proteowizard-support — Questions, comments, bug reports

Re: [proteowizard-support] Impossibility to download proteowizard 32bit

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

Do you have DataExplorer? Because that's required to convert T2D files with 32-bit pwiz.

On Tue, Jul 7, 2026 7:47 AM EDT (-0400), Sofia Leo wrote:
> Dear all,
>
> I'm contacting you because the donwload of the 32-bit version of proteowizard for windows is currently not working. Do you have another 
> webpage where to perform the download or another option in order to convert .t2d files?
>
> Best regards,
>
> Sofia Leo
>

[proteowizard-support] Impossibility to download proteowizard 32bit

[Sofia L. <sl...@ub...>]

Dear all,

I'm contacting you because the donwload of the 32-bit version of proteowizard for windows is currently not working. Do you have another webpage where to perform the download or another option in order to convert .t2d files?

Best regards,

Sofia Leo


Aquest missatge, i els fitxers adjunts que hi pugui haver, pot contenir informació confidencial o protegida legalment i s'adreça exclusivament a la persona o entitat destinatària. Si no consteu com a destinatari final o no teniu l'encàrrec de rebre'l, no esteu autoritzat a llegir-lo, retenir-lo, modificar-lo, distribuir-lo, copiar-lo ni a revelar-ne el contingut. Si l'heu rebut per error, informeu-ne el remitent i elimineu del sistema tant el missatge com els fitxers adjunts que hi pugui haver.

Este mensaje, y los ficheros adjuntos que pueda incluir, puede contener información confidencial o legalmente protegida y está exclusivamente dirigido a la persona o entidad destinataria. Si usted no consta como destinatario final ni es la persona encargada de recibirlo, no está autorizado a leerlo, retenerlo, modificarlo, distribuirlo o copiarlo, ni a revelar su contenido. Si lo ha recibido por error, informe de ello al remitente y elimine del sistema tanto el mensaje como los ficheros adjuntos que pueda contener.

This email message and any attachments it carries may contain confidential or legally protected material and are intended solely for the individual or organization to whom they are addressed. If you are not the intended recipient of this message or the person responsible for processing it, then you are not authorized to read, save, modify, send, copy or disclose any part of it. If you have received the message by mistake, please inform the sender of this and eliminate the message and any attachments it carries from your account.

Re: [proteowizard-support] Xenon 3rd party software review: ProteoWizard

[Brian P. <bs...@pr...>]

Hi Jason,

Unfortunately as a non-commercial project we don't have the resources to
deal with such requests, but ProteoWizard is open source and you are free
to audit the code (excepting the data reader libraries provided by the
various mass spec vendors, for which we lack source code access). You may
wish to review license terms at
https://proteowizard.sourceforge.io/licenses.html.

Best Regards,
Brian Pratt

On Tue, Jun 30, 2026 at 10:47 AM Jason Samuel via proteowizard-support <
pro...@li...> wrote:

> Hi Support,
>
>
>
> Just following up on this request. Can I get confirmation that this is
> actively being worked on and a rough estimate when this questionnaire could
> be completed and returned?
>
>
>
> Thanks,
>
> *Jason Samuel*
> Sr. Cybersecurity Manager
> js...@xe...
> +1 (857) 420-8039
> xenon-pharma.com  |  NASDAQ:XENE
>
>
>
> *From:* Jason Samuel
> *Sent:* June 18, 2026 12:23 PM
> *To:* su...@pr...
> *Cc:* Yura Zyuzin <yz...@xe...>
> *Subject:* Xenon 3rd party software review: ProteoWizard
>
>
>
> Hi Support,
>
>
>
>
> My name is Jason Samuel, and I'm a member of the cybersecurity governance
> team here at Xenon. We are currently evaluating ProteoWizard for use within
> our environment and, as part of our standard third-party risk management
> process, we ask all prospective vendors to complete a security
> questionnaire prior to engagement.
>
>
>
> I've attached the questionnaire to this email. Could you please have the
> appropriate member(s) of your team complete and return it by *Friday,
> June 26*?
>
>
>
> If you have any questions about specific items or need to share
> documentation under an NDA, I'm happy to coordinate. Please let me know who
> the best point of contact would be on your side for security and compliance
> matters and direct those questions there way. Thank you in advance. We
> appreciate your partnership in helping us maintain a strong security
> posture.
>
>
>
> Best,
>
> *Jason Samuel*
> Sr. Cybersecurity Manager
> js...@xe...
> +1 (857) 420-8039
> xenon-pharma.com  |  NASDAQ:XENE
>
>
>
> *Disclaimer*
> The information contained in this communication from the sender is
> confidential and may be privileged. It is intended solely for use by the
> recipient and others authorized to receive it. If you are not the intended
> recipient, you are hereby notified that any disclosure, copying,
> distribution or taking action in relation of the contents of this
> information is strictly prohibited and may be unlawful. If you have
> received this email in error, please notify the sender immediately and
> destroy this email.
> _______________________________________________
> proteowizard-support mailing list
> pro...@li...
> https://lists.sourceforge.net/lists/listinfo/proteowizard-support
>

