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From: Chambers, M. <mat...@gm...> - 2026-04-29 14:07:50
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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 > |
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From: Gregory S. <GS...@me...> - 2026-04-29 14:03:27
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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/> [A close up of a text Description automatically generated]<https://mtbln.co/awrq6y> Link for discovery panel webinar promotion: https://mtbln.co/awrq6y DISCLAIMER: This email and any file transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee, you should not disseminate, distribute or copy this e-mail. Please notify the sender or the system manager and delete or destroy this email and any attachment immediately. |
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From: Joseph O. <Jos...@UT...> - 2026-04-20 20:45:09
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Hi Matt, Thanks for the quick reply! From: Chambers, Matthew <mat...@gm...> Sent: Monday, April 20, 2026 3:40 PM To: Joseph Otto <Jos...@UT...>; su...@pr... Subject: Re: [proteowizard-support] De-charge MS2 Hi Joe, Unfortunately we don't have a charge deconvolution filter in msconvert/pwiz. The turbocharger filter can assign precursor charge states, but I don't think it does anything for fragment charge states. -Matt On Mon, Apr 20, 2026 4: 34 PM Hi Joe, Unfortunately we don't have a charge deconvolution filter in msconvert/pwiz. The turbocharger filter can assign precursor charge states, but I don't think it does anything for fragment charge states. -Matt On Mon, Apr 20, 2026 4:34 PM EDT (-0400), Joseph Otto wrote: Good afternoon, I’m converting some Thermo raw files to MGFs using MSConvert. I was wondering if you had any recommendations for de-charging the MS2 spectra or outputting the charge state of the MS2 fragments when making the MGF file? The image below is from a Matrix Science Mascot set of slides I found online. I think this is the same as deconvoluting the MS2 spectra. The settings I used this time are in the image below also. Thank you, Joe [cid:image001.png@01DCD0DC.9F88AFB0] [cid:image002.png@01DCD0DC.9F88AFB0] ############################################## Joe Otto, Ph.D. Senior Research Scientist Proteomics Core Facility UT Southwestern Medical Center 5323 Harry Hines Blvd. Rm.Y4.306 Dallas, TX 75390 ############################################## ________________________________ UT Southwestern Medical Center The future of medicine, today. _______________________________________________ proteowizard-support mailing list pro...@li...<mailto:pro...@li...> https://lists.sourceforge.net/lists/listinfo/proteowizard-support<https://urldefense.com/v3/__https:/lists.sourceforge.net/lists/listinfo/proteowizard-support__;!!MznTZTSvDXGV0Co!FIL_gX0tDkvIpxj0kHnviGKd_Y-EqnClT4ZqWdlh6Xl_txVu5lTNn57YGSezJMfumC4HIopDl2dW258knJ2EB5dGUts4YKIaV-Gp$> |
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From: Chambers, M. <mat...@gm...> - 2026-04-20 20:40:02
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Hi Joe, Unfortunately we don't have a charge deconvolution filter in msconvert/pwiz. The turbocharger filter can assign precursor charge states, but I don't think it does anything for fragment charge states. -Matt On Mon, Apr 20, 2026 4:34 PM EDT (-0400), Joseph Otto wrote: > > Good afternoon, > > I’m converting some Thermo raw files to MGFs using MSConvert. I was wondering if you had any recommendations for de-charging the MS2 > spectra or outputting the charge state of the MS2 fragments when making the MGF file? The image below is from a Matrix Science Mascot set > of slides I found online. I think this is the same as deconvoluting the MS2 spectra. > > The settings I used this time are in the image below also. > > Thank you, > > Joe > > ############################################## > > *Joe Otto, Ph.D.* > > Senior Research Scientist > > Proteomics Core Facility > > UT Southwestern Medical Center > > 5323 Harry Hines Blvd. Rm.Y4.306 > > Dallas, TX 75390 > > ############################################## > > > -------------------------------------------------------------------------------------------------------------------------------------------- > > UTSouthwestern > > Medical Center > > The future of medicine, today. > > > > _______________________________________________ > proteowizard-support mailing list > pro...@li... > https://lists.sourceforge.net/lists/listinfo/proteowizard-support |
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From: Joseph O. <Jos...@UT...> - 2026-04-20 20:34:54
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Good afternoon, I'm converting some Thermo raw files to MGFs using MSConvert. I was wondering if you had any recommendations for de-charging the MS2 spectra or outputting the charge state of the MS2 fragments when making the MGF file? The image below is from a Matrix Science Mascot set of slides I found online. I think this is the same as deconvoluting the MS2 spectra. The settings I used this time are in the image below also. Thank you, Joe [cid:image001.png@01DCD0DB.1EE48420] [cid:image002.png@01DCD0DB.2EB8CAF0] ############################################## Joe Otto, Ph.D. Senior Research Scientist Proteomics Core Facility UT Southwestern Medical Center 5323 Harry Hines Blvd. Rm.Y4.306 Dallas, TX 75390 ############################################## ________________________________ UT Southwestern Medical Center The future of medicine, today. |
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From: Chambers, M. <mat...@gm...> - 2026-04-14 14:27:12
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Hi Arjun, Convert WIFF to mzML, probably with peak picking enabled. See if you get comparable results. If not, ask DIANN developers what settings to use to convert to mzML. Hope this helps, -Matt On Tue, Apr 14, 2026 8:30 AM EDT (-0400), Arjun Bhardwaj wrote: > > Dear Proteowizad, > > I hope you are doing well. > > My name is Arjun Bhardwaj, and I am a PhD scholar at RCB, Faridabad. I am writing to seek your guidance regarding data analysis using > DIA-NN for our LiP-MS experiments. > > We have successfully performed the analysis using DIA-NN (version 2.3.2) on a Windows system. However, due to the large data volume, the > processing time was quite long (approximately 15 days). To improve efficiency, we are now attempting to run DIA-NN on a high-performance > computing (HPC) system (IBDC, India) using Linux. > > While we have optimized the parameters on the HPC environment, we are encountering an issue during data conversion. Specifically, DIA-NN > appears to rely on .dll files for converting WIFF files to mzML format, which are not supported in the Linux environment. > > Could you kindly advise on how to handle this conversion step on Linux, or suggest any alternative workflow or tools that would allow us > to process WIFF files for DIA-NN analysis in an HPC setup? > > We would greatly appreciate your guidance on this matter. > > Thank you for your time and support. > > Kind regards, > Arjun Bhardwaj > PhD Scholar > Regional Centre for Biotechnology (RCB), Faridabad > India > > > > _______________________________________________ > proteowizard-support mailing list > pro...@li... > https://lists.sourceforge.net/lists/listinfo/proteowizard-support |
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From: Arjun B. <arj...@rc...> - 2026-04-14 12:30:47
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Dear Proteowizad, I hope you are doing well. My name is Arjun Bhardwaj, and I am a PhD scholar at RCB, Faridabad. I am writing to seek your guidance regarding data analysis using DIA-NN for our LiP-MS experiments. We have successfully performed the analysis using DIA-NN (version 2.3.2) on a Windows system. However, due to the large data volume, the processing time was quite long (approximately 15 days). To improve efficiency, we are now attempting to run DIA-NN on a high-performance computing (HPC) system (IBDC, India) using Linux. While we have optimized the parameters on the HPC environment, we are encountering an issue during data conversion. Specifically, DIA-NN appears to rely on .dll files for converting WIFF files to mzML format, which are not supported in the Linux environment. Could you kindly advise on how to handle this conversion step on Linux, or suggest any alternative workflow or tools that would allow us to process WIFF files for DIA-NN analysis in an HPC setup? We would greatly appreciate your guidance on this matter. Thank you for your time and support. Kind regards, Arjun Bhardwaj PhD Scholar Regional Centre for Biotechnology (RCB), Faridabad India |
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From: Marek, T. J <tim...@ui...> - 2026-03-26 21:16:33
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I think we figured this out. Thank you, Tim M From: Chambers, Matthew <mat...@gm...> Sent: Thursday, March 26, 2026 12:33 PM To: Marek, Tim J <tim...@ui...>; su...@pr... Subject: Re: [External] Re: [proteowizard-support] Access Issues You don't often get email from mat...@gm...<mailto:mat...@gm...>. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> How about on other computers? And the other binaries, msconvert.exe (command line) and seems.exe? On Thu, Mar 26, 2026 12:24 PM EDT (-0400), Marek, Tim J wrote: I have tried both. Also tried installing while logged in as admin and running the program as admin. Same result so far. Thank you, Tim M From: Chambers, Matthew <mat...@gm...><mailto:mat...@gm...> Sent: Thursday, March 26, 2026 11:18 AM To: Marek, Tim J <tim...@ui...><mailto:tim...@ui...>; su...@pr...<mailto:su...@pr...> Subject: [External] Re: [proteowizard-support] Access Issues You don't often get email from mat...@gm...<mailto:mat...@gm...>. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> Hi Tim, I just downloaded and installed the latest build for all users and was able to run MSConvertGUI without a problem. So I'm not sure what could be causing this. Have you tried installing for just the current user instead of for all users (which installs to Program Files)? -Matt On Thu, Mar 26, 2026 12:02 PM EDT (-0400), Marek, Tim J via proteowizard-support wrote: We have users who have used ProteoWizard in the past and just updated to new computers. When we install ProteoWizard for them we get the following error when attempting to run the program. This happens even if I try to run the program as administrator. Any ideas on what the issue may be? [cid:image001.png@01DCBD3B.E0A98B40] Thank you, |
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From: Chambers, M. <mat...@gm...> - 2026-03-26 17:33:21
