param.default {InterpretMSSpectrum}

Default parameter list for InterpretMSSpectrum.

Description

Default parameter list for InterpretMSSpectrum.

Usage

data(param.default)

Format

A data frame with 22 observations on the following 3 variables:

ionization

ESI or APCI – will influence expected peak width and precision as well as adducts.

ionmode

positive or negative – will influence expected adducts.

allowed_elements

Passed to Rdisop in formula generation.

maxElements

Passed to Rdisop in formula generation.

minElements

Passed to Rdisop in formula generation.

substitutions

Will be deprecated in the future.

quick_isos

TRUE = via Rdisop, FALSE = via enviPat (often more correct)

score_cutoff

Specifies initial filtering step threshold per fragment. Sum Formulas with score_i < score_cutoff*max(score) will be removed.

neutral_loss_cutoff

Specifies the allowed deviation in mDa for neutral losses to be accepted from the provided neutral loss list.

Details

Default parameter list used by InterpretMSSpectrum, serving also as a template for custom lists. Basically every option which needs to be modified rarely went in here. Specific parameter set modifications (i.e. for 'APCIpos') are provided and can be called using the character string as a shortcut. Alternatively, a named list can be provided where all contained parameters will receive the new specified values.