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Re: [proteowizard-support] msconvert data-compression problem
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From: Chambers, M. <mat...@gm...> - 2026-05-27 13:53:05
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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...> > *Skickat:* den 26 maj 2026 17:53 > *Till:* Magnus Sellstedt <mag...@um...>; Brian Pratt <bs...@pr...> > *Kopia:* su...@pr... <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 > > Skickat från Outlook för Android <https://aka.ms/AAb9ysg> > -------------------------------------------------------------------------------------------------------------------------------------------- > *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 > _______________________________________________ > proteowizard-support mailing list > pro...@li... <mailto:pro...@li...> > https://lists.sourceforge.net/lists/listinfo/proteowizard-support > <https://lists.sourceforge.net/lists/listinfo/proteowizard-support> > > > > _______________________________________________ proteowizard-support mailing list pro...@li... > <mailto:pro...@li...> https://lists.sourceforge.net/lists/listinfo/proteowizard-support > <https://lists.sourceforge.net/lists/listinfo/proteowizard-support> > > > |