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How about on other computers? And the other binaries, msconvert.exe (command line) and seems.exe? On Thu, Mar 26, 2026 12:24 PM EDT (-0400), Marek, Tim J wrote: > > I have tried both. Also tried installing while logged in as admin and running the program as admin. Same result so far. > > Thank you, > > Tim M > > *From:*Chambers, Matthew <mat...@gm...> > *Sent:* Thursday, March 26, 2026 11:18 AM > *To:* Marek, Tim J <tim...@ui...>; su...@pr... > *Subject:* [External] Re: [proteowizard-support] Access Issues > > > > > You don't often get email from mat...@gm.... Learn why this is important <https://aka.ms/LearnAboutSenderIdentification> > > > > Hi Tim, > > I just downloaded and installed the latest build for all users and was able to run MSConvertGUI without a problem. So I'm not sure what > could be causing this. Have you tried installing for just the current user instead of for all users (which installs to Program Files)? > > -Matt > > On Thu, Mar 26, 2026 12:02 PM EDT (-0400), Marek, Tim J via proteowizard-support wrote: > > We have users who have used ProteoWizard in the past and just updated to new computers. When we install ProteoWizard for them we get > the following error when attempting to run the program. This happens even if I try to run the program as administrator. Any ideas on > what the issue may be? > > Thank you, > |
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From: Marek, T. J <tim...@ui...> - 2026-03-26 16:24:36
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I have tried both. Also tried installing while logged in as admin and running the program as admin. Same result so far. Thank you, Tim M From: Chambers, Matthew <mat...@gm...> Sent: Thursday, March 26, 2026 11:18 AM To: Marek, Tim J <tim...@ui...>; su...@pr... Subject: [External] Re: [proteowizard-support] Access Issues You don't often get email from mat...@gm...<mailto:mat...@gm...>. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> Hi Tim, I just downloaded and installed the latest build for all users and was able to run MSConvertGUI without a problem. So I'm not sure what could be causing this. Have you tried installing for just the current user instead of for all users (which installs to Program Files)? -Matt On Thu, Mar 26, 2026 12:02 PM EDT (-0400), Marek, Tim J via proteowizard-support wrote: We have users who have used ProteoWizard in the past and just updated to new computers. When we install ProteoWizard for them we get the following error when attempting to run the program. This happens even if I try to run the program as administrator. Any ideas on what the issue may be? [cid:image001.png@01DCBD13.131F29F0] Thank you, |
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From: Chambers, M. <mat...@gm...> - 2026-03-26 16:24:31
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Hi Tim, I just downloaded and installed the latest build for all users and was able to run MSConvertGUI without a problem. So I'm not sure what could be causing this. Have you tried installing for just the current user instead of for all users (which installs to Program Files)? -Matt On Thu, Mar 26, 2026 12:02 PM EDT (-0400), Marek, Tim J via proteowizard-support wrote: > > We have users who have used ProteoWizard in the past and just updated to new computers. When we install ProteoWizard for them we get the > following error when attempting to run the program. This happens even if I try to run the program as administrator. Any ideas on what > the issue may be? > > Thank you, > > |
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From: Marek, T. J <tim...@ui...> - 2026-03-26 16:02:20
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We have users who have used ProteoWizard in the past and just updated to new computers. When we install ProteoWizard for them we get the following error when attempting to run the program. This happens even if I try to run the program as administrator. Any ideas on what the issue may be? [cid:image001.png@01DCBD0F.F8F18850] Thank you, Tim J Marek Senior IT Support Consultant CPHB N148A College of Public Health, University of Iowa Iowa City, Ia 52242-5000 Phone: (319) 384-3843 Email: Tim...@ui...<mailto:Tim...@ui...> College of Public-Health Support Call: X43838 email: cph...@ui...<mailto:cph...@ui...> http://www.public-health.uiowa.edu/it |
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From: Paul-Albert A. S. <pau...@ba...> - 2026-03-09 12:43:24
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Hi Brian, After exporting the files with the latest version, we think that we might have spotted a problem with the current implementation of the pwiz_Reader_Bruker. It seems that only UV information from specifically selected UV channels but not the full DAD spectrum is exported. At least we cannot find UV information in the .mzML when we have not selected specific UV channels in the method. Example where we have selected two specific wavelengths and where we can see UV information in the exported .mzML file: [cid:image005.png@01DCAFB7.59E3F5A0] Can you confirm this or did we overlook something? Best Paul From: Paul-Albert Anselm Schneide Sent: Sunday, February 22, 2026 10:51 AM To: 'Brian Pratt' <bs...@pr...>; Catharina Erbacher <cat...@ba...> Cc: Chambers, Matthew <mat...@gm...>; su...@pr... Subject: RE: [proteowizard-support] [EXT] Re: Missing UV/DAD data in mzML files Hi Brian, Thanks, that helped! The version we used for conversion is not the most recent one, and therefore I cannot see the data blocks. Apparently, we use "pwiz_Reader_Bruker" version="3.0.24272". @Catharina<mailto:cat...@ba...>: Can you download the most recent version from here: ProteoWizard: Download<https://proteowizard.sourceforge.io/download.html> I just checked and it should be 3.0.26052. Thanks Paul From: Brian Pratt <bs...@pr...<mailto:bs...@pr...>> Sent: Friday, February 20, 2026 6:17 PM To: Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>> Cc: Chambers, Matthew <mat...@gm...<mailto:mat...@gm...>>; su...@pr...<mailto:su...@pr...>; Catharina Erbacher <cat...@ba...<mailto:cat...@ba...>> Subject: Re: [proteowizard-support] [EXT] Re: Missing UV/DAD data in mzML files Hi Paul, Using the file you provided back when we started: After conversion you should, for example, find this towards the end the output: <chromatogram index="3" id="DAD: Signal A, 205.0 nm/Bw:4.0 nm Ref 360.0 nm/Bw:100.0 nm" defaultArrayLength="1187"> <cvParam cvRef="MS" accession="MS:1000812" name="absorption chromatogram" value=""/> <cvParam cvRef="MS" accession="MS:1000809" name="chromatogram title" value="DAD: Signal A, 205.0 nm/Bw:4.0 nm Ref 360.0 nm/Bw:100.0 nm"/> <userParam name="Instrument" value="Agilent ICF System"/> <binaryDataArrayList count="2"> Up towards the top you should find something like <software id="pwiz_Reader_Bruker" version="3.0.26050"> <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/> </software> What's the value for "version" that you see? Brian On Fri, Feb 20, 2026 at 1:33 AM Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>> wrote: Thank you, Matthew. I am afraid that I cannot find the UV information. What is the <cvParam cvRef= > I should search for to find the respective data blocks? And just to make sure we are working with the correct bundle, we use the one that can be downloaded here: ProteoWizard: Download<https://proteowizard.sourceforge.io/download.html> Best Paul From: Chambers, Matthew <mat...@gm...<mailto:mat...@gm...>> Sent: Thursday, February 12, 2026 5:09 PM To: Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>>; Brian Pratt <bs...@pr...<mailto:bs...@pr...>> Cc: su...@pr...<mailto:su...@pr...>; Catharina Erbacher <cat...@ba...<mailto:cat...@ba...>> Subject: Re: [proteowizard-support] [EXT] Re: Missing UV/DAD data in mzML files It'll show up as chromatograms at the end of the file (before the index). On Thu, Feb 12, 2026 10:30 AM EST (-0500), Paul-Albert Anselm Schneide via proteowizard-support wrote: Hi Brian, Sorry that I have to disturb you again with the Bruker data... We have exported some files with the latest version of your parser but still struggle to find the DAD information. Could you maybe send me/us the documentation for where this can be found in the .xml tree? Best Paul From: Brian Pratt <bs...@pr...><mailto:bs...@pr...> Sent: Thursday, January 8, 2026 6:14 PM To: Paul-Albert Anselm Schneide <pau...@ba...><mailto:pau...@ba...> Cc: Catharina Erbacher <cat...@ba...><mailto:cat...@ba...>; su...@pr...<mailto:su...@pr...> Subject: Re: [EXT] Re: [proteowizard-support] Missing UV/DAD data in mzML files The work got tangled up with accompanying UI improvements to SeeMS and Skyline, and it was just completed yesterday. I was going to notify you this morning after the final build and test, which is complete now. Download the current package and you should be ready to go. Thanks for your help on this. Brian On Thu, Jan 8, 2026 at 12:56 AM Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>> wrote: Hi Brian, Hope you had a got start to 2026! Just wanted to ask if you’ve already had the time to fix the converter? 😊 Best Paul From: Brian Pratt <bs...@pr...<mailto:bs...@pr...>> Sent: Thursday, December 11, 2025 6:08 PM To: Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>> Cc: Catharina Erbacher <cat...@ba...<mailto:cat...@ba...>>; su...@pr...<mailto:su...@pr...> Subject: Re: [EXT] Re: [proteowizard-support] Missing UV/DAD data in mzML files I expect I can get this done early next week. On Thu, Dec 11, 2025 at 4:32 AM Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>> wrote: Dear Brian, Thanks a lot for the update and sounds great! Do you have an idea on how long it might take to develop the new converter that can parse the UV information? Best Paul From: Brian Pratt <bs...@pr...<mailto:bs...@pr...>> Sent: Wednesday, December 10, 2025 10:53 PM To: Catharina Erbacher <cat...@ba...<mailto:cat...@ba...>> Cc: Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>>; su...@pr...<mailto:su...@pr...> Subject: Re: [EXT] Re: [proteowizard-support] Missing UV/DAD data in mzML files Just a quick update - I've gotten some good information from our friends at Bruker and I'll be moving forward with this. Brian On Mon, Nov 24, 2025 at 12:26 AM Catharina Erbacher <cat...@ba...<mailto:cat...@ba...>> wrote: Hi Brian, this is great news! Thanks a lot! Kind regards, Catharina Dr. Catharina Erbacher Lab Team Leader LC-MS Mobile: +49 151 11795362, Email: cat...@ba...<mailto:cat...@ba...> Postal Address: BASF SE, RGS/AL, Carl-Bosch-Strasse 38, 67056 Ludwigshafen am Rhein, Germany [cid:image001.png@01DCAFB6.CD3F2B10] BASF SE, Registered Office: 67056 Ludwigshafen, Germany Registration Court: Amtsgericht Ludwigshafen, Registration No.: HRB 6000 Chairman of the Supervisory Board: Kurt Bock Board of Executive Directors: Markus Kamieth, Chairman; Dirk Elvermann, Michael Heinz, Anup Kothari, Stephan Kothrade, Katja Scharpwinkel Information on data protection can be found here: https://www.basf.com/global/en/legal/data-protection-at-basf.html From: Brian Pratt <bs...@pr...<mailto:bs...@pr...>> Sent: Saturday, November 22, 2025 2:09 AM To: Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>> Cc: su...