Detect centroiding in <dataProcessing> tag

[skinnider]

The attached file HILIC_CON_BASA_567795.mzXML (from MTBLS103) contains centroided MS spectra:

  <dataProcessing centroided="1">
   <software type="conversion" name="trapper" version="4.3.1 (build Sep  9 2009 12:29:13)" />
  </dataProcessing>

However, because the centroided attribute is not set for every <scan> tag individually, but instead is set just once for the entire experiment in <dataProcessing>, mzR does not detect that these are centroided spectra:

> dat = Spectra("HILIC_CON_BASA_567795.mzXML", source = MsBackendMzR())
> table(spectraData(dat)$centroided)

FALSE
  768

In comparison, C18_CON_BASA_688344.mzXML from the same accession has the centroided attribute set for every individual spectrum and mzR correctly detects that these are all centroided spectra.

Is there a workaround for this, to detect that the HILIC file does indeed contain centroided spectra?

Files (too big for upload):
C18_CON_BASA_688344.mzXML
HILIC_CON_BASA_567795.mzXML

[lgatto]

There's an isCentroided() method from the Spectra that will estimate the mode from the spectra. Here's the relevant extract from ?isCentroided:

        • ‘isCentroided()’: a heuristic approach assessing if the
          spectra in ‘object’ are in profile or centroided mode. The
          function takes the ‘qtl’th quantile top peaks, then
          calculates the difference between adjacent m/z value and
          returns ‘TRUE’ if the first quartile is greater than ‘k’.
          (See ‘Spectra:::.isCentroided()’ for the code.)