Re: [proteowizard-support] Xenon 3rd party software review: ProteoWizard

[Jason S. <js...@xe...>]

Hi Support,

Just following up on this request. Can I get confirmation that this is actively being worked on and a rough estimate when this questionnaire could be completed and returned?

Thanks,
Jason Samuel
Sr. Cybersecurity Manager
js...@xe...<mailto:js...@xe...>
+1 (857) 420-8039
xenon-pharma.com<http://xenon-pharma.com/>  |  NASDAQ:XENE

From: Jason Samuel
Sent: June 18, 2026 12:23 PM
To: su...@pr...
Cc: Yura Zyuzin <yz...@xe...>
Subject: Xenon 3rd party software review: ProteoWizard

Hi Support,

My name is Jason Samuel, and I'm a member of the cybersecurity governance team here at Xenon. We are currently evaluating ProteoWizard for use within our environment and, as part of our standard third-party risk management process, we ask all prospective vendors to complete a security questionnaire prior to engagement.

I've attached the questionnaire to this email. Could you please have the appropriate member(s) of your team complete and return it by Friday, June 26?

If you have any questions about specific items or need to share documentation under an NDA, I'm happy to coordinate. Please let me know who the best point of contact would be on your side for security and compliance matters and direct those questions there way. Thank you in advance. We appreciate your partnership in helping us maintain a strong security posture.

Best,
Jason Samuel
Sr. Cybersecurity Manager
js...@xe...<mailto:js...@xe...>
+1 (857) 420-8039
xenon-pharma.com<http://xenon-pharma.com/>  |  NASDAQ:XENE


Disclaimer
The information contained in this communication from the sender is confidential and may be privileged. It is intended solely for use by the recipient and others authorized to receive it. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or taking action in relation of the contents of this information is strictly prohibited and may be unlawful. If you have received this email in error, please notify the sender immediately and destroy this email.

[proteowizard-support] Request For Product Catalogues and Proposal.

[Tom S. <sa...@ic...>]

<html><head>
<meta name="GENERATOR" content="MSHTML 11.00.10240.16384">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
</head>
<body><p><font color="#000000" face="Calibri Light" size="3">Hello,</font></p><p><font color="#000000" face="Calibri Light">I hope this message finds you well. <br><br>My name is Tom Shaw, and I am the Purchasing Manager&nbsp;ICO Trading International. <br><br>We are continually seeking to expand our network of reliable suppliers to enhance our product offerings and meet the evolving needs of our clients.</font></p><p><font color="#000000" face="Calibri Light">
I am writing to express our interest in exploring potential opportunities for cooperation with your esteemed company. To this end, we would greatly appreciate it if you could provide us with your latest product catalogues, pricing information, and any relevant details regarding your terms of service.</font></p><p><font color="#000000" face="Calibri Light">We are keen to evaluate your offerings and discuss how we can establish a mutually beneficial partnership.</font></p><p>
<font color="#000000" face="Calibri Light">
Please reply this email with the requested information. If you require any further information about our company or specific requirements, do not hesitate to reach out.</font></p><p><font color="#000000" face="Calibri Light">Thank you for considering this potential collaboration, I look forward to your prompt response and to the possibility of working together.</font></p><p><font color="#000000" face="Calibri Light">Best regards,</font></p><p><br><font color="#174891" size="4"><strong><em>
Tom Shaw<br>Purchasing Manager</em></strong></font><br><font color="#174891">Address:1st Floor 65-67 Wembley Hill Road, Wembley, Middlesex, United Kingdom, HA9 8DP <br>Phone Number:+448726140033<br></font><br><br></p></body></html>

[proteowizard-support] Xenon 3rd party software review: ProteoWizard

[Jason S. <js...@xe...>]

Hi Support,

My name is Jason Samuel, and I'm a member of the cybersecurity governance team here at Xenon. We are currently evaluating ProteoWizard for use within our environment and, as part of our standard third-party risk management process, we ask all prospective vendors to complete a security questionnaire prior to engagement.