@pr...<mailto:su...@pr...>; Catharina Erbacher <cat...@ba...<mailto:cat...@ba...>> Subject: Re: [EXT] Re: [proteowizard-support] Missing UV/DAD data in mzML files Sie erhalten nicht häufig E-Mails von bs...@pr...<mailto:bs...@pr...>. Erfahren Sie, warum dies wichtig ist<https://aka.ms/LearnAboutSenderIdentification> Just an update, we're working with Bruker to see if there's some readily available code for handling this. Brian On Tue, Nov 18, 2025 at 12:55 PM Brian Pratt <bs...@pr...<mailto:bs...@pr...>> wrote: Unfortunately this looks like a fairly sizeable change - the Bruker API doesn't provide this information directly. I can see where it's located in a sqlite file, but it's not trivial to interpret and extract. I do agree that it's useful information but I can't get to this right away. It's also not clear to me just how standard the information is, given that it's actually Agilent equipment doing that measurement rather than anything Bruker produces? On Mon, Nov 17, 2025 at 2:45 PM Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>> wrote: Great! Thanks a lot Brian, for getting back to us. Looking forward to hearing from you. Best Paul From: Brian Pratt <bs...@pr...<mailto:bs...@pr...>> Sent: Monday, November 17, 2025 8:14 PM To: Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>> Cc: su...@pr...<mailto:su...@pr...>; Catharina Erbacher <cat...@ba...<mailto:cat...@ba...>> Subject: Re: [EXT] Re: [proteowizard-support] Missing UV/DAD data in mzML files Sie erhalten nicht häufig E-Mails von bs...@pr...<mailto:bs...@pr...>. Erfahren Sie, warum dies wichtig ist<https://aka.ms/LearnAboutSenderIdentification> I have the data, thanks, and can confirm that we seem to ignore that information. I'll see what can be done about that. Brian On Fri, Nov 14, 2025 at 12:30 AM Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>> wrote: Hi Brian, Thanks a lot for your fast response. Please try if you can access this example data file via the shared link: [zip icon]Akzeptanztest_20250320_PG03238_kep101_94_1_2962.d.zip<https://basf-my.sharepoint.com/:u:/g/personal/schnep18_basfad_basf_net/ER6T09UuRZNLlE9Ana8LTDYBrzblpoNW1JYqP-PLL0ftAg?e=HUW455> Best Paul From: Brian Pratt <bs...@pr...<mailto:bs...@pr...>> Sent: Wednesday, November 12, 2025 5:51 PM To: Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>> Cc: su...@pr...<mailto:su...@pr...>; Catharina Erbacher <cat...@ba...<mailto:cat...@ba...>> Subject: [EXT] Re: [proteowizard-support] Missing UV/DAD data in mzML files Sie erhalten nicht häufig E-Mails von bs...@pr...<mailto:bs...@pr...>. Erfahren Sie, warum dies wichtig ist<https://aka.ms/LearnAboutSenderIdentification> Happy to have a look at this - can you provide some sample data? Brian Pratt On Wed, Nov 12, 2025 at 4:55 AM Paul-Albert Anselm Schneide via proteowizard-support <pro...@li...<mailto:pro...@li...>> wrote: Dear ProteoWizard Support Team, We are facing issues with conversion of Bruker raw data files (see picture below) to .mzML format using ProteoWIzard. Specifically, we noticed that there is no UV/DAD information in the converted mzML files. The measurements were conducted on a Bruker TIMS-TOF. Is this a common issue and do you have any suggestions for how we can convert the files into a readable format that stores MS and UV/DAD information? [cid:image003.png@01DCAFB6.CD3F2B10] Thank you very much in advance! Best Paul Beste Grüße/ Kind regards Dr. Paul-Albert Schneide Laborleiter F&E, Chemometrics@BASF Email: pau...@ba...<mailto:pau...@ba...> Postal Address: BASF SE, RGA/AD, Carl-Bosch-Strasse 38, 67056 Ludwigshafen am Rhein, Germany [cid:image004.png@01DCAFB6.CD3F2B10] BASF SE, Registered Office: 67056 Ludwigshafen, Germany Registration Court: Amtsgericht Ludwigshafen, Registration No.: HRB 6000 Chairman of the Supervisory Board: Kurt Bock Board of Executive Directors: Markus Kamieth, Chairman; Dirk Elvermann, Michael Heinz, Anup Kothari, Stephan Kothrade, Katja Scharpwinkel _______________________________________________ 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 |
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From: Chambers, M. <mat...@gm...> - 2026-03-02 16:26:13
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Hi Joseph, There's only a couple --chromatogramFilter options (not nearly as many as --filter for spectrum filters). One is "index" and the other is "lockmassRefiner". You can use the index filter to select only chromatogram index 5: --chromatogramFilter "index 5" That is the only filter available right now for subsetting the chromatogram list. Hope this helps, -Matt On Sat, Feb 28, 2026 7:01 PM EST (-0500), Joseph Otto wrote: > > Hi Matt, > > You’ve helped me out before with converting LC-MS chromatogram data to a txt file. I parse out data from the text files to use in other > tools. We recently got an EvoSep Eno system and the primary LC pressure trace that I want is seen in SeeMS. I usually use these options > and they work well. “--text --filter "msLevel 42-" “ How could I adjust it to include the pump pressure highlighted below? It is Pump > Pressure 24, index 5. > > Thank you, > > Joe > > *From:* Chambers, Matthew <mat...@gm...> > *Sent:* Tuesday, June 18, 2024 9:55 AM > *To:* Joseph Otto <Jos...@UT...>; su...@pr... > *Subject:* Re: [proteowizard-support] Pump Pressure output - Thermo MS files > > It's a custom text format meant to make the hierarchical XML models and binary base64 encoded data easy to read by text. It's not a > tabular format at all. Basically you'd parse it line by line. Store the last seen spectrum/chromatogram id, then when you get to the > binary data array at the spectrum id, you associate that data with the last seen id. > > On 6/17/2024 4:55 PM, Joseph Otto wrote: > > Thank you. > > What is the .txt format that is output by this? Is there a set of parsing rules available? > > Thanks, > > Joe > > *From:* Chambers, Matthew <mat...@gm...> <mailto:mat...@gm...> > *Sent:* Friday, June 14, 2024 1:00 PM > *To:* Joseph Otto <Jos...@UT...> <mailto:Jos...@UT...>; su...@pr... > *Subject:* Re: [proteowizard-support] Pump Pressure output - Thermo MS files > > --text --filter "msLevel 42" > to get text output for just the chromatograms. > > On 6/14/2024 1:21 PM, Joseph Otto wrote: > > Oh great! That was an easy fix. > > Do you have a suggestion for what might be the quickest settings to extract the pressure data from a raw file using MSconvert > commandline? > > Thanks, > > Joe > > *From:* Chambers, Matthew <mat...@gm...> <mailto:mat...@gm...> > *Sent:* Friday, June 14, 2024 11:55 AM > *To:* Joseph Otto <Jos...@UT...> <mailto:Jos...@UT...>; su...@pr... > *Subject:* Re: [proteowizard-support] Pump Pressure output - Thermo MS files > > Download a newer ProteoWizard. I see Pump Pressure in SeeMS' chromatogram list. > > On 6/14/2024 12:35 PM, Joseph Otto wrote: > > Hi Matt, > > Thank you for the quick response. > > I’m not seeing it in SeeMS unless I’m not looking in the right place. See the screenshots below. > > An example raw file can be downloaded here: temp > <https://urldefense.com/v3/__https:/365utsouthwestern-my.sharepoint.com/:f:/g/personal/joseph_otto_utsouthwestern_edu/EppThtdCZsVJp75A8e5IYxQBGXJxQte_Cwgu9Kcb7358jg?e=gwll2x__;!!MznTZTSvDXGV0Co!DJMAYyvnUv0b9tNpEjCOgsv_TF2k3FMPuXa7T0rVJ7-qwMR8zM1qbyIKzBXdJQyxBeDFyabd25Xskljnb_JsBQd0oDZxKmE3ZBF6$> > > > https://365utsouthwestern-my.sharepoint.com/:f:/g/personal/joseph_otto_utsouthwestern_edu/EppThtdCZsVJp75A8e5IYxQBGXJxQte_Cwgu9Kcb7358jg?e=gwll2x > <https://urldefense.com/v3/__https:/365utsouthwestern-my.sharepoint.com/:f:/g/personal/joseph_otto_utsouthwestern_edu/EppThtdCZsVJp75A8e5IYxQBGXJxQte_Cwgu9Kcb7358jg?e=gwll2x__;!!MznTZTSvDXGV0Co!DJMAYyvnUv0b9tNpEjCOgsv_TF2k3FMPuXa7T0rVJ7-qwMR8zM1qbyIKzBXdJQyxBeDFyabd25Xskljnb_JsBQd0oDZxKmE3ZBF6$> > > It is the same file that is shown in the example. > > Thank you, > > Joe > > > > > > > > > > *From:* Chambers, Matthew <mat...@gm...> <mailto:mat...@gm...> > *Sent:* Friday, June 14, 2024 11:26 AM > *To:* Joseph Otto <Jos...@UT...> <mailto:Jos...@UT...>; su...@pr... > *Subject:* Re: [proteowizard-support] Pump Pressure output - Thermo MS files > > *EXTERNAL MAIL* > > Hi Joseph, > > Do you see a pump pressure trace when you open the RAW with SeeMS? If so, the trace (chromatogram) should be there when you > convert the file to mzML. If not, send us your RAW file and I'll see about adding support for getting the pressure from it. > > I don't think we have a way to export chromatograms to tabular text but there is a --text format in msconvert that produces a > hierarchical output (kind of like YAML, but it's not) which will have the spectrum and chromatogram data points in plain text. > It would be extremely verbose though so you'd probably want to filter out all the spectra (--filter "msLevel 42" would do the > trick) > > Hope this helps, > -Matt > > > > > On 6/14/2024 11:28 AM, Joseph Otto wrote: > > Good morning, > > I’d like to extract the pressure information from thermo *.raw files. From looking at the github for msconvert, it looks > like I should be able to pull it out, but I’m not sure how. A screenshot of the data is attached. An example raw file is > available for download at the link below as well. > > Ideally, I could extract it to a simple text format along with TIC data from the MS. > > Could you help me to extract the needed data using MSconvert if it is possible? > > temp > <https://urldefense.com/v3/__https:/365utsouthwestern-my.sharepoint.com/:f:/g/personal/joseph_otto_utsouthwestern_edu/EppThtdCZsVJp75A8e5IYxQBGXJxQte_Cwgu9Kcb7358jg?e=gwll2x__;!!MznTZTSvDXGV0Co!DJMAYyvnUv0b9tNpEjCOgsv_TF2k3FMPuXa7T0rVJ7-qwMR8zM1qbyIKzBXdJQyxBeDFyabd25Xskljnb_JsBQd0oDZxKmE3ZBF6$> > > > https://365utsouthwestern-my.sharepoint.com/:f:/g/personal/joseph_otto_utsouthwestern_edu/EppThtdCZsVJp75A8e5IYxQBGXJxQte_Cwgu9Kcb7358jg?e=gwll2x > <https://urldefense.com/v3/__https:/365utsouthwestern-my.sharepoint.com/:f:/g/personal/joseph_otto_utsouthwestern_edu/EppThtdCZsVJp75A8e5IYxQBGXJxQte_Cwgu9Kcb7358jg?e=gwll2x__;!!MznTZTSvDXGV0Co!DJMAYyvnUv0b9tNpEjCOgsv_TF2k3FMPuXa7T0rVJ7-qwMR8zM1qbyIKzBXdJQyxBeDFyabd25Xskljnb_JsBQd0oDZxKmE3ZBF6$> > > > > > > > Thank you, > > Joe > > *CAUTION: *This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's > email address before replying. > > -------------------------------------------------------------------------------------------------------------------------------------------- > > *UT**Southwestern* > > Medical Center > > > The future of medicine, today. > |
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From: Joseph O. <Jos...@UT...> - 2026-03-01 00:02:22
