deviation (+/-) of m/z within an EIC, `mzclust`
`ppm`	`dmzgap`, given in ppm (TRUE) or as absolute value (FALSE)
`drtgap`	RT gap width for partitioning, `mzpart`
`drtsmall`	Peak definition - RT window of a peak; cp. `minpeak` argument
`drtdens`	Maximum length of EICs, `mzclust`
`drtfill`	RT gap length to be filled, `mzpick`
`drttotal`	Maximum RT length of a single peak, `mzpick`
`minpeak`	Peak definition - minimum number of measurements per peak to found in windows of `drtsmall` and `dmzsmall`, `mzpick`
`recurs`	Maximum number of peaks within one EIC, `mzpick`
`weight`	Weight for assigning measurements to a peak, `mzpick`
`SB`	Signal-to-base ratio, `mzpick`
`SN`	Signal-to-noise ratio, `mzpick`
`minint`	Minimum intensity of a peak, `mzpick`
`maxint`	Peaks above this intensity are alwas included, regardless of checks for `SB` or `SN`, `mzpick`
`ended`	Within the peak detection recursion set by argument `recurs`, how often can a peak detection fail, to end the recursion? `mzpick`
`ion_mode`	"positive" or "negative" ionization. Otherwise set to FALSE, see details.
`progbar`	Show a progress bar (TRUE or FALSE)? May only work under Windows OS.

For further details on the parameter settings, please refer to the arguments of the underlying functions readMSdata, mzagglom, mzclust and mzpick. ion_mode allows to filter scans of a specific polarity from .mzXML files, if not set to FALSE; useful for files acquired under polarity switching.

Folder with .csv peak tables, each containing columns with: m/z (mean m/z of peak measurements), var_m/z (m/z variation of peak measurements), max_int (base-line corrected maximum intensity), sum_int (sum of all base-line corrected peak measurement intensities), RT (retention time at maximum intensity), minRT (start peak RT), maxRT (end peak RT), peak# (peak ID number), EIC# (EIC ID number), Score (not yet implemented)

Martin Loos

readMSdata mzagglom mzclust mzpick plotMSlist