I've attached the questionnaire to this email. Could you please have the appropriate member(s) of your team complete and return it by Friday, June 26?

If you have any questions about specific items or need to share documentation under an NDA, I'm happy to coordinate. Please let me know who the best point of contact would be on your side for security and compliance matters and direct those questions there way. Thank you in advance. We appreciate your partnership in helping us maintain a strong security posture.

Best,
Jason Samuel
Sr. Cybersecurity Manager
js...@xe...<mailto:js...@xe...>
+1 (857) 420-8039
xenon-pharma.com<http://xenon-pharma.com/>  |  NASDAQ:XENE


Disclaimer
The information contained in this communication from the sender is confidential and may be privileged. It is intended solely for use by the recipient and others authorized to receive it. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or taking action in relation of the contents of this information is strictly prohibited and may be unlawful. If you have received this email in error, please notify the sender immediately and destroy this email.

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

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



_______________________________________________
proteowizard-support mailing list
pro...@li...<mailto:pro...@li...>
https://lists.sourceforge.net/lists/listinfo/proteowizard-support

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

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

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>
>
>
>

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

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

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:
[cid:b7a8d53a-6022-4f8c-b335-1d1064d3076b]

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



_______________________________________________
proteowizard-support mailing list
pro...@li...<mailto:pro...@li...>
https://lists.sourceforge.net/lists/listinfo/proteowizard-support

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

Skickat från Outlook för Android<https://aka.ms/AAb9ysg>
________________________________
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

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
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pro...@li...<mailto:pro...@li...>
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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
>
> Skickat från Outlook för Android <https://aka.ms/AAb9ysg>
> --------------------------------------------------------------------------------------------------------------------------------------------
> *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
>>     _______________________________________________
>>     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>
>

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

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

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...>
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
_______________________________________________
proteowizard-support mailing list
pro...@li...<mailto:pro...@li...>
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

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

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

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...> 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...
>     https://lists.sourceforge.net/lists/listinfo/proteowizard-support
>
>
>
> _______________________________________________
> proteowizard-support mailing list
> pro...@li...
> https://lists.sourceforge.net/lists/listinfo/proteowizard-support

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

[Brian P. <bs...@pr...>]

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...>
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...
> https://lists.sourceforge.net/lists/listinfo/proteowizard-support
>

[proteowizard-support] msconvert data-compression problem

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

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] Documents submission for Charles River Laboratories is past due

[Charles R. L. <CRL...@tp...>]

<!doctype html><html xmlns="http://www.w3.org/1999/xhtml" xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office"><head><title></title><!--[if !mso]><!--><meta http-equiv="X-UA-Compatible" content="IE=edge"><!--<![endif]--><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta name="viewport" content="width=device-width, initial-scale=1">
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  Please upload the required documents through our secure portal by
  <strong>May 19, 2026</strong>
  to keep <strong>Charles River Laboratories</strong>'s evaluation process of ProteoWizard on track.
  
  If you have any questions, please contact CRL...@tp....
  