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Hi Matt, You’ve helped me out before with converting LC-MS chromatogram data to a txt file. I parse out data from the text files to use in other tools. We recently got an EvoSep Eno system and the primary LC pressure trace that I want is seen in SeeMS. I usually use these options and they work well. “--text --filter "msLevel 42-" “ How could I adjust it to include the pump pressure highlighted below? It is Pump Pressure 24, index 5. Thank you, Joe [cid:image001.png@01DCA8DC.54933FC0] From: Chambers, Matthew <mat...@gm...> Sent: Tuesday, June 18, 2024 9:55 AM To: Joseph Otto <Jos...@UT...>; su...@pr... Subject: Re: [proteowizard-support] Pump Pressure output - Thermo MS files It's a custom text format meant to make the hierarchical XML models and binary base64 encoded data easy to read by text. It's not a tabular format at all. Basically you'd parse it line by line. Store the last seen spectrum/chromatogram id, then when you get to the binary data array at the spectrum id, you associate that data with the last seen id. On 6/17/2024 4:55 PM, Joseph Otto wrote: Thank you. What is the .txt format that is output by this? Is there a set of parsing rules available? Thanks, Joe From: Chambers, Matthew <mat...@gm...><mailto:mat...@gm...> Sent: Friday, June 14, 2024 1:00 PM To: Joseph Otto <Jos...@UT...><mailto:Jos...@UT...>; su...@pr...<mailto:su...@pr...> Subject: Re: [proteowizard-support] Pump Pressure output - Thermo MS files --text --filter "msLevel 42" to get text output for just the chromatograms. On 6/14/2024 1:21 PM, Joseph Otto wrote: Oh great! That was an easy fix. Do you have a suggestion for what might be the quickest settings to extract the pressure data from a raw file using MSconvert commandline? Thanks, Joe From: Chambers, Matthew <mat...@gm...><mailto:mat...@gm...> Sent: Friday, June 14, 2024 11:55 AM To: Joseph Otto <Jos...@UT...><mailto:Jos...@UT...>; su...@pr...<mailto:su...@pr...> Subject: Re: [proteowizard-support] Pump Pressure output - Thermo MS files Download a newer ProteoWizard. I see Pump Pressure in SeeMS' chromatogram list. On 6/14/2024 12:35 PM, Joseph Otto wrote: Hi Matt, Thank you for the quick response. I’m not seeing it in SeeMS unless I’m not looking in the right place. See the screenshots below. An example raw file can be downloaded here: temp<https://urldefense.com/v3/__https:/365utsouthwestern-my.sharepoint.com/:f:/g/personal/joseph_otto_utsouthwestern_edu/EppThtdCZsVJp75A8e5IYxQBGXJxQte_Cwgu9Kcb7358jg?e=gwll2x__;!!MznTZTSvDXGV0Co!DJMAYyvnUv0b9tNpEjCOgsv_TF2k3FMPuXa7T0rVJ7-qwMR8zM1qbyIKzBXdJQyxBeDFyabd25Xskljnb_JsBQd0oDZxKmE3ZBF6$> https://365utsouthwestern-my.sharepoint.com/:f:/g/personal/joseph_otto_utsouthwestern_edu/EppThtdCZsVJp75A8e5IYxQBGXJxQte_Cwgu9Kcb7358jg?e=gwll2x<https://urldefense.com/v3/__https:/365utsouthwestern-my.sharepoint.com/:f:/g/personal/joseph_otto_utsouthwestern_edu/EppThtdCZsVJp75A8e5IYxQBGXJxQte_Cwgu9Kcb7358jg?e=gwll2x__;!!MznTZTSvDXGV0Co!DJMAYyvnUv0b9tNpEjCOgsv_TF2k3FMPuXa7T0rVJ7-qwMR8zM1qbyIKzBXdJQyxBeDFyabd25Xskljnb_JsBQd0oDZxKmE3ZBF6$> It is the same file that is shown in the example. Thank you, Joe From: Chambers, Matthew <mat...@gm...><mailto:mat...@gm...> Sent: Friday, June 14, 2024 11:26 AM To: Joseph Otto <Jos...@UT...><mailto:Jos...@UT...>; su...@pr...<mailto:su...@pr...> Subject: Re: [proteowizard-support] Pump Pressure output - Thermo MS files EXTERNAL MAIL Hi Joseph, Do you see a pump pressure trace when you open the RAW with SeeMS? If so, the trace (chromatogram) should be there when you convert the file to mzML. If not, send us your RAW file and I'll see about adding support for getting the pressure from it. I don't think we have a way to export chromatograms to tabular text but there is a --text format in msconvert that produces a hierarchical output (kind of like YAML, but it's not) which will have the spectrum and chromatogram data points in plain text. It would be extremely verbose though so you'd probably want to filter out all the spectra (--filter "msLevel 42" would do the trick) Hope this helps, -Matt On 6/14/2024 11:28 AM, Joseph Otto wrote: Good morning, I’d like to extract the pressure information from thermo *.raw files. From looking at the github for msconvert, it looks like I should be able to pull it out, but I’m not sure how. A screenshot of the data is attached. An example raw file is available for download at the link below as well. Ideally, I could extract it to a simple text format along with TIC data from the MS. Could you help me to extract the needed data using MSconvert if it is possible? temp<https://urldefense.com/v3/__https:/365utsouthwestern-my.sharepoint.com/:f:/g/personal/joseph_otto_utsouthwestern_edu/EppThtdCZsVJp75A8e5IYxQBGXJxQte_Cwgu9Kcb7358jg?e=gwll2x__;!!MznTZTSvDXGV0Co!DJMAYyvnUv0b9tNpEjCOgsv_TF2k3FMPuXa7T0rVJ7-qwMR8zM1qbyIKzBXdJQyxBeDFyabd25Xskljnb_JsBQd0oDZxKmE3ZBF6$> https://365utsouthwestern-my.sharepoint.com/:f:/g/personal/joseph_otto_utsouthwestern_edu/EppThtdCZsVJp75A8e5IYxQBGXJxQte_Cwgu9Kcb7358jg?e=gwll2x<https://urldefense.com/v3/__https:/365utsouthwestern-my.sharepoint.com/:f:/g/personal/joseph_otto_utsouthwestern_edu/EppThtdCZsVJp75A8e5IYxQBGXJxQte_Cwgu9Kcb7358jg?e=gwll2x__;!!MznTZTSvDXGV0Co!DJMAYyvnUv0b9tNpEjCOgsv_TF2k3FMPuXa7T0rVJ7-qwMR8zM1qbyIKzBXdJQyxBeDFyabd25Xskljnb_JsBQd0oDZxKmE3ZBF6$> Thank you, Joe CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying. ________________________________ UT Southwestern Medical Center The future of medicine, today. |
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From: Paul-Albert A. S. <pau...@ba...> - 2026-02-22 09:51:17
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Hi Brian, Thanks, that helped! The version we used for conversion is not the most recent one, and therefore I cannot see the data blocks. Apparently, we use "pwiz_Reader_Bruker" version="3.0.24272". @Catharina<mailto:cat...@ba...>: Can you download the most recent version from here: ProteoWizard: Download<https://proteowizard.sourceforge.io/download.html> I just checked and it should be 3.0.26052. Thanks Paul From: Brian Pratt <bs...@pr...> Sent: Friday, February 20, 2026 6:17 PM To: Paul-Albert Anselm Schneide <pau...@ba...> Cc: Chambers, Matthew <mat...@gm...>; su...@pr...; Catharina Erbacher <cat...@ba...> Subject: Re: [proteowizard-support] [EXT] Re: Missing UV/DAD data in mzML files Hi Paul, Using the file you provided back when we started: After conversion you should, for example, find this towards the end the output: <chromatogram index="3" id="DAD: Signal A, 205.0 nm/Bw:4.0 nm Ref 360.0 nm/Bw:100.0 nm" defaultArrayLength="1187"> <cvParam cvRef="MS" accession="MS:1000812" name="absorption chromatogram" value=""/> <cvParam cvRef="MS" accession="MS:1000809" name="chromatogram title" value="DAD: Signal A, 205.0 nm/Bw:4.0 nm Ref 360.0 nm/Bw:100.0 nm"/> <userParam name="Instrument" value="Agilent ICF System"/> <binaryDataArrayList count="2"> Up towards the top you should find something like <software id="pwiz_Reader_Bruker" version="3.0.26050"> <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/> </software> What's the value for "version" that you see? Brian On Fri, Feb 20, 2026 at 1:33 AM Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>> wrote: Thank you, Matthew. I am afraid that I cannot find the UV information. What is the <cvParam cvRef= > I should search for to find the respective data blocks? And just to make sure we are working with the correct bundle, we use the one that can be downloaded here: ProteoWizard: Download<https://proteowizard.sourceforge.io/download.html> Best Paul From: Chambers, Matthew <mat...@gm...<mailto:mat...@gm...>> Sent: Thursday, February 12, 2026 5:09 PM To: Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>>; Brian Pratt <bs...@pr...<mailto:bs...@pr...>> Cc: su...@pr...<mailto:su...@pr...>; Catharina Erbacher <cat...@ba...<mailto:cat...@ba...>> Subject: Re: [proteowizard-support] [EXT] Re: Missing UV/DAD data in mzML files It'll show up as chromatograms at the end of the file (before the index). On Thu, Feb 12, 2026 10:30 AM EST (-0500), Paul-Albert Anselm Schneide via proteowizard-support wrote: Hi Brian, Sorry that I have to disturb you again with the Bruker data... We have exported some files with the latest version of your parser but still struggle to find the DAD information. Could you maybe send me/us the documentation for where this can be found in the .xml tree? Best Paul From: Brian Pratt <bs...@pr...><mailto:bs...@pr...> Sent: Thursday, January 8, 2026 6:14 PM To: Paul-Albert Anselm Schneide <pau...@ba...><mailto:pau...@ba...> Cc: Catharina Erbacher <cat...@ba...><mailto:cat...@ba...>; su...@pr...<mailto:su...@pr...> Subject: Re: [EXT] Re: [proteowizard-support] Missing UV/DAD data in mzML files The work got tangled up with accompanying UI improvements to SeeMS and Skyline, and it was just completed yesterday. I was going to notify you this morning after the final build and test, which is complete now. Download the current package and you should be ready to go. Thanks for your help on this. Brian On Thu, Jan 8, 2026 at 12:56 AM Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>> wrote: Hi Brian, Hope you had a got start to 2026! Just wanted to ask if you’ve already had the time to fix the converter? 😊 Best Paul From: Brian Pratt <bs...@pr...<mailto:bs...@pr...>> Sent: Thursday, December 11, 2025 6:08 PM To: Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>> Cc: Catharina Erbacher <cat...@ba...<mailto:cat...@ba...>>; su...@pr...<mailto:su...@pr...> Subject: Re: [EXT] Re: [proteowizard-support] Missing UV/DAD data in mzML files I expect I can get this done early next week. On Thu, Dec 11, 2025 at 4:32 AM Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>> wrote: Dear Brian, Thanks a lot for the update and sounds great! Do you have an idea on how long it might take to develop the new converter that can parse the UV information? Best Paul From: Brian Pratt <bs...@pr...<mailto:bs...@pr...>> Sent: Wednesday, December 10, 2025 10:53 PM To: Catharina Erbacher <cat...@ba...<mailto:cat...@ba...>> Cc: Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>>; su...@pr...<mailto:su...@pr...> Subject: Re: [EXT] Re: [proteowizard-support] Missing UV/DAD data in mzML files Just a quick update - I've gotten some good information from our friends at Bruker and I'll be moving forward with this. Brian On Mon, Nov 24, 2025 at 12:26 AM Catharina Erbacher <cat...@ba...<mailto:cat...@ba...>> wrote: Hi Brian, this is great news! Thanks a lot! Kind regards, Catharina Dr. Catharina Erbacher Lab Team Leader LC-MS Mobile: +49 151 11795362, Email: cat...@ba...<mailto:cat...@ba...> Postal Address: BASF SE, RGS/AL, Carl-Bosch-Strasse 38, 67056 Ludwigshafen am Rhein, Germany [cid:image001.png@01DCA3E8.723CCE40] BASF SE, Registered Office: 67056 Ludwigshafen, Germany Registration Court: Amtsgericht Ludwigshafen, Registration No.: HRB 6000 Chairman of the Supervisory Board: Kurt Bock Board of Executive Directors: Markus Kamieth, Chairman; Dirk Elvermann, Michael Heinz, Anup Kothari, Stephan Kothrade, Katja Scharpwinkel Information on data protection can be found here: https://www.basf.com/global/en/legal/data-protection-at-basf.html From: Brian Pratt <bs...@pr...<mailto:bs...@pr...>> Sent: Saturday, November 22, 2025 2:09 AM To: Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>> Cc: su...