Error: Mix-up of MS and MS2-data in EIC-extraction

[LeonSaal]

Hi Kristian,

as I was trying out the package I noticed, that during EIC extraction, it seems as if no distinction is made between the MS levels.
This can be seen in the following plotChroms() output from seconds 130 onwards.
You can clearly see the eight precursors in DDA-MS2-mode with higher acquisition rate and the MS1-scan in between.

The analysis up to that point was based on inst/cpc.pdf, where file is one of my analyses with MS1 and MS2-level:

msraw = MSnbase::readMSData(
  files = file,
  msLevel. = 1,
  centroided = TRUE,
  mode = "onDisk"
)

xd <-
  xcms::findChromPeaks(
    msraw,
    param = xcms::CentWaveParam(
      ppm = 60,
      peakwidth = c(5, 50),
      fitgauss = T,
      noise = 200,
      integrate = 2,
      prefilter = c(5, 1000),
      verboseColumns = T,
      mzdiff = 0.01
    ),
    msLevel = 1L
  )

cpc <-
  cpc::filter_xcms_peaklist(
    xd = xd,
    return_type = "cpc",
    param = cpc::cpcProcParam(
      min_sn = 10,
      min_pts = 10,
      min_intensity = 2000
    )
  )


cpc::plotPeaks(cpc, peakIdx="CP0001")

Am I missing an important setting or is the package only applicable to raw data without MS2-data?

Kind regards,

Leon