Spectrum2-class {MSnbase} | R Documentation

## 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 <lg390@cam.ac.uk>

### See Also

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

[Package MSnbase version 2.12.0 Index]