@pr...<mailto:su...@pr...>; Catharina Erbacher <cat...@ba...<mailto:cat...@ba...>> Subject: Re: [EXT] Re: [proteowizard-support] Missing UV/DAD data in mzML files Sie erhalten nicht häufig E-Mails von bs...@pr...<mailto:bs...@pr...>. Erfahren Sie, warum dies wichtig ist<https://aka.ms/LearnAboutSenderIdentification> Just an update, we're working with Bruker to see if there's some readily available code for handling this. Brian On Tue, Nov 18, 2025 at 12:55 PM Brian Pratt <bs...@pr...<mailto:bs...@pr...>> wrote: Unfortunately this looks like a fairly sizeable change - the Bruker API doesn't provide this information directly. I can see where it's located in a sqlite file, but it's not trivial to interpret and extract. I do agree that it's useful information but I can't get to this right away. It's also not clear to me just how standard the information is, given that it's actually Agilent equipment doing that measurement rather than anything Bruker produces? On Mon, Nov 17, 2025 at 2:45 PM Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>> wrote: Great! Thanks a lot Brian, for getting back to us. Looking forward to hearing from you. Best Paul From: Brian Pratt <bs...@pr...<mailto:bs...@pr...>> Sent: Monday, November 17, 2025 8:14 PM To: Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>> Cc: su...@pr...<mailto:su...@pr...>; Catharina Erbacher <cat...@ba...<mailto:cat...@ba...>> Subject: Re: [EXT] Re: [proteowizard-support] Missing UV/DAD data in mzML files Sie erhalten nicht häufig E-Mails von bs...@pr...<mailto:bs...@pr...>. Erfahren Sie, warum dies wichtig ist<https://aka.ms/LearnAboutSenderIdentification> I have the data, thanks, and can confirm that we seem to ignore that information. I'll see what can be done about that. Brian On Fri, Nov 14, 2025 at 12:30 AM Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>> wrote: Hi Brian, Thanks a lot for your fast response. Please try if you can access this example data file via the shared link: [zip icon]Akzeptanztest_20250320_PG03238_kep101_94_1_2962.d.zip<https://basf-my.sharepoint.com/:u:/g/personal/schnep18_basfad_basf_net/ER6T09UuRZNLlE9Ana8LTDYBrzblpoNW1JYqP-PLL0ftAg?e=HUW455> Best Paul From: Brian Pratt <bs...@pr...<mailto:bs...@pr...>> Sent: Wednesday, November 12, 2025 5:51 PM To: Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>> Cc: su...@pr...<mailto:su...@pr...>; Catharina Erbacher <cat...@ba...<mailto:cat...@ba...>> Subject: [EXT] Re: [proteowizard-support] Missing UV/DAD data in mzML files Sie erhalten nicht häufig E-Mails von bs...@pr...<mailto:bs...@pr...>. Erfahren Sie, warum dies wichtig ist<https://aka.ms/LearnAboutSenderIdentification> Happy to have a look at this - can you provide some sample data? Brian Pratt On Wed, Nov 12, 2025 at 4:55 AM Paul-Albert Anselm Schneide via proteowizard-support <pro...@li...<mailto:pro...@li...>> wrote: Dear ProteoWizard Support Team, We are facing issues with conversion of Bruker raw data files (see picture below) to .mzML format using ProteoWIzard. Specifically, we noticed that there is no UV/DAD information in the converted mzML files. The measurements were conducted on a Bruker TIMS-TOF. Is this a common issue and do you have any suggestions for how we can convert the files into a readable format that stores MS and UV/DAD information? [cid:image003.png@01DCA3E8.723CCE40] Thank you very much in advance! Best Paul Beste Grüße/ Kind regards Dr. Paul-Albert Schneide Laborleiter F&E, Chemometrics@BASF Email: pau...@ba...<mailto:pau...@ba...> Postal Address: BASF SE, RGA/AD, Carl-Bosch-Strasse 38, 67056 Ludwigshafen am Rhein, Germany [cid:image004.png@01DCA3E8.723CCE40] BASF SE, Registered Office: 67056 Ludwigshafen, Germany Registration Court: Amtsgericht Ludwigshafen, Registration No.: HRB 6000 Chairman of the Supervisory Board: Kurt Bock Board of Executive Directors: Markus Kamieth, Chairman; Dirk Elvermann, Michael Heinz, Anup Kothari, Stephan Kothrade, Katja Scharpwinkel _______________________________________________ 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 |
|
From: Brian P. <bs...@pr...> - 2026-02-20 17:17:39
|
Hi Paul,
Using the file you provided back when we started:
After conversion you should, for example, find this towards the end the
output:
<chromatogram index="3" id="DAD: Signal A, 205.0 nm/Bw:4.0 nm Ref
360.0 nm/Bw:100.0 nm" defaultArrayLength="1187">
<cvParam cvRef="MS" accession="MS:1000812" name="absorption
chromatogram" value=""/>
<cvParam cvRef="MS" accession="MS:1000809" name="chromatogram
title" value="DAD: Signal A, 205.0 nm/Bw:4.0 nm Ref 360.0 nm/Bw:100.0 nm"/>
<userParam name="Instrument" value="Agilent ICF System"/>
<binaryDataArrayList count="2">
Up towards the top you should find something like
<software id="pwiz_Reader_Bruker" *version="3.0.26050"*>
<cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard
software" value=""/>
</software>
What's the value for "version" that you see?
Brian
On Fri, Feb 20, 2026 at 1:33 AM Paul-Albert Anselm Schneide <
pau...@ba...> wrote:
> Thank you, Matthew. I am afraid that I cannot find the UV information.
> What is the <cvParam cvRef= > I should search for to find the respective
> data blocks?
>
> And just to make sure we are working with the correct bundle, we use the
> one that can be downloaded here: ProteoWizard: Download
> <https://proteowizard.sourceforge.io/download.html>
>
>
>
> Best
>
> Paul
>
>
>
> *From:* Chambers, Matthew <mat...@gm...>
> *Sent:* Thursday, February 12, 2026 5:09 PM
> *To:* Paul-Albert Anselm Schneide <pau...@ba...>; Brian Pratt <
> bs...@pr...>
> *Cc:* su...@pr...; Catharina Erbacher <
> cat...@ba...>
> *Subject:* Re: [proteowizard-support] [EXT] Re: Missing UV/DAD data in
> mzML files
>
>
>
> It'll show up as chromatograms at the end of the file (before the index).
>
> On Thu, Feb 12, 2026 10:30 AM EST (-0500), Paul-Albert Anselm Schneide via
> proteowizard-support wrote:
>
> Hi Brian,
>
>
>
> Sorry that I have to disturb you again with the Bruker data... We have
> exported some files with the latest version of your parser but still
> struggle to find the DAD information. Could you maybe send me/us the
> documentation for where this can be found in the .xml tree?
>
>
>
> Best
>
> Paul
>
>
>
> *From:* Brian Pratt <bs...@pr...> <bs...@pr...>
> *Sent:* Thursday, January 8, 2026 6:14 PM
> *To:* Paul-Albert Anselm Schneide <pau...@ba...>
> <pau...@ba...>
> *Cc:* Catharina Erbacher <cat...@ba...>
> <cat...@ba...>; su...@pr...
> *Subject:* Re: [EXT] Re: [proteowizard-support] Missing UV/DAD data in
> mzML files
>
>
>
> The work got tangled up with accompanying UI improvements to SeeMS and
> Skyline, and it was just completed yesterday. I was going to notify you
> this morning after the final build and test, which is complete now.
> Download the current package and you should be ready to go. Thanks for your
> help on this.
>
>
>
> Brian
>
>
>
> On Thu, Jan 8, 2026 at 12:56 AM Paul-Albert Anselm Schneide <
> pau...@ba...> wrote:
>
> Hi Brian,
>
>
>
> Hope you had a got start to 2026! Just wanted to ask if you’ve already had
> the time to fix the converter? 😊
>
>
>
> Best
>
> Paul
>
>
>
> *From:* Brian Pratt <bs...@pr...>
> *Sent:* Thursday, December 11, 2025 6:08 PM
> *To:* Paul-Albert Anselm Schneide <pau...@ba...>
> *Cc:* Catharina Erbacher <cat...@ba...>;
> su...@pr...
> *Subject:* Re: [EXT] Re: [proteowizard-support] Missing UV/DAD data in
> mzML files
>
>
>
> I expect I can get this done early next week.
>
>
>
> On Thu, Dec 11, 2025 at 4:32 AM Paul-Albert Anselm Schneide <
> pau...@ba...> wrote:
>
> Dear Brian,
>
>
>
> Thanks a lot for the update and sounds great! Do you have an idea on how
> long it might take to develop the new converter that can parse the UV
> information?
>
>
>
> Best
>
> Paul
>
>
>
> *From:* Brian Pratt <bs...@pr...>
> *Sent:* Wednesday, December 10, 2025 10:53 PM
> *To:* Catharina Erbacher <cat...@ba...>
> *Cc:* Paul-Albert Anselm Schneide <pau...@ba...>;
> su...@pr...
> *Subject:* Re: [EXT] Re: [proteowizard-support] Missing UV/DAD data in
> mzML files
>
>
>
> Just a quick update - I've gotten some good information from our friends
> at Bruker and I'll be moving forward with this.
>
>
>
> Brian
>
>
>
> On Mon, Nov 24, 2025 at 12:26 AM Catharina Erbacher <
> cat...@ba...> wrote:
>
> Hi Brian,
>
>
>
> this is great news! Thanks a lot!
>
>
>
> Kind regards,
>
> Catharina
>
>
>
>
> *Dr. Catharina Erbacher*
> Lab Team Leader LC-MS
>
>
>
> Mobile: +49 151 11795362, Email: cat...@ba...
> Postal Address: BASF SE, RGS/AL, Carl-Bosch-Strasse 38, 67056 Ludwigshafen
> am Rhein, Germany
>
> BASF SE, Registered Office: 67056 Ludwigshafen, Germany
>
> Registration Court: Amtsgericht Ludwigshafen, Registration No.: HRB 6000
>
> Chairman of the Supervisory Board: Kurt Bock
>
> Board of Executive Directors:
>
> Markus Kamieth, Chairman;
>
> Dirk Elvermann, Michael Heinz, Anup Kothari, Stephan Kothrade, Katja
> Scharpwinkel
>
>
>
> Information on data protection can be found here: *https://www.basf.com/global/en/legal/data-protection-at-basf.html
> <https://www.basf.com/global/en/legal/data-protection-at-basf.html>*
>
>
>
> *From:* Brian Pratt <bs...@pr...>
> *Sent:* Saturday, November 22, 2025 2:09 AM
> *To:* Paul-Albert Anselm Schneide <pau...@ba...>
> *Cc:* su...@pr...; Catharina Erbacher <
> cat...@ba...>
> *Subject:* Re: [EXT] Re: [proteowizard-support] Missing UV/DAD data in
> mzML files
>
>
>
> Sie erhalten nicht häufig E-Mails von bs...@pr.... Erfahren
> Sie, warum dies wichtig ist
> <https://aka.ms/LearnAboutSenderIdentification>
>
> Just an update, we're working with Bruker to see if there's some
> readily available code for handling this.
>
>
>
> Brian
>
>
>
> On Tue, Nov 18, 2025 at 12:55 PM Brian Pratt <bs...@pr...>
> wrote:
>
> Unfortunately this looks like a fairly sizeable change - the Bruker API
> doesn't provide this information directly. I can see where it's located in
> a sqlite file, but it's not trivial to interpret and extract. I do agree
> that it's useful information but I can't get to this right away.
>
>
>
> It's also not clear to me just how standard the information is, given that
> it's actually Agilent equipment doing that measurement rather than anything
> Bruker produces?
>
>
>
> On Mon, Nov 17, 2025 at 2:45 PM Paul-Albert Anselm Schneide <
> pau...@ba...> wrote:
>
> Great! Thanks a lot Brian, for getting back to us. Looking forward to
> hearing from you.
>
>
>
> Best
>
> Paul
>
>
>
> *From:* Brian Pratt <bs...@pr...>
> *Sent:* Monday, November 17, 2025 8:14 PM
> *To:* Paul-Albert Anselm Schneide <pau...@ba...>
> *Cc:* su...@pr...; Catharina Erbacher <
> cat...@ba...>
> *Subject:* Re: [EXT] Re: [proteowizard-support] Missing UV/DAD data in
> mzML files
>
>
>
> Sie erhalten nicht häufig E-Mails von bs...@pr.... Erfahren
> Sie, warum dies wichtig ist
> <https://aka.ms/LearnAboutSenderIdentification>
>
> I have the data, thanks, and can confirm that we seem to ignore that
> information. I'll see what can be done about that.