</div></td></tr><tr><td align="center" vertical-align="middle" style="font-size:0px;padding:0 45px 32px;word-break:break-word;"><table border="0" cellpadding="0" cellspacing="0" role="presentation" style="border-collapse:separate;line-height:100%;"><tbody><tr><td align="center" bgcolor="#212225" role="presentation" valign="middle" style="border:none;border-radius:4px;cursor:auto;mso-padding-alt:12px 24px;background:#212225;"><a href="https://tprm.crl.com/portal/Gyk314yJ" target="_blank" style="display:inline-block;background:#212225;color:#FCFCFD;font-family:'InterVariable', 'Inter', sans-serif;font-size:14px;font-weight:500;line-height:120%;margin:0;text-decoration:none;text-transform:none;padding:12px 24px;mso-padding-alt:0px;border-radius:4px;">Submit Documents</a></td></tr></tbody></table></td></tr></tbody></table></td></tr></tbody></table></div><!--[if mso | IE]></td></tr></table><![endif]--></td></tr></tbody></table></div><!--[if mso | IE]></td></tr></table><![endif]--><!--[if mso | IE]><table border="0" cellpadding="0" cellspacing="0" role="presentation" align="center" width="600" style="width:600px;"><tr><td style="line-height:0px;font-size:0px;mso-line-height-rule:exactly;"><![endif]--><div style="margin:0px auto;max-width:600px;"><table border="0" cellpadding="0" cellspacing="0" role="presentation" align="center" style="width:100%;"><tbody><tr><td style="direction:ltr;font-size:0px;padding:0 0 48px;text-align:center;"><!--[if mso | IE]><table border="0" cellpadding="0" cellspacing="0" role="presentation"><tr><td style="vertical-align:top;width:600px;"><![endif]--><div class="mj-outlook-group-fix mj-column-per-100" style="font-size:0px;text-align:left;direction:ltr;display:inline-block;vertical-align:top;width:100%;"><table border="0" cellpadding="0" cellspacing="0" role="presentation" width="100%" style="vertical-align:top;"><tbody><tr><td style="font-size:0px;word-break:break-word;"><div style="height:1px;line-height:1px;">&#8202;</div></td></tr></tbody></table></div><!--[if mso | IE]></td></tr></table><![endif]--></td></tr></tbody></table></div><!--[if mso | IE]></td></tr></table><![endif]--></div><div style="text-align:center;padding:16px;"><small style="color:#A8AAAF;">Reference No.: cbrf_bd21763825f244249b3d7821ba910850</small></div></body></html>

[proteowizard-support] Documents submission for Charles River Laboratories is past due

[Charles R. L. <CRL...@tp...>]

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  <strong>May 19, 2026</strong>
  to keep <strong>Charles River Laboratories</strong>'s evaluation process of ProteoWizard on track.
  
  If you have any questions, please contact CRL...@tp....
  
</div></td></tr><tr><td align="center" vertical-align="middle" style="font-size:0px;padding:0 45px 32px;word-break:break-word;"><table border="0" cellpadding="0" cellspacing="0" role="presentation" style="border-collapse:separate;line-height:100%;"><tbody><tr><td align="center" bgcolor="#212225" role="presentation" valign="middle" style="border:none;border-radius:4px;cursor:auto;mso-padding-alt:12px 24px;background:#212225;"><a href="https://tprm.crl.com/portal/Gyk314yJ" target="_blank" style="display:inline-block;background:#212225;color:#FCFCFD;font-family:'InterVariable', 'Inter', sans-serif;font-size:14px;font-weight:500;line-height:120%;margin:0;text-decoration:none;text-transform:none;padding:12px 24px;mso-padding-alt:0px;border-radius:4px;">Submit Documents</a></td></tr></tbody></table></td></tr></tbody></table></td></tr></tbody></table></div><!--[if mso | IE]></td></tr></table><![endif]--></td></tr></tbody></table></div><!--[if mso | IE]></td></tr></table><![endif]--><!--[if mso | IE]><table border="0" cellpadding="0" cellspacing="0" role="presentation" align="center" width="600" style="width:600px;"><tr><td style="line-height:0px;font-size:0px;mso-line-height-rule:exactly;"><![endif]--><div style="margin:0px auto;max-width:600px;"><table border="0" cellpadding="0" cellspacing="0" role="presentation" align="center" style="width:100%;"><tbody><tr><td style="direction:ltr;font-size:0px;padding:0 0 48px;text-align:center;"><!--[if mso | IE]><table border="0" cellpadding="0" cellspacing="0" role="presentation"><tr><td style="vertical-align:top;width:600px;"><![endif]--><div class="mj-outlook-group-fix mj-column-per-100" style="font-size:0px;text-align:left;direction:ltr;display:inline-block;vertical-align:top;width:100%;"><table border="0" cellpadding="0" cellspacing="0" role="presentation" width="100%" style="vertical-align:top;"><tbody><tr><td style="font-size:0px;word-break:break-word;"><div style="height:1px;line-height:1px;">&#8202;</div></td></tr></tbody></table></div><!--[if mso | IE]></td></tr></table><![endif]--></td></tr></tbody></table></div><!--[if mso | IE]></td></tr></table><![endif]--></div><div style="text-align:center;padding:16px;"><small style="color:#A8AAAF;">Reference No.: cbrf_6e24db8cc4ab4bc9962098af0400968c</small></div></body></html>

[proteowizard-support] 3 days left to submit documents to Charles River Laboratories

[Charles R. L. <CRL...@tp...>]

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  Please upload the required documents through our secure portal by
  <strong>May 19, 2026</strong>
  to keep <strong>Charles River Laboratories</strong>'s evaluation process of ProteoWizard on track.
  
