calculateFragments-methods {MSnbase}

R Documentation

Calculate ions produced by fragmentation.

Description

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

Arguments

sequence	character, peptide sequence.
object	Object of class "Spectrum2" or "missing" .
tolerance	numeric tolerance between the theoretical and measured MZ values (only available if object is not missing).
method	method used for for duplicated matches. Choose "highest" or "closest" to select the peak with the highest intensity respectively the closest MZ in the tolerance range. If "all" is given all possible matches in the tolerance range are reported (only available if object is not missing).
type	character vector of target ions; possible values: c("a", "b", "c", "x", "y", "z"); default: type=c("b", "y").
z	numeric desired charge state; default z=1.
modifications	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 if TRUE (default) the used modifications are printed.

Methods

signature(sequence = "character", object = "missing", ...)

Calculates the theoretical fragments for a peptide sequence. Returns a data.frame with the columns c("mz", "ion", "type", "pos", "z", "seq").

signature(sequence = "character", object = "Spectrum2", ...)

Calculates and matches the theoretical fragments for a peptide sequence and a "Spectrum2" object. The ... arguments are passed to the internal functions. Currently tolerance, method and relative are supported.

You could change the tolerance (default 0.1) and decide whether this tolerance should be applied relative to the target m/z (relative = TRUE) or absolute (default relative = FALSE) to match the theoretical fragment MZ with the MZ of the spectrum. When (relative = TRUE) the mass tolerance window is set to target mz +/- (target mz * tolerance) and target mz +/- tolerance otherwise. In cases of multiple matches use method to select the peak with the highest intensity (method = "highest", default) respectively closest MZ (method = "closes"). If method = "all" is set all possible matches in the current tolerance range are reported. Returns the same data.frame as above but the mz column represents the matched MZ values of the spectrum. Additionally there is a column error that contains the difference between the observed MZ (from the spectrum) to the theoretical fragment MZ.

Author(s)

Sebastian Gibb <mail@sebastiangibb.de>

Examples

## find path to a mzXML file
file <- dir(system.file(package = "MSnbase", dir = "extdata"),
            full.name = TRUE, pattern = "mzXML$")

## create basic MSnExp
msexp <- readMSData(file, centroided = FALSE)

## centroid them
msexp <- pickPeaks(msexp)

## 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)

calculateFragments("VESITARHGEVLQLRPK", msexp[[1]])

## 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)

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