"readMSData" unable to read uncorrupted mzML file

[MuyaoXi9271]

Hi expert,

The major issue is that the values of collision energy are all 0 in the DDA data obtained from negative mode when reading .mzml file by function "readMSData". They are available in the .d file. Initially, .d file was converted into .mzML file by msconvert.

Then I tried other approaches to convert .d file generated from Bruker into a .mzML file by DataAnalysis (v5.2 and v5.3 developed by Bruker)

"readMSData" could read the .mzML file converted from DataAnalysis (v5.2) and the values of collision energy are all 0 as well

But "readMSData" could not read .mzML file from DataAnalysis (v5.3) and receive the error "Error in pwizModule$open(filename): [MSDataFile::readFile()] Unsupported file format". I guess there are some changes from v5.2 into v5.3

Do I need to provide .mzML file to let you know what is wrong with the error? And I receive a reply from the developer at Bruker that "what part of the analysis is needed for the import to work since we do not. Maybe they are able to tell by your findings what is needed and we can check if this included in further versions of DA."

I appreciate any help you could provide and I am looking forward to receiving your reply.

Bests, Muyao

[sneumann]

Hi, yes, without the mzML files there is little we can do. You can open the mzML with an editor and have a look what CE is embedded in the parts. Bruker also used to have a "CompassXport" command line tool for the conversion, but I dont know if that works for timsTOF class of instruments. Yours, Steffen

[MuyaoXi9271]

Hi Steffen,

When I open the .mzml file and find that information that is ""

Is it ok?

Bests, Muyao

[sneumann]

In our mzML from a Bruker I find <cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="20.000000" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt"/> but if yours has "" then there is little xcms can do. Yours, Steffen

[MuyaoXi9271]

<cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="10.000000" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt"/>

It is that I find from my .zmML file. Sorry for nothing in the previous comment.

Bests, Muyao

[MuyaoXi9271]

Hi, yes, without the mzML files there is little we can do. You can open the mzML with an editor and have a look what CE is embedded in the parts. Bruker also used to have a "CompassXport" command line tool for the conversion, but I dont know if that works for timsTOF class of instruments. Yours, Steffen

As far as I know, CompassXport is not used anymore. Bests, Muyao

[MuyaoXi9271]

Hi Steffen,

How is the process going? I still have a problem reading the .mzML file from Bruker dataanalysis 5.3 by function "readMSData" and receive the error "Original error was: Error in pwizModule$open(filename): [MSDataFile::readFile()] Unsupported file format". Could I share the file with you privately to see what happened? That could also help to optimize this function.

Bests, Muyao

[sneumann]

I can't locate your file (anymore ?), so nothing I can test. Yours, Steffen

[MuyaoXi9271]

I would like to send the file to you privately in terms of GDPR. Is it ok?

I really need your help.

Bests, Muyao

[sneumann]

Hi, the quick (and not satisfying) answer is: is Proteowizard itself can't open the file, there is nothing XCMS can do:

sneumann@laptop:~/Downloads$ mscat test_mix7.mzML
[MSDataFile::readFile()] Unsupported file format.

using the super-simple mscat from https://proteowizard.sourceforge.io/tools/tools_base.html. So before xcms can do anything, the mzML conversion needs to be debugged/fixed. You could consider opening a ticket at https://github.com/ProteoWizard. Yours, Steffen