MS Annotation in R

Description Usage Arguments Value Author(s) References

This is a wrapper function for GenForm, requiring MS, MS/MS, ion settings and directories.

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RunGenForm(ms_file, msms_file, ion, GenFormDir, ResultsDir,ppm=5, acc=15,
elements="CHNOPS",ff="", dbe=TRUE, oei=TRUE, mz=0, exist=TRUE, an_loss=TRUE,an_loss_limit=500,
sort=FALSE, cleanMSMS=FALSE)

`ms_file`	File name of a plain text, two column file (e.g. `MS.txt`) containing space-separated mz and intensity values of the MS1 spectrum (full scan). The most intense peak is taken as "m" unless this is defined with `"mz"`.
`msms_file`	A plain text, two column file (e.g. `MSMS.txt`) containing space-separated mz and intensity values of the tandem (MS2) spectrum, i.e. the fragments. While GenForm can be run without MSMS, this function requires its use at this stage.
`ion`	Ion setting to use. Options: `c("-e","+e","-H","+H","+Na")`.
`GenFormDir`	Directory containing `GenForm.exe`.
`ResultsDir`	Directory to save the GenForm results. Existing files will be overwritten.
`ppm`	Accuracy setting for MS1 (default `5` ppm).
`acc`	Accuracy setting for MS2 (default `15` ppm).
`elements`	Selection of elements to consider. Default `"CHNOPS"`, implemented are `"CHBrClFINOPSSi"`.
`ff`	A "fuzzy formula" input to offer more control beyond `elements`. This should be in format `C0-6H0-20O1-3`.
`dbe`	Default `TRUE` writes double bond equivalents to output; `FALSE` suppresses this output.
`oei`	Default `TRUE` allows odd electron ions for explaining MS/MS peaks, `FALSE` means only even electron ions are considered.
`mz`	If mz is >0, this is the mass GenForm will use to calculate the formulas, considering the `ion` setting. Default is the most intense peak in `ms_file`.
`exist`	Default `TRUE` activates the existance filter (allowing only formulae for which at least one structural formula exists). `FALSE` is not recommended for most use cases.
`an_loss`	Activate the annotation of MSMS fragments with subformulas and losses.
`an_loss_limit`	Define the cut-off limit for annotating subformulas and losses. For many peaks and formulas, this becomes time consuming and produces massive files of limited use.
`sort`	Default `FALSE` will produce default output. If `TRUE`, generates an additional sorted file sorted by combined match value.
`cleanMSMS`	Default `FALSE`. If `TRUE`, produces an additional cleaned MSMS file containing only peaks with subformula annotation.