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

[Chambers, M. <mat...@gm...>]

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...>
> *Sent:* Tuesday, May 26, 2026 5:03:20 PM
> *To:* Brian Pratt <bs...@pr...>; Magnus Sellstedt <mag...@um...>
> *Cc:* su...@pr... <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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