calculateFragments: Calculate ions produced by fragmentation

In rformassspectrometry/PSM: Handling and Managing Peptide Spectrum Matches

Calculate ions produced by fragmentation

Description

These method calculates a-, b-, c-, x-, y- and z-ions produced by fragmentation.

Available methods

• The default method with signature sequence = "character" and object = "missing" calculates the theoretical fragments for a peptide sequence. It returns a data.frame with the columns mz, ion, type, pos, z and seq.

• Additional method can be defined that will adapt their behaviour based on spectra defined in object. See for example the MSnbase package that implements a method for objects of class Spectrum2.

Usage

## S4 method for signature 'character,missing'
calculateFragments(
  sequence,
  type = c("b", "y"),
  z = 1,
  modifications = c(C = 57.02146),
  neutralLoss = defaultNeutralLoss(),
  verbose = TRUE
)

Arguments

sequence	character() providing a peptide sequence.
type	character vector of target ions; possible values: c("a", "b", "c", "x", "y", "z"). Default is type = c("b", "y").
z	numeric with desired charge state; default is 1.
modifications	A named numeric vector of used modifications. The name must correspond to the one-letter-code of the modified amino acid and the numeric value must represent the mass that should be added to the original amino accid mass, default: Carbamidomethyl modifications = c(C = 57.02146). Use Nterm or Cterm as names for modifications that should be added to the amino respectively carboxyl-terminus.
neutralLoss	list, it has to have two named elments, namely water and ammonia that contain a character vector which type of neutral loss should be calculated. Currently neutral loss on the C terminal "Cterm", at the amino acids c("D", "E", "S", "T") for "water" (shown with an ⁠_⁠) and c("K", "N", "Q", "R") for "ammonia" (shown with an *) are supported. There is a helper function `defaultNeutralLoss()` that returns the correct list. It has two arguments `disableWaterLoss` and `disableAmmoniaLoss` to remove single neutral loss options. See the example section for use cases.
verbose	logical(1). If TRUE (default) the used modifications are printed.

Value

The methods with oject = "missing" returns a data.frame.

Author(s)

Sebastian Gibb [e-mail]

Examples

## calculate fragments for ACE with default modification
calculateFragments("ACE", modifications = c(C = 57.02146))

## calculate fragments for ACE with an addition N-terminal modification
calculateFragments("ACE", modifications = c(C = 57.02146, Nterm = 229.1629))

## calculate fragments for ACE without any modifications
calculateFragments("ACE", modifications = NULL)

calculateFragments("VESITARHGEVLQLRPK",
                   type = c("a", "b", "c", "x", "y", "z"),
                   z = 1:2)

## neutral loss
defaultNeutralLoss()

## disable water loss on the C terminal
defaultNeutralLoss(disableWaterLoss="Cterm")

## real example
calculateFragments("PQR")
calculateFragments("PQR",
                   neutralLoss=defaultNeutralLoss(disableWaterLoss="Cterm"))
calculateFragments("PQR",
                   neutralLoss=defaultNeutralLoss(disableAmmoniaLoss="Q"))

## disable neutral loss completely
calculateFragments("PQR", neutralLoss=NULL)

rformassspectrometry/PSM documentation built on Dec. 13, 2024, 7:27 a.m.