Spectrum2-class: The "Spectrum2" Class for MSn Spectra

In lgatto/MSnbase: Base Functions and Classes for Mass Spectrometry and Proteomics

The "Spectrum2" Class for MSn Spectra

Description

Spectrum2 extends the "Spectrum" class and introduces several MS2 specific attributes in addition to the slots in "Spectrum". Since version 1.99.2, this class is used for any MS levels > 1. Spectrum2 are not created directly but are contained in the assayData slot of an "MSnExp".

In version 1.19.12, the polarity slot had been added to the "Spectrum" class (previously in "Spectrum1"). Hence, "Spectrum2" objects created prior to this change will not be valid anymore, since they will miss the polarity slots. Object can be appropriately updated using the updateObject method.

Slots

See the "Spectrum" class for inherited slots.

merged:

Object of class "numeric" indicating of how many combination the current spectrum is the result of.

precScanNum:

Object of class "integer" indicating the precursor MS scan index in the original input file. Accessed with the precScanNum or precAcquisitionNum methods.

precursorMz:

Object of class "numeric" providing the precursor ion MZ value.

precursorIntensity:

Object of class "numeric" providing the precursor ion intensity.

precursorCharge:

Object of class "integer" indicating the precursor ion charge.

collisionEnergy:

Object of class "numeric" indicating the collision energy used to fragment the parent ion.

Extends

Class "Spectrum", directly. Class "Versioned", by class "Spectrum", distance 2.

Methods

See "Spectrum" for additional accessors and methods for Spectrum2 objects.

precursorMz(object)

Returns the precursor MZ value as a numeric.

precursorMz(object)

Returns the precursor scan number in the original data file as an integer.

precursorIntensity(object)

Returns the precursor intensity as a numeric.

precursorCharge(object)

Returns the precursor intensity as a integer.

collisionEnergy(object)

Returns the collision energy as an numeric.

removeReporters(object, ...)

Removes all reporter ion peaks. See removeReporters documentation for more details and examples.

precAcquisitionNum:

Returns the precursor's acquisition number.

precScanNum:

See precAcquisitionNum.

calculateFragments

signature(sequence = "character", object = "Spectrum2"): Calculates and matches the theoretical fragments of a peptide sequence with the ones observed in a spectrum. See calculateFragments documentation for more details and examples.

Author(s)

Laurent Gatto

See Also

Virtual super-class "Spectrum", "Spectrum1" for MS1 spectra and "MSnExp" for a full experiment container.

lgatto/MSnbase documentation built on Nov. 12, 2024, 10:58 a.m.