search

sneumann / mzR

This is the git repository matching the Bioconductor package mzR: parser for netCDF, mzXML, mzData and mzML files (mass spectrometry data)
42 stars 28 forks source link

Support of EAD DDA files #277

Closed htmonkey closed 2 years ago

htmonkey commented 2 years ago

Hi, it seems that mzR isn't extracting MSn spectra acquired by DDA-EAD on a SCIEX ZenoTOF 7600. All is fine with DDA-CID runs, but Msn spectra are reported empty in the case of EAD.

Exemplary file: https://polybox.ethz.ch/index.php/s/M5qcKW5NiJYU7Xs

of <- openMSfile('EAD_30msec15KE_SPLASH_2.mzML')
sh <- header(of)
sh2 <- sh[sh$msLevel == 2, ]
ms2spectra <- peaks(of, sh2$seqNum)
ms2spectra[1]
[[1]]
     mz intensity
jorainer commented 2 years ago

Hi Nicola,

can proteowizard (more recent versions) correctly import the data? Maybe we would need to update the proteowizard libraries within mzR @sneumann ?

htmonkey commented 2 years ago

Yes: all EAD files converted by pwiz include complete MS2 scans. I can see everything with TOPPview. mzR finds the MS2 scans, but doesn't manage to pull the MS2 spectra.

In the meantime, I tested several files and pwiz versions. The issue doesn't seem to be related to the pwiz version, but to the file. In one case it actually worked with pwiz+mzR. Unfortunately the vast majority of DDA-EAD files doesn't. Fishy.

Just in case, I added the raw data of a file (wiff & wiff2) to the same link.

htmonkey commented 2 years ago

I figured out the issue. It wasn't caused by mzR or Pwiz, but by some odd centroiding phenomenon by the SCIEX software. Funnily enough, TOPPview shows an MS2 spectrum even if the scan doesn't contain any binary data. Whatever. I'll close the issue. Thx!

jorainer commented 2 years ago

Thanks for letting us know!