Re: [proteowizard-support] msconvert data-compression problem

[Magnus S. <mag...@um...>]

I copied the command line using the button for this in the GUI. I don't remember exactly what it said, but it contained the zlib=off option. I will try again tomorrow when I'm back at work.
/Magnus

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________________________________
From: Chambers, Matthew <mat...@gm...>
Sent: Tuesday, May 26, 2026 5:53:08 PM
To: Magnus Sellstedt <mag...@um...>; Brian Pratt <bs...@pr...>
Cc: su...@pr... <su...@pr...>
Subject: Re: [proteowizard-support] msconvert data-compression problem

I tested msconvert with --zlib=off and -zoff and both produces mzML without zlib compression. Also tested MSConvertGUI with Use Zlib compression unchecked and that worked as well. What exact command-line did you use?

On Tue, May 26, 2026 11:13 AM EDT (-0400), Magnus Sellstedt wrote:
Yes, I have tried to turn off the zlib compression both in the GUI and from the command line, but it didn't work.
/Magnus

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________________________________
From: Chambers, Matthew <mat...@gm...><mailto:mat...@gm...>
Sent: Tuesday, May 26, 2026 5:03:20 PM
To: Brian Pratt <bs...@pr...><mailto:bs...@pr...>; Magnus Sellstedt <mag...@um...><mailto:mag...@um...>
Cc: su...@pr...<mailto:su...@pr...> <su...@pr...><mailto:su...@pr...>
Subject: Re: [proteowizard-support] msconvert data-compression problem

Hi Magnus,

A couple years ago I flipped msconvert from needing the -z flag to turn on zlib compression to turning it on by default, which means you need "--zlib=off" to turn it off. There's just not that many tools that don't support compression, and it makes a huge difference in output file size. If you use the --zlib=off flag and still get compressed files let me know that's definitely a bug.

Hope this helps,
-Matt


On Mon, May 25, 2026 12:33 PM EDT (-0400), Brian Pratt wrote:
Hi Magnus,

That would be surprising - are you certain of this? What are you seeing from the downstream application? Do your mzML files contain anything like the following?

            <binaryDataArray encodedLength="1863392">
              <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>
              <cvParam cvRef="MS" accession="MS:1000574" name="zlib compression" value=""/>
              <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>

Best regards,

Brian Pratt

On Mon, May 25, 2026 at 1:13 AM Magnus Sellstedt <mag...@um...<mailto:mag...@um...>> wrote:
Hello,

I am using msconvert to convert Agilent d.files to uncompressed mzML-files. This has worked fine previously, but after a download of a recent version of msconvert, the mzML-files now appear to be somewhat compressed regardless of if I turn zlib-compression on or off via the GUI. My downstream application does not work on compressed files. How can I generate the uncompressed mzML-files?

Best
Magnus Sellstedt
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