AdductSpec-class {adductomicsR} | R Documentation

## AdductSpec class

### Description

The AdductSpec class contains dynamic noise filtered composite MS/MS spectra and their corresponding MS1 scan isotopic patterns. Produced by adductSpecGen() from mzXML files.

### Usage

    x

### Format

An object of class `NULL` of length 0.

### Value

dynamic noise filtered composite MS/MS spectra and their corresponding MS1 scan isotopic patterns

### Slots

`adductMS2spec`

  list of adduct MS2 spectras

`groupMS2spec`

  list of group MS2 spectras

`metaData`

  dataframe of metadata from mzXML

`aaResSeqs`

  matrix of amino acid sequences

`specPepMatches`

  list of spectra peptide matches

`specPepCompSpec`

  list of comp spectra peptide matches

`sumAdductType`

  dataframe of adduct types

`Peptides`

  dataframe of peptides under study

`rtDevModels`

  list of rtDevModels

`targetTable`

  dataframe target table

`file.paths`

  character of file path

`Parameters`

  dataframe of parameters

### Methods

c

  `signature(object = "AdductSpec")`: Concatenates the spectra information.

Specfile.paths

  `signature(object = "AdductSpec")`: Accesses the file paths.

adductMS2spec

  `signature(object = "AdductSpec")`: Accesses the adduct MS2 spectral information.

metaData

  `signature(object = "AdductSpec")`: Accesses the scan metadata.

Parameters

  `signature(object = "AdductSpec")`: Accesses the user parameters.

groupMS2spec

  `signature(object = "AdductSpec")`: Accesses the spectral information for the grouped MS2 spectra.

rtDevModels

  `signature(object = "AdductSpec")`: Accesses the retention time deviation models.

sumAdductType

  `signature(object = "AdductSpec")`: Accesses the total adduct types.

Peptides

  `signature(object = "AdductSpec")`: Accesses the peptide information.

specPepMatches

  `signature(object = "AdductSpec")`: Accesses the peptide matches in the spectra.

### Author(s)

JL Hayes jlhayes1982@gmail.com

[Package adductomicsR version 1.6.0 Index]