>
>
>
> Brian
>
>
>
> On Fri, Nov 14, 2025 at 12:30 AM Paul-Albert Anselm Schneide <
> pau...@ba...> wrote:
>
> Hi Brian,
>
>
>
> Thanks a lot for your fast response. Please try if you can access this
> example data file via the shared link:
>
> [image: zip icon]Akzeptanztest_20250320_PG03238_kep101_94_1_2962.d.zip
> <https://basf-my.sharepoint.com/:u:/g/personal/schnep18_basfad_basf_net/ER6T09UuRZNLlE9Ana8LTDYBrzblpoNW1JYqP-PLL0ftAg?e=HUW455>
>
>
>
> Best
>
> Paul
>
>
>
> *From:* Brian Pratt <bs...@pr...>
> *Sent:* Wednesday, November 12, 2025 5:51 PM
> *To:* Paul-Albert Anselm Schneide <pau...@ba...>
> *Cc:* su...@pr...; Catharina Erbacher <
> cat...@ba...>
> *Subject:* [EXT] Re: [proteowizard-support] Missing UV/DAD data in mzML
> files
>
>
>
> Sie erhalten nicht häufig E-Mails von bs...@pr.... Erfahren
> Sie, warum dies wichtig ist
> <https://aka.ms/LearnAboutSenderIdentification>
>
> Happy to have a look at this - can you provide some sample data?
>
>
>
> Brian Pratt
>
>
>
> On Wed, Nov 12, 2025 at 4:55 AM Paul-Albert Anselm Schneide via
> proteowizard-support <pro...@li...> wrote:
>
> Dear ProteoWizard Support Team,
>
>
>
> We are facing issues with conversion of Bruker raw data files (see picture
> below) to .mzML format using ProteoWIzard. Specifically, we noticed that
> there is no UV/DAD information in the converted mzML files. The
> measurements were conducted on a Bruker TIMS-TOF. Is this a common issue
> and do you have any suggestions for how we can convert the files into a
> readable format that stores MS and UV/DAD information?
>
>
>
>
>
> Thank you very much in advance!
>
>
>
> Best
>
> Paul
>
>
>
> Beste Grüße/ Kind regards
> * Dr. Paul-Albert Schneide*
> Laborleiter F&E, Chemometrics@BASF
>
>
>
> Email: pau...@ba...
> Postal Address: BASF SE, RGA/AD, Carl-Bosch-Strasse 38, 67056 Ludwigshafen
> am Rhein, Germany
>
> BASF SE, Registered Office: 67056 Ludwigshafen, Germany
>
> Registration Court: Amtsgericht Ludwigshafen, Registration No.: HRB 6000
>
> Chairman of the Supervisory Board: Kurt Bock
>
> Board of Executive Directors:
>
> Markus Kamieth, Chairman;
>
> Dirk Elvermann, Michael Heinz, Anup Kothari, Stephan Kothrade, Katja
> Scharpwinkel
>
>
>
> _______________________________________________
> 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
>
>
>
|
|
From: Paul-Albert A. S. <pau...@ba...> - 2026-02-20 09:33:33
|
Thank you, Matthew. I am afraid that I cannot find the UV information. What is the <cvParam cvRef= > I should search for to find the respective data blocks? And just to make sure we are working with the correct bundle, we use the one that can be downloaded here: ProteoWizard: Download<https://proteowizard.sourceforge.io/download.html> Best Paul From: Chambers, Matthew <mat...@gm...> Sent: Thursday, February 12, 2026 5:09 PM To: Paul-Albert Anselm Schneide <pau...@ba...>; Brian Pratt <bs...@pr...> Cc: su...@pr...; Catharina Erbacher <cat...@ba...> Subject: Re: [proteowizard-support] [EXT] Re: Missing UV/DAD data in mzML files It'll show up as chromatograms at the end of the file (before the index). On Thu, Feb 12, 2026 10:30 AM EST (-0500), Paul-Albert Anselm Schneide via proteowizard-support wrote: Hi Brian, Sorry that I have to disturb you again with the Bruker data... We have exported some files with the latest version of your parser but still struggle to find the DAD information. Could you maybe send me/us the documentation for where this can be found in the .xml tree? Best Paul From: Brian Pratt <bs...@pr...><mailto:bs...@pr...> Sent: Thursday, January 8, 2026 6:14 PM To: Paul-Albert Anselm Schneide <pau...@ba...><mailto:pau...@ba...> Cc: Catharina Erbacher <cat...@ba...><mailto:cat...@ba...>; su...@pr...<mailto:su...@pr...> Subject: Re: [EXT] Re: [proteowizard-support] Missing UV/DAD data in mzML files The work got tangled up with accompanying UI improvements to SeeMS and Skyline, and it was just completed yesterday. I was going to notify you this morning after the final build and test, which is complete now. Download the current package and you should be ready to go. Thanks for your help on this. Brian On Thu, Jan 8, 2026 at 12:56 AM Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>> wrote: Hi Brian, Hope you had a got start to 2026! Just wanted to ask if you’ve already had the time to fix the converter? 😊 Best Paul From: Brian Pratt <bs...@pr...<mailto:bs...@pr...>> Sent: Thursday, December 11, 2025 6:08 PM To: Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>> Cc: Catharina Erbacher <cat...@ba...<mailto:cat...@ba...>>; su...@pr...<mailto:su...@pr...> Subject: Re: [EXT] Re: [proteowizard-support] Missing UV/DAD data in mzML files I expect I can get this done early next week. On Thu, Dec 11, 2025 at 4:32 AM Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>> wrote: Dear Brian, Thanks a lot for the update and sounds great! Do you have an idea on how long it might take to develop the new converter that can parse the UV information? Best Paul From: Brian Pratt <bs...@pr...<mailto:bs...@pr...>> Sent: Wednesday, December 10, 2025 10:53 PM To: Catharina Erbacher <cat...@ba...<mailto:cat...@ba...>> Cc: Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>>; su...@pr...<mailto:su...@pr...> Subject: Re: [EXT] Re: [proteowizard-support] Missing UV/DAD data in mzML files Just a quick update - I've gotten some good information from our friends at Bruker and I'll be moving forward with this. Brian On Mon, Nov 24, 2025 at 12:26 AM Catharina Erbacher <cat...@ba...<mailto:cat...@ba...>> wrote: Hi Brian, this is great news! Thanks a lot! Kind regards, Catharina Dr. Catharina Erbacher Lab Team Leader LC-MS Mobile: +49 151 11795362, Email: cat...@ba...<mailto:cat...@ba...> Postal Address: BASF SE, RGS/AL, Carl-Bosch-Strasse 38, 67056 Ludwigshafen am Rhein, Germany [cid:image001.png@01DCA24D.920A1CB0] BASF SE, Registered Office: 67056 Ludwigshafen, Germany Registration Court: Amtsgericht Ludwigshafen, Registration No.: HRB 6000 Chairman of the Supervisory Board: Kurt Bock Board of Executive Directors: Markus Kamieth, Chairman; Dirk Elvermann, Michael Heinz, Anup Kothari, Stephan Kothrade, Katja Scharpwinkel Information on data protection can be found here: https://www.basf.com/global/en/legal/data-protection-at-basf.html From: Brian Pratt <bs...@pr...<mailto:bs...@pr...>> Sent: Saturday, November 22, 2025 2:09 AM To: Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>> Cc: su...@pr...<mailto:su...@pr...>; Catharina Erbacher <cat...@ba...<mailto:cat...@ba...>> Subject: Re: [EXT] Re: [proteowizard-support] Missing UV/DAD data in mzML files Sie erhalten nicht häufig E-Mails von bs...@pr...<mailto:bs...@pr...>. Erfahren Sie, warum dies wichtig ist<https://aka.ms/LearnAboutSenderIdentification> Just an update, we're working with Bruker to see if there's some readily available code for handling this. Brian On Tue, Nov 18, 2025 at 12:55 PM Brian Pratt <bs...@pr...<mailto:bs...@pr...>> wrote: Unfortunately this looks like a fairly sizeable change - the Bruker API doesn't provide this information directly. I can see where it's located in a sqlite file, but it's not trivial to interpret and extract. I do agree that it's useful information but I can't get to this right away. It's also not clear to me just how standard the information is, given that it's actually Agilent equipment doing that measurement rather than anything Bruker produces? On Mon, Nov 17, 2025 at 2:45 PM Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>> wrote: Great! Thanks a lot Brian, for getting back to us. Looking forward to hearing from you. Best Paul From: Brian Pratt <bs...@pr...<mailto:bs...@pr...>> Sent: Monday, November 17, 2025 8:14 PM To: Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>> Cc: su...@pr...<mailto:su...@pr...>; Catharina Erbacher <cat...@ba...<mailto:cat...@ba...>> Subject: Re: [EXT] Re: [proteowizard-support] Missing UV/DAD data in mzML files Sie erhalten nicht häufig E-Mails von bs...@pr...<mailto:bs...@pr...>. Erfahren Sie, warum dies wichtig ist<https://aka.ms/LearnAboutSenderIdentification> I have the data, thanks, and can confirm that we seem to ignore that information. I'll see what can be done about that. Brian On Fri, Nov 14, 2025 at 12:30 AM Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>> wrote: Hi Brian, Thanks a lot for your fast response. Please try if you can access this example data file via the shared link: [zip icon]Akzeptanztest_20250320_PG03238_kep101_94_1_2962.d.zip<https://basf-my.sharepoint.com/:u:/g/personal/schnep18_basfad_basf_net/ER6T09UuRZNLlE9Ana8LTDYBrzblpoNW1JYqP-PLL0ftAg?e=HUW455> Best Paul From: Brian Pratt <bs...@pr...<mailto:bs...@pr...>> Sent: Wednesday, November 12, 2025 5:51 PM To: Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>> Cc: su...@pr...<mailto:su...@pr...>; Catharina Erbacher <cat...@ba...<mailto:cat...@ba...>> Subject: [EXT] Re: [proteowizard-support] Missing UV/DAD data in mzML files Sie erhalten nicht häufig E-Mails von bs...@pr...<mailto:bs...@pr...>. Erfahren Sie, warum dies wichtig ist<https://aka.ms/LearnAboutSenderIdentification> Happy to have a look at this - can you provide some sample data? Brian Pratt On Wed, Nov 12, 2025 at 4:55 AM Paul-Albert Anselm Schneide via proteowizard-support <pro...@li...<mailto:pro...@li...>> wrote: Dear ProteoWizard Support Team, We are facing issues with conversion of Bruker raw data files (see picture below) to .mzML format using ProteoWIzard. Specifically, we noticed that there is no UV/DAD information in the converted mzML files. The measurements were conducted on a Bruker TIMS-TOF. Is this a common issue and do you have any suggestions for how we can convert the files into a readable format that stores MS and UV/DAD information? [cid:image003.png@01DCA24D.920A1CB0] Thank you very much in advance! Best Paul Beste Grüße/ Kind regards Dr. Paul-Albert Schneide Laborleiter F&E, Chemometrics@BASF Email: pau...@ba...<mailto:pau...@ba...> Postal Address: BASF SE, RGA/AD, Carl-Bosch-Strasse 38, 67056 Ludwigshafen am Rhein, Germany [cid:image004.png@01DCA24D.920A1CB0] BASF SE, Registered Office: 67056 Ludwigshafen, Germany Registration Court: Amtsgericht Ludwigshafen, Registration No.: HRB 6000 Chairman of the Supervisory Board: Kurt Bock Board of Executive Directors: Markus Kamieth, Chairman; Dirk Elvermann, Michael Heinz, Anup Kothari, Stephan Kothrade, Katja Scharpwinkel _______________________________________________ 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 |
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From: Chambers, M. <mat...@gm...> - 2026-02-12 16:08:51