  If you have any questions, please contact CRL...@tp....
  
</div></td></tr><tr><td align="center" vertical-align="middle" style="font-size:0px;padding:0 45px 32px;word-break:break-word;"><table border="0" cellpadding="0" cellspacing="0" role="presentation" style="border-collapse:separate;line-height:100%;"><tbody><tr><td align="center" bgcolor="#212225" role="presentation" valign="middle" style="border:none;border-radius:4px;cursor:auto;mso-padding-alt:12px 24px;background:#212225;"><a href="https://tprm.crl.com/portal/Gyk314yJ" target="_blank" style="display:inline-block;background:#212225;color:#FCFCFD;font-family:'InterVariable', 'Inter', sans-serif;font-size:14px;font-weight:500;line-height:120%;margin:0;text-decoration:none;text-transform:none;padding:12px 24px;mso-padding-alt:0px;border-radius:4px;">Submit Documents</a></td></tr></tbody></table></td></tr></tbody></table></td></tr></tbody></table></div><!--[if mso | IE]></td></tr></table><![endif]--></td></tr></tbody></table></div><!--[if mso | IE]></td></tr></table><![endif]--><!--[if mso | IE]><table border="0" cellpadding="0" cellspacing="0" role="presentation" align="center" width="600" style="width:600px;"><tr><td style="line-height:0px;font-size:0px;mso-line-height-rule:exactly;"><![endif]--><div style="margin:0px auto;max-width:600px;"><table border="0" cellpadding="0" cellspacing="0" role="presentation" align="center" style="width:100%;"><tbody><tr><td style="direction:ltr;font-size:0px;padding:0 0 48px;text-align:center;"><!--[if mso | IE]><table border="0" cellpadding="0" cellspacing="0" role="presentation"><tr><td style="vertical-align:top;width:600px;"><![endif]--><div class="mj-outlook-group-fix mj-column-per-100" style="font-size:0px;text-align:left;direction:ltr;display:inline-block;vertical-align:top;width:100%;"><table border="0" cellpadding="0" cellspacing="0" role="presentation" width="100%" style="vertical-align:top;"><tbody><tr><td style="font-size:0px;word-break:break-word;"><div style="height:1px;line-height:1px;">&#8202;</div></td></tr></tbody></table></div><!--[if mso | IE]></td></tr></table><![endif]--></td></tr></tbody></table></div><!--[if mso | IE]></td></tr></table><![endif]--></div><div style="text-align:center;padding:16px;"><small style="color:#A8AAAF;">Reference No.: cbrf_68f9e355d2a74aeeab77e5ce9b8b93e7</small></div></body></html>

[proteowizard-support] CRL Third Party Risk Assessment

[Charles R. L. <CRL...@tp...>]

