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

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

Ok, thank you!

I will adjust my processing scripts to assume 32 bits intensity data. Although the GUI does not work to turn off zlib compression on my computer, I now know how to handle it by running the command line version so I can continue processing my data.

/Magnus


________________________________
Från: Chambers, Matthew <mat...@gm...>
Skickat: den 27 maj 2026 15:52
Till: Magnus Sellstedt <mag...@um...>; Brian Pratt <bs...@pr...>
Kopia: su...@pr... <su...@pr...>
Ämne: Re: Sv: [proteowizard-support] msconvert data-compression problem

AFAIK there's no instrument with intensity data precise enough to need more than 32-bit precision. So 64/32 has always been the msconvert default, or should have been. I think maybe there was a bug in the GUI I fixed a while ago that the 64-bit radio button was interpreted as 64/64. I should rename that label to just say "m/z encoding precision". I was able to reproduce the GUI issue with --zlib=off not being passed to the "Show command line" option, but when the GUI itself ran the conversion, it had zlib off like it was supposed to.

-Matt


On Wed, May 27, 2026 3:41 AM EDT (-0400), Magnus Sellstedt wrote:
I have tested again and for me it does not work to turn off the zlib compression in the GUI - the output data is still compressed. When I click the "show command line" button in the GUI it does not contain the --zlib=off option:


However, I have how now managed to turn off the zlib compression in the command line version by adding the --zlib=off option.

I did then noticed that the converted data is now stored in 32 bits in the intensity arrays, but 64 bits in the mass arrays. Previous versions of msconvert stored both arrays in 64 bits. Is that something that can be controlled?

/Magnus




________________________________
Från: Chambers, Matthew <mat...@gm...><mailto:mat...@gm...>
Skickat: den 26 maj 2026 17:53
Till: Magnus Sellstedt <mag...@um...><mailto:mag...@um...>; Brian Pratt <bs...@pr...><mailto:bs...@pr...>
Kopia: su...@pr...<mailto:su...@pr...> <su...@pr...><mailto:su...@pr...>
Ämne: 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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