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It'll show up as chromatograms at the end of the file (before the index). On Thu, Feb 12, 2026 10:30 AM EST (-0500), Paul-Albert Anselm Schneide via proteowizard-support wrote: > > Hi Brian, > > Sorry that I have to disturb you again with the Bruker data... We have exported some files with the latest version of your parser but > still struggle to find the DAD information. Could you maybe send me/us the documentation for where this can be found in the .xml tree? > > Best > > Paul > > *From:*Brian Pratt <bs...@pr...> > *Sent:* Thursday, January 8, 2026 6:14 PM > *To:* Paul-Albert Anselm Schneide <pau...@ba...> > *Cc:* Catharina Erbacher <cat...@ba...>; su...@pr... > *Subject:* Re: [EXT] Re: [proteowizard-support] Missing UV/DAD data in mzML files > > The work got tangled up with accompanying UI improvements to SeeMS and Skyline, and it was just completed yesterday. I was going to notify > you this morning after the final build and test, which is complete now. Download the current package and you should be ready to go. Thanks > for your help on this. > > Brian > > On Thu, Jan 8, 2026 at 12:56 AM Paul-Albert Anselm Schneide <pau...@ba...> wrote: > > Hi Brian, > > Hope you had a got start to 2026! Just wanted to ask if you’ve already had the time to fix the converter? 😊 > > Best > > Paul > > *From:*Brian Pratt <bs...@pr...> > *Sent:* Thursday, December 11, 2025 6:08 PM > *To:* Paul-Albert Anselm Schneide <pau...@ba...> > *Cc:* Catharina Erbacher <cat...@ba...>; su...@pr... > *Subject:* Re: [EXT] Re: [proteowizard-support] Missing UV/DAD data in mzML files > > I expect I can get this done early next week. > > On Thu, Dec 11, 2025 at 4:32 AM Paul-Albert Anselm Schneide <pau...@ba...> wrote: > > Dear Brian, > > Thanks a lot for the update and sounds great! Do you have an idea on how long it might take to develop the new converter that can > parse the UV information? > > Best > > Paul > > *From:*Brian Pratt <bs...@pr...> > *Sent:* Wednesday, December 10, 2025 10:53 PM > *To:* Catharina Erbacher <cat...@ba...> > *Cc:* Paul-Albert Anselm Schneide <pau...@ba...>; su...@pr... > *Subject:* Re: [EXT] Re: [proteowizard-support] Missing UV/DAD data in mzML files > > Just a quick update - I've gotten some good information from our friends at Bruker and I'll be moving forward with this. > > Brian > > On Mon, Nov 24, 2025 at 12:26 AM Catharina Erbacher <cat...@ba...> wrote: > > Hi Brian, > > this is great news! Thanks a lot! > > Kind regards, > > Catharina > > * > **Dr. Catharina Erbacher* > Lab Team Leader LC-MS > > Mobile: +49 151 11795362, Email: cat...@ba... > Postal Address: BASF SE, RGS/AL, Carl-Bosch-Strasse 38, 67056 Ludwigshafen am Rhein, Germany > > BASF SE, Registered Office: 67056 Ludwigshafen, Germany > > Registration Court: Amtsgericht Ludwigshafen, Registration No.: HRB 6000 > > Chairman of the Supervisory Board: Kurt Bock > > Board of Executive Directors: > > Markus Kamieth, Chairman; > > Dirk Elvermann, Michael Heinz, Anup Kothari, Stephan Kothrade, Katja Scharpwinkel > > Information on data protection can be found here: _https://www.basf.com/global/en/legal/data-protection-at-basf.html > <https://www.basf.com/global/en/legal/data-protection-at-basf.html>_ > > *From:*Brian Pratt <bs...@pr...> > *Sent:* Saturday, November 22, 2025 2:09 AM > *To:* Paul-Albert Anselm Schneide <pau...@ba...> > *Cc:* su...@pr...; Catharina Erbacher <cat...@ba...> > *Subject:* Re: [EXT] Re: [proteowizard-support] Missing UV/DAD data in mzML files > > > > > Sie erhalten nicht häufig E-Mails von bs...@pr.... Erfahren Sie, warum dies wichtig ist > <https://aka.ms/LearnAboutSenderIdentification> > > > > Just an update, we're working with Bruker to see if there's some readily available code for handling this. > > Brian > > On Tue, Nov 18, 2025 at 12:55 PM Brian Pratt <bs...@pr...> wrote: > > Unfortunately this looks like a fairly sizeable change - the Bruker API doesn't provide this information directly. I can > see where it's located in a sqlite file, but it's not trivial to interpret and extract. I do agree that it's useful > information but I can't get to this right away. > > It's also not clear to me just how standard the information is, given that it's actually Agilent equipment doing that > measurement rather than anything Bruker produces? > > On Mon, Nov 17, 2025 at 2:45 PM Paul-Albert Anselm Schneide <pau...@ba...> wrote: > > Great! Thanks a lot Brian, for getting back to us. Looking forward to hearing from you. > > Best > > Paul > > *From:*Brian Pratt <bs...@pr...> > *Sent:* Monday, November 17, 2025 8:14 PM > *To:* Paul-Albert Anselm Schneide <pau...@ba...> > *Cc:* su...@pr...; Catharina Erbacher <cat...@ba...> > *Subject:* Re: [EXT] Re: [proteowizard-support] Missing UV/DAD data in mzML files > > > > > Sie erhalten nicht häufig E-Mails von bs...@pr.... Erfahren Sie, warum dies wichtig ist > <https://aka.ms/LearnAboutSenderIdentification> > > > > I have the data, thanks, and can confirm that we seem to ignore that information. I'll see what can be done about that. > > Brian > > On Fri, Nov 14, 2025 at 12:30 AM Paul-Albert Anselm Schneide <pau...@ba...> wrote: > > Hi Brian, > > Thanks a lot for your fast response. Please try if you can access this example data file via the shared link: > > zip iconAkzeptanztest_20250320_PG03238_kep101_94_1_2962.d.zip > <https://basf-my.sharepoint.com/:u:/g/personal/schnep18_basfad_basf_net/ER6T09UuRZNLlE9Ana8LTDYBrzblpoNW1JYqP-PLL0ftAg?e=HUW455> > > Best > > Paul > > *From:*Brian Pratt <bs...@pr...> > *Sent:* Wednesday, November 12, 2025 5:51 PM > *To:* Paul-Albert Anselm Schneide <pau...@ba...> > *Cc:* su...@pr...; Catharina Erbacher <cat...@ba...> > *Subject:* [EXT] Re: [proteowizard-support] Missing UV/DAD data in mzML files > > > > > Sie erhalten nicht häufig E-Mails von bs...@pr.... Erfahren Sie, warum dies wichtig ist > <https://aka.ms/LearnAboutSenderIdentification> > > > > Happy to have a look at this - can you provide some sample data? > > Brian Pratt > > On Wed, Nov 12, 2025 at 4:55 AM Paul-Albert Anselm Schneide via proteowizard-support > <pro...@li...> wrote: > > Dear ProteoWizard Support Team, > > We are facing issues with conversion of Bruker raw data files (see picture below) to .mzML format using > ProteoWIzard. Specifically, we noticed that there is no UV/DAD information in the converted mzML files. The > measurements were conducted on a Bruker TIMS-TOF. Is this a common issue and do you have any suggestions for > how we can convert the files into a readable format that stores MS and UV/DAD information? > > Thank you very much in advance! > > Best > > Paul > > Beste Grüße/ Kind regards* > Dr. Paul-Albert Schneide* > Laborleiter F&E, Chemometrics@BASF > > Email: pau...@ba... <mailto:pau...@ba...> > Postal Address: BASF SE, RGA/AD, Carl-Bosch-Strasse 38, 67056 Ludwigshafen am Rhein, Germany > > BASF SE, Registered Office: 67056 Ludwigshafen, Germany > > Registration Court: Amtsgericht Ludwigshafen, Registration No.: HRB 6000 > > Chairman of the Supervisory Board: Kurt Bock > > Board of Executive Directors: > > Markus Kamieth, Chairman; > > Dirk Elvermann, Michael Heinz, Anup Kothari, Stephan Kothrade, Katja Scharpwinkel > > _______________________________________________ > 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 |
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From: Paul-Albert A. S. <pau...@ba...> - 2026-02-12 15:31:14
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Hi Brian, Sorry that I have to disturb you again with the Bruker data... We have exported some files with the latest version of your parser but still struggle to find the DAD information. Could you maybe send me/us the documentation for where this can be found in the .xml tree? Best Paul From: Brian Pratt <bs...@pr...> Sent: Thursday, January 8, 2026 6:14 PM To: Paul-Albert Anselm Schneide <pau...@ba...> Cc: Catharina Erbacher <cat...@ba...>; su...@pr... Subject: Re: [EXT] Re: [proteowizard-support] Missing UV/DAD data in mzML files The work got tangled up with accompanying UI improvements to SeeMS and Skyline, and it was just completed yesterday. I was going to notify you this morning after the final build and test, which is complete now. Download the current package and you should be ready to go. Thanks for your help on this. Brian On Thu, Jan 8, 2026 at 12:56 AM Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>> wrote: Hi Brian, Hope you had a got start to 2026! Just wanted to ask if you’ve already had the time to fix the converter? 😊 Best Paul From: Brian Pratt <bs...@pr...<mailto:bs...@pr...>> Sent: Thursday, December 11, 2025 6:08 PM To: Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>> Cc: Catharina Erbacher <cat...@ba...<mailto:cat...@ba...>>; su...@pr...<mailto:su...@pr...> Subject: Re: [EXT] Re: [proteowizard-support] Missing UV/DAD data in mzML files I expect I can get this done early next week. On Thu, Dec 11, 2025 at 4:32 AM Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>> wrote: Dear Brian, Thanks a lot for the update and sounds great! Do you have an idea on how long it might take to develop the new converter that can parse the UV information? Best Paul From: Brian Pratt <bs...@pr...<mailto:bs...@pr...>> Sent: Wednesday, December 10, 2025 10:53 PM To: Catharina Erbacher <cat...@ba...<mailto:cat...@ba...>> Cc: Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>>; su...@pr...<mailto:su...@pr...> Subject: Re: [EXT] Re: [proteowizard-support] Missing UV/DAD data in mzML files Just a quick update - I've gotten some good information from our friends at Bruker and I'll be moving forward with this. Brian On Mon, Nov 24, 2025 at 12:26 AM Catharina Erbacher <cat...@ba...<mailto:cat...@ba...>> wrote: Hi Brian, this is great news! Thanks a lot! Kind regards, Catharina Dr. Catharina Erbacher Lab Team Leader LC-MS Mobile: +49 151 11795362, Email: cat...@ba...<mailto:cat...@ba...> Postal Address: BASF SE, RGS/AL, Carl-Bosch-Strasse 38, 67056 Ludwigshafen am Rhein, Germany [cid:image001.png@01DC9C3C.F0B66B90] BASF SE, Registered Office: 67056 Ludwigshafen, Germany Registration Court: Amtsgericht Ludwigshafen, Registration No.: HRB 6000 Chairman of the Supervisory Board: Kurt Bock Board of Executive Directors: Markus Kamieth, Chairman; Dirk Elvermann, Michael Heinz, Anup Kothari, Stephan Kothrade, Katja Scharpwinkel Information on data protection can be found here: https://www.basf.com/global/en/legal/data-protection-at-basf.html From: Brian Pratt <bs...@pr...<mailto:bs...@pr...>> Sent: Saturday, November 22, 2025 2:09 AM To: Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>> Cc: su...@pr...<mailto:su...@pr...>; Catharina Erbacher <cat...@ba...<mailto:cat...@ba...>> Subject: Re: [EXT] Re: [proteowizard-support] Missing UV/DAD data in mzML files Sie erhalten nicht häufig E-Mails von bs...@pr...<mailto:bs...@pr...>. Erfahren Sie, warum dies wichtig ist<https://aka.ms/LearnAboutSenderIdentification> Just an update, we're working with Bruker to see if there's some readily available code for handling this. Brian On Tue, Nov 18, 2025 at 12:55 PM Brian Pratt <bs...@pr...<mailto:bs...@pr...