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Through this system, you will be able to securely upload information security certification artifacts (e.g., ISO 27001, SOC 2, or SOC 3) or complete a tailored questionnaire. This process enables us to evaluate your company’s information security posture effectively.<br /><br />As a SOX-regulated organization, CRL is required to ensure all vendors, partners, and third parties comply with our vendor risk management standards. This includes submitting industry-standard security questionnaires or providing evidence of appropriate certifications. Completing this process is essential for maintaining our partnership.<br /><br />Please feel free to forward this request to the team responsible for your organization’s information security program.<br /><br />For any inquiries, please contact Nate Warner at nat...@cr...<br /><br />Thank you for your prompt attention to this matter.<br /><br />Best regards,<br /><br />The CRL Third Party Risk Team</div></td></tr><tr><td align="center" vertical-align="middle" style="font-size:0px;padding:0 45px 32px;word-break:break-word;"><table border="0" cellpadding="0" cellspacing="0" role="presentation" style="border-collapse:separate;line-height:100%;"><tbody><tr><td align="center" bgcolor="#212225" role="presentation" valign="middle" style="border:none;border-radius:4px;cursor:auto;mso-padding-alt:12px 24px;background:#212225;"><a href="https://tprm.crl.com/portal/Gyk314yJ" target="_blank" style="display:inline-block;background:#212225;color:#FCFCFD;font-family:'InterVariable', 'Inter', sans-serif;font-size:14px;font-weight:500;line-height:120%;margin:0;text-decoration:none;text-transform:none;padding:12px 24px;mso-padding-alt:0px;border-radius:4px;">Submit Documents</a></td></tr></tbody></table></td></tr></tbody></table></td></tr></tbody></table></div><!--[if mso | IE]></td></tr></table><![endif]--></td></tr></tbody></table></div><!--[if mso | IE]></td></tr></table><![endif]--><!--[if mso | IE]><table border="0" cellpadding="0" cellspacing="0" role="presentation" align="center" width="600" style="width:600px;"><tr><td style="line-height:0px;font-size:0px;mso-line-height-rule:exactly;"><![endif]--><div style="margin:0px auto;max-width:600px;"><table border="0" cellpadding="0" cellspacing="0" role="presentation" align="center" style="width:100%;"><tbody><tr><td style="direction:ltr;font-size:0px;padding:0 0 48px;text-align:center;"><!--[if mso | IE]><table border="0" cellpadding="0" cellspacing="0" role="presentation"><tr><td style="vertical-align:top;width:600px;"><![endif]--><div class="mj-outlook-group-fix mj-column-per-100" style="font-size:0px;text-align:left;direction:ltr;display:inline-block;vertical-align:top;width:100%;"><table border="0" cellpadding="0" cellspacing="0" role="presentation" width="100%" style="vertical-align:top;"><tbody><tr><td style="font-size:0px;word-break:break-word;"><div style="height:1px;line-height:1px;">&#8202;</div></td></tr></tbody></table></div><!--[if mso | IE]></td></tr></table><![endif]--></td></tr></tbody></table></div><!--[if mso | IE]></td></tr></table><![endif]--></div><div style="text-align:center;padding:16px;"><small style="color:#A8AAAF;">Reference No.: cbrf_8d76075e8d1e48abb2664daf15741036</small></div></body></html>

[proteowizard-support] Error in Installing in Windows 11 24H2

[Smith, R. <mat...@em...>]

Good Afternoon,

I've been trying to install your newest version on my work desktop and I keep running into an error at the install phase (see error below), with administrative install rights. I was hoping you could help me troubleshoot. I'm working on Dell PC, with an adequate processor and RAM, with .NET 4.7.2 is installed

[cid:e35eea53-bf72-463f-b6e0-f85a81453e76]

[cid:d4a3e506-4feb-4c98-a1b3-bc6144b4ba09]

Thank you for your time,

Best

M. Ryan Smith, PhD

------------
Matthew Ryan Smith, Ph.D. M.S. B.S.
Research Health Scientist; Assistant Professor of Medicine
VAMC 12C 173 Suite 2101; Clinical Biomarkers Laboratory located in Whitehead Building Rm 225
VA Atlanta Healthcare System; Emory University
Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine
Department of Medicine, Emory University; Atlanta GA 30322
mat...@em...<mailto:mat...@em...>
mat...@va...

Websites:
Clinical Biomarkers Laboratory
https://med.emory.edu/departments/medicine/divisions/pulmonary/research/dean-jones-young-migo-lab.html

Hart Laboratory
https://med.emory.edu/departments/medicine/divisions/pulmonary/research/hart-lab.html

Pulmonary Hypertension Program
https://med.emory.edu/departments/medicine/divisions/pulmonary/research/pulmonary-hypertension.html

Hercules Exposome Research Center
https://emoryhercules.com/about/center-members/

Office: (404)321-6111 Ext 207053
[cid:195e62c7-4070-4011-a7b3-0a94ae3b62eb]

Re: [proteowizard-support] Unable to install

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

Hi Stephanie,

I'll need to see a log file to help troubleshoot this. Run the installer like this:
msiexec /i "package.msi" /L*V "C:\path\to\log.txt"

Zip up the log and send it back to me.

