Add validatePSM(), a function that wraps multiple checks to validate PSMs

[guideflandre]

This PR adds a few functions (metrics used through checks), a wrapper function validatePSM(), corresponding tests and a vignette, as well as example data bundled with the package. The example data is a subset of ?MsDataHub::Boekweg2022. There is a spectra object and a PSM object. They are used to describe validatePSM in the examples as well as in the vignette. They can also be used for other functions.

validatePSM is a wrapper for multiple validation metrics/checks based on spectral or identification characteristics.

It mainly includes:

• checkABpresence() : TRUE if the a2-b2 fragments are both
  present.

• checkXYpresence() : TRUE if the x2-y2 fragments are both
  present.

• checkOverlap() : Detects a gap in the coverage of b- and y-ions.
  Returns FALSE when a gap is found (b- and y-ions do not jointly
  cover the full sequence), which may indicate an unsearched
  modification. Returns TRUE when b- and y-ions overlap, further
  confirming the identification.

• checkShiftConsistency() : In case of modifications present:
  returns the percentage of potential mass shifts actually matched.
  If not applicable because there are no modifications: NA.

• checkParentIonIntensity() : The relative intensity of the parent
  ion over the base peak. A value close to 1 indicates poor
  fragmentation.

• checkPrecursorPurity() returns a numeric vector of length
  length(x). Each value is the ratio of the most-intense peak to
  the total intensity within the isolation window of the
  corresponding MS1 scan, as computed by
  Spectra::precursorPurity(). MS1 spectra and MS2 spectra with no
  preceding MS1 scan return NA.

validatePSM() returns a dataframe with the results for each of these functions:

[guideflandre]

These metrics can then be added to a PSM object or Spectra object by matching the spectrumId, which make them useful for rescoring.