>> wrote: Unfortunately this looks like a fairly sizeable change - the Bruker API doesn't provide this information directly. I can see where it's located in a sqlite file, but it's not trivial to interpret and extract. I do agree that it's useful information but I can't get to this right away. It's also not clear to me just how standard the information is, given that it's actually Agilent equipment doing that measurement rather than anything Bruker produces? On Mon, Nov 17, 2025 at 2:45 PM Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>> wrote: Great! Thanks a lot Brian, for getting back to us. Looking forward to hearing from you. Best Paul From: Brian Pratt <bs...@pr...<mailto:bs...@pr...>> Sent: Monday, November 17, 2025 8:14 PM To: Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>> Cc: su...@pr...<mailto:su...@pr...>; Catharina Erbacher <cat...@ba...<mailto:cat...@ba...>> Subject: Re: [EXT] Re: [proteowizard-support] Missing UV/DAD data in mzML files Sie erhalten nicht häufig E-Mails von bs...@pr...<mailto:bs...@pr...>. Erfahren Sie, warum dies wichtig ist<https://aka.ms/LearnAboutSenderIdentification> I have the data, thanks, and can confirm that we seem to ignore that information. I'll see what can be done about that. Brian On Fri, Nov 14, 2025 at 12:30 AM Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>> wrote: Hi Brian, Thanks a lot for your fast response. Please try if you can access this example data file via the shared link: [zip icon]Akzeptanztest_20250320_PG03238_kep101_94_1_2962.d.zip<https://basf-my.sharepoint.com/:u:/g/personal/schnep18_basfad_basf_net/ER6T09UuRZNLlE9Ana8LTDYBrzblpoNW1JYqP-PLL0ftAg?e=HUW455> Best Paul From: Brian Pratt <bs...@pr...<mailto:bs...@pr...>> Sent: Wednesday, November 12, 2025 5:51 PM To: Paul-Albert Anselm Schneide <pau...@ba...<mailto:pau...@ba...>> Cc: su...@pr...<mailto:su...@pr...>; Catharina Erbacher <cat...@ba...<mailto:cat...@ba...>> Subject: [EXT] Re: [proteowizard-support] Missing UV/DAD data in mzML files Sie erhalten nicht häufig E-Mails von bs...@pr...<mailto:bs...@pr...>. Erfahren Sie, warum dies wichtig ist<https://aka.ms/LearnAboutSenderIdentification> Happy to have a look at this - can you provide some sample data? Brian Pratt On Wed, Nov 12, 2025 at 4:55 AM Paul-Albert Anselm Schneide via proteowizard-support <pro...@li...<mailto:pro...@li...>> wrote: Dear ProteoWizard Support Team, We are facing issues with conversion of Bruker raw data files (see picture below) to .mzML format using ProteoWIzard. Specifically, we noticed that there is no UV/DAD information in the converted mzML files. The measurements were conducted on a Bruker TIMS-TOF. Is this a common issue and do you have any suggestions for how we can convert the files into a readable format that stores MS and UV/DAD information? [cid:image003.png@01DC9C3C.F0B66B90] Thank you very much in advance! Best Paul Beste Grüße/ Kind regards Dr. Paul-Albert Schneide Laborleiter F&E, Chemometrics@BASF Email: pau...@ba...<mailto:pau...@ba...> Postal Address: BASF SE, RGA/AD, Carl-Bosch-Strasse 38, 67056 Ludwigshafen am Rhein, Germany [cid:image004.png@01DC9C3C.F0B66B90] BASF SE, Registered Office: 67056 Ludwigshafen, Germany Registration Court: Amtsgericht Ludwigshafen, Registration No.: HRB 6000 Chairman of the Supervisory Board: Kurt Bock Board of Executive Directors: Markus Kamieth, Chairman; Dirk Elvermann, Michael Heinz, Anup Kothari, Stephan Kothrade, Katja Scharpwinkel _______________________________________________ proteowizard-support mailing list pro...@li...<mailto:pro...@li...> https://lists.sourceforge.net/lists/listinfo/proteowizard-support |
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From: Brian P. <bs...@pr...> - 2026-02-09 14:39:27
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Hi Chris, I believe you can obtain that python code from the authors of the manuscript you cited. It's not anything we maintain or distribute. Best regards, Brian Pratt On Mon, Feb 9, 2026 at 1:33 AM Christopher Thorley <chr...@vr...> wrote: > Dear ProteoWizard, > > I wonder if you can help. We are trying to setup data processing > capability on a Thermo Exploris 480 Mass Spec in Hybrid DIA mode > using ProteoWizard. > > Documentation (Title Supplement "Hyrid-DIA: Intelligent Data Acquisition > Integrates Targeted and Discovery Proteomics to analyze Phospho signaling > in Single Spheroids") we are using referring to a ProteoWizard > installation which references a python file called *MSx_Extractor.py.* > > We have installed *ProteoWizard 3.0.26029 *which gives us the MSConverter > GUI but no evidence of the *MSx_Extractor.py* within the installation > directory. > > Are the docs we are using just out of date? Is there another process we > should follow with the latest version of ProteoWizard for this usecase? > > Thanks Chris > > > This email message and any attachments are confidential and intended for > use by the addressee(s) only. If you are not the intended recipient, please > notify me immediately by replying to this message, and destroy all copies > of this message and any attachments. Thank you. > For information on how Vertex processes personal data, please see our Global > Privacy Notice <https://www.vrtx.com/international-privacy/> > _______________________________________________ > proteowizard-support mailing list > pro...@li... > https://lists.sourceforge.net/lists/listinfo/proteowizard-support > |
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From: Christopher T. <chr...@vr...> - 2026-02-09 09:33:41
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Dear ProteoWizard, I wonder if you can help. We are trying to setup data processing capability on a Thermo Exploris 480 Mass Spec in Hybrid DIA mode using ProteoWizard. Documentation (Title Supplement "Hyrid-DIA: Intelligent Data Acquisition Integrates Targeted and Discovery Proteomics to analyze Phosphosignaling in Single Spheroids") we are using referring to a ProteoWizard installation which references a python file called MSx_Extractor.py. We have installed ProteoWizard 3.0.26029 which gives us the MSConverter GUI but no evidence of the MSx_Extractor.py within the installation directory. Are the docs we are using just out of date? Is there another process we should follow with the latest version of ProteoWizard for this usecase? Thanks Chris This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you. For information on how Vertex processes personal data, please see our Global Privacy Notice<https://www.vrtx.com/international-privacy/> |
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From: Connie M. P. <con...@ke...> - 2026-02-04 16:47:39
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Hi Nick, Thank you for this. The issue was a compatibility problem with the script indexing within the file, which was appropriate for when the script was developed but different in the newer version. The older version has fixed the problem. Best regards, Connie From: Nick Shulman <nicksh@u.washington.edu> Sent: Wednesday, 4 February 2026 16:43 To: Connie Mae Petroeschevsky <con...@ke...> Cc: su...@pr... Subject: Re: [proteowizard-support] Older version availability I have some old ProteoWizard installers here: https://proteome.gs.washington.edu/~nicksh/ProteowizardInstallers/ Version 3.0.22223<https://proteome.gs.washington.edu/~nicksh/ProteowizardInstallers/pwiz-setup-3.0.22223.8c29d2e-x86_64.msi> is the closest in time to the version you are asking for. Are you getting some sort of error when you run your script with the current version of MSConvert? -- Nick On Wed, Feb 4, 2026 at 4:50 AM Connie Mae Petroeschevsky <con...@ke...<mailto:con...@ke...>> wrote: Dear ProteoWizard support, I am looking to install an older version of MS Convert that is compatible with a script that I need to run. The version is MSConvert: ProteoWizard 3.0.22271.8860818. I can’t seem to access the TeamCity link with the older version. Could you please provide an updated link? Many Thanks, Connie --- Dr. Connie Petroeschevsky Postdoctoral Researcher - Lanekoff Group Centre of Excellence: Chemical Mechanisms of Life Dept. of Chemistry for Life Sciences (BMC), Uppsala University mail: con...@ke...<mailto:con...@ke...> När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy _______________________________________________ proteowizard-support mailing list pro...@li...<mailto:pro...@li...> https://lists.sourceforge.net/lists/listinfo/proteowizard-support VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. |
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From: Nick S. <nicksh@u.washington.edu> - 2026-02-04 15:42:56
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I have some old ProteoWizard installers here: https://proteome.gs.washington.edu/~nicksh/ProteowizardInstallers/ Version 3.0.22223 <https://proteome.gs.washington.edu/~nicksh/ProteowizardInstallers/pwiz-setup-3.0.22223.8c29d2e-x86_64.msi> is the closest in time to the version you are asking for. Are you getting some sort of error when you run your script with the current version of MSConvert? -- Nick On Wed, Feb 4, 2026 at 4:50 AM Connie Mae Petroeschevsky < con...@ke...> wrote: > Dear ProteoWizard support, > > > > I am looking to install an older version of MS Convert that is compatible > with a script that I need to run. The version is MSConvert: ProteoWizard > 3.0.22271.8860818. I can’t seem to access the TeamCity link with the > older version. Could you please provide an updated link? > > > > Many Thanks, > > Connie > > > > --- > > *Dr. Connie Petroeschevsky* > > Postdoctoral Researcher - Lanekoff Group > > Centre of Excellence: Chemical Mechanisms of Life > > Dept. of Chemistry for Life Sciences (BMC), Uppsala University > > mail: con...@ke... > > > > > > > > > > > När du har kontakt med oss på Uppsala universitet med e-post så innebär > det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör > det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ > > E-mailing Uppsala University means that we will process your personal > data. For more information on how this is performed, please read here: > http://www.uu.se/en/about-uu/data-protection-policy > _______________________________________________ > proteowizard-support mailing list > pro...@li... > https://lists.sourceforge.net/lists/listinfo/proteowizard-support > |
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From: Connie M. P. <con...@ke...> - 2026-02-04 12:50:02
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Dear ProteoWizard support, I am looking to install an older version of MS Convert that is compatible with a script that I need to run. The version is MSConvert: ProteoWizard 3.0.22271.8860818. I can’t seem to access the TeamCity link with the older version. Could you please provide an updated link? Many Thanks, Connie --- Dr. Connie Petroeschevsky Postdoctoral Researcher - Lanekoff Group Centre of Excellence: Chemical Mechanisms of Life Dept. of Chemistry for Life Sciences (BMC), Uppsala University mail: con...@ke...<mailto:con...@ke...> När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy |
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