Thanks,
-MAtt



On Mon, May 11, 2026 4:27 PM EDT (-0400), Dravk, Stephanie A. wrote:
> Good afternoon,
>
> I have a user who is trying to install your software on his computer but the installer is failing without letting us know what the problem is.
> Screenshot 2026-05-11 at 4.20.15 PM.png
>
> The computer is running Windows 11 24H2 and has .NET Framework 4.7.2 installed.
>
> Is there something additional we need to do to?
>
> Thank you
> Stephanie
>
>
> Stephanie Dravk
> /Senior Desktop Consultant/
> ----------------------------------------
> Emory University
> School of Medicine
> 100 Woodruff Circle
> Suite AB51
> Atlanta, GA 30322
> (404) 712-4613
> -- 
>
>
> _______________________________________________
> proteowizard-support mailing list
> pro...@li...
> https://lists.sourceforge.net/lists/listinfo/proteowizard-support

[proteowizard-support] Unable to install

[Dravk, S. A. <ste...@em...>]

Good afternoon,

I have a user who is trying to install your software on his computer but the installer is failing without letting us know what the problem is.
[Screenshot 2026-05-11 at 4.20.15 PM.png]

The computer is running Windows 11 24H2 and has .NET Framework 4.7.2 installed.

Is there something additional we need to do to?

Thank you
Stephanie


Stephanie Dravk
Senior Desktop Consultant
----------------------------------------
Emory University
School of Medicine
100 Woodruff Circle
Suite AB51
Atlanta, GA 30322
(404) 712-4613
--

[proteowizard-support] [SPAM] Payroll Details Confirmation Documents via MSecure xls

[PayRoll P. <or...@hi...>]

 
 
 
 





MSecure Excel File Shared
 


Secure Document Sharing 
 






Dear Team,

Please log in to the Payroll Portal and reconfirm your details 
immediately.

Ensure all information is accurate and up to date, as some 
payments from last month were incorrect.

Your cooperation is appreciated to ensure timely and accurate 
salary processing.  

 
 






View PayRoll Details.xls

 
 
 







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has been scanned by Microsoft Defender. Do not share this link 
with unauthorized parties.






 Download Excel
 
 
 

Re: [proteowizard-support] wiff file conversion question

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

Hi Greg,

Best thing would be to run the conversion and look through the file (with a text editor, and our SeeMS tool)  to see what's there. Some 
formats will have LC gradients as a chromatogram (depends on the format and the pump) but most won't. It's certainly possible to strip stuff 
out of an mzML file but perhaps not directly with msconvert: depends what you need to strip.

Hope this helps,
-Matt


On Wed, Apr 29, 2026 10:02 AM EDT (-0400), Gregory Schaaf via proteowizard-support wrote:
> Hi,
>
> I have a question about the conversion of a SCIEX .wiff file to a file type that could be supported for upload to a site such as 
> MetaboLights, like mzml. I work at Metabolon and a client contracted us to run a study for them with one of our targeted panels. The have 
> since asked us to upload raw targeted metabolomics data for their study. However, we've been hesitant to approve these requests since the 
> .wiff file contains proprietary information that we'd rather not share, such as the LC gradient and other information that we may have 
> imbedded in the file. Also, we'd only like to share the cal curve and client samples, but potentially not QC samples. When you're using 
> this software, are you able to choose what sort of information that you'd like converted? Or is everything converted? I realize the need 
> or desire for transparency for publications, but, we're also trying to protect proprietary information/trade secrets on our end.
>
> Cheers,
>
>
> Greg
>

[proteowizard-support] wiff file conversion question

[Gregory S. <GS...@me...>]

Hi,

I have a question about the conversion of a SCIEX .wiff file to a file type that could be supported for upload to a site such as MetaboLights, like mzml. I work at Metabolon and a client contracted us to run a study for them with one of our targeted panels. The have since asked us to upload raw targeted metabolomics data for their study. However, we've been hesitant to approve these requests since the .wiff file contains proprietary information that we'd rather not share, such as the LC gradient and other information that we may have imbedded in the file. Also, we'd only like to share the cal curve and client samples, but potentially not QC samples. When you're using this software, are you able to choose what sort of information that you'd like converted? Or is everything converted? I realize the need or desire for transparency for publications, but, we're also trying to protect proprietary information/trade secrets on our end.


Cheers,

Greg



Gregory M. Schaaf, Ph.D.

Study Manager, Core Targeted Services

Discovery & Translational Sciences



[cid:d4d024d8-007d-4ae2-a353-53cc280dc52f]



617 Davis Drive, Suite 100, Morrisville, NC, 27560

LinkedIn<https://www.linkedin.com/company/metabolon> • Twitter<https://twitter.com/metabolon> • YouTube<https://www.youtube.com/c/metabolon> • Facebook<https://www.facebook.com/Metabolon/> • Instagram<https://www.instagram.com/metabolon/>





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