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From: Davide B. <dav...@ma...> - 2024-04-07 19:43:52
|
<html><head></head><body><div style="font-family: Verdana;font-size: 12.0px;"><div>Hello,</div> <div> </div> <div>I have a Linux Mint 20 machine, and I have an urgent need to make this proteowizard docker image work.</div> <div> </div> <div>I tried to launch a docker container with proteowizard utilities inside of it, but it seems that i cannot run it interactively, I receive an help page instead: </div> <div>docker run -it --rm -v /home/pc/master/deadlines_assignments_papers_lectures/proteomics/Exercises/exercise-1-denovo:/data chambm/pwiz-skyline-i-agree-to-the-vendor-licenses<br/> Usage: msconvert [options] [filemasks]<br/> Convert mass spec data file formats.</div> <div>Return value: # of failed files.<br/> </div> <div>When I try to use seeMS utility, which should be fundamental in order to visualise peaks and understanding what is going on, I continue to receive error messages of every type:</div> <div>pc@pc:~$ docker run -it --rm \<br/> > -v /home/pc/master/deadlines_assignments_papers_lectures/proteomics/Exercises:/data \<br/> > --env DISPLAY=$DISPLAY --volume /tmp/.X11-unix:/tmp/.X11-unix \<br/> > chambm/pwiz-skyline-i-agree-to-the-vendor-licenses \<br/> > wine seeMS /exercise-1-denovo/Ex1-HCD-OT-OT.raw<br/> X Error of failed request: BadValue (integer parameter out of range for operation)<br/> Major opcode of failed request: 130 (MIT-SHM)<br/> Minor opcode of failed request: 3 (X_ShmPutImage)<br/> Value in failed request: 0x560<br/> Serial number of failed request: 2164<br/> Current serial number in output stream: 2168<br/> pc@pc:~$ docker run -it --rm -e WINEDEBUG=-all -v /home/pc/master/deadlines_assignments_papers_lectures/proteomics/Exercises:/data chambm/pwiz-skyline-i-agree-to-the-vendor-licenses wine seeMS /data/Ex1-HCD-OT-OT.raw<br/> pc@pc:~$ docker run -it --rm -e WINEDEBUG=-all -v /home/pc/master/deadlines_assignments_papers_lectures/proteomics/Exercises/exercise-1-denovo:/data chambm/pwiz-skyline-i-agree-to-the-vendor-licenses wine seeMS Ex1-HCD-OT-OT.raw<br/> pc@pc:~$ docker run -it --rm -v /home/pc/master/deadlines_assignments_papers_lectures/proteomics/Exercises/exercise-1-denovo:/data --volume /tmp/.X11-unix:/tmp/.X11-unix chambm/pwiz-skyline-i-agree-to-the-vendor-licenses wine seeMS Ex1-HCD-OT-OT.raw<br/> pc@pc:~$ docker run -it --rm \<br/> > -e WINEDEBUGSHM=-all \<br/> > -v /home/pc/master/deadlines_assignments_papers_lectures/proteomics/Exercises/exercise-1-denovo:/data \<br/> > --env DISPLAY=$DISPLAY \<br/> > --volume /tmp/.X11-unix:/tmp/.X11-unix \<br/> > chambm/pwiz-skyline-i-agree-to-the-vendor-licenses \<br/> > wine seeMS /data/Ex1-HCD-OT-OT.raw<br/> X Error of failed request: BadValue (integer parameter out of range for operation)<br/> Major opcode of failed request: 130 (MIT-SHM)<br/> Minor opcode of failed request: 3 (X_ShmPutImage)<br/> Value in failed request: 0x560<br/> Serial number of failed request: 2163<br/> Current serial number in output stream: 2167<br/> Are you sure that the utility for visualising raw ms data is included in the docker image? It seems that i cannot launch seeMS in any way.</div> <div> </div> <div>On the other hand, the command :</div> <div> </div> <div>docker run -it --rm -e WINEDEBUG=-all -v /home/pc/master/deadlines_assignments_papers_lectures/proteomics/Exercises/exercise-1-denovo:/data chambm/pwiz-skyline-i-agree-to-the-vendor-licenses wine msconvert /data/Ex1-HCD-OT-OT.raw works fine:</div> <div> </div> <div>format: mzML m/z: Compression-Zlib, 64-bit intensity: Compression-Zlib, 32-bit rt: Compression-Zlib, 64-bit ByteOrder_LittleEndian indexed="true" outputPath: . extension: .mzML contactFilename: runIndexSet: spectrum list filters: chromatogram list filters: filenames: /data\Ex1-HCD-OT-OT.raw processing file: /data\Ex1-HCD-OT-OT.raw calculating source file checksums writing output file: .\Ex1-HCD-OT-OT.mzML</div> <div> </div> <div>I also used xhost +local:pc, as suggested, regarding possible issues with X11 forwarding. </div> <div> </div> <div>pc@pc:~$ wine --version<br/> wine-9.0<br/> </div></div></body></html> |
From: Chambers, M. <mat...@gm...> - 2024-04-05 15:55:22
|
Hi Charlie, Sorry for the delay. This was actually an easy one to answer after viewing your mzXML: it only has a single spectrum! Mspicture works by plotting 3d spectra where X is m/z, Y is time, and Z is intensity (represented as a color scale). So it won't work with a single spectrum and it also needs scan times in the data (but it should give a better error message). Any LC data will have times, but I'm not sure about MALDI. Are you trying to do imaging MALDI? Is that spectrum from just a single MALDI spot? -Matt On 3/27/2024 12:37 PM, Charles Sweet wrote: > Hi Matt, > Thanks for the followup. A sample of the mzXML files I'm using is attached, and the command's I've tried are: > > mspicture test.mzXML > mspicture --mzLow=1200 --mzHigh=2000 test.mzXML > > Both return the following: > [Pseudo2DGel::Impl::update] unknown mass analyzer type, assuming ion trap > vector::_M_range_check > > Is it possible that this is due to it being a MALDI spectrum and not LC-MS? I was hoping to adapt the tool go generate gel-view versions > of simple MALDI spectra but perhaps this is not possible. > > Best. > Charlie > > -------------------------------------------------------------------------------------------------------- > Charles R. Sweet, Ph.D. > Associate Professor of Biochemistry and Biology > Chemistry Department > United States Naval Academy > Annapolis, MD 21402 > sw...@us... > https://sites.google.com/usna.edu/sweetlab/home/ > (410) 293-6643 (office) > (410) 293-2218 (fax) > > ** For use by intended recipient only. If you are not the intended > recipient, delete this email and notify the sender. ** > -------------------------------------------------------------------------------------------------------- > > > On Wed, Mar 27, 2024 at 11:05 AM Chambers, Matthew <mat...@gm...> wrote: > > Hi Charlie, > > This usually indicates that mspicture is making an assumption about the input data that isn't holding true. If you provide an example > file > and command-line triggering the error I can look into fixing it or at least giving a better error message. > > Thanks, > -Matt > > > On 3/25/2024 6:03 PM, Charles Sweet via proteowizard-support wrote: > > Dear Proteowizard support, > > I am using mspicture in linux command line with Proteowizard installed through Bioconda. (conda v. 23.5, Proteowizard > v.3.0.9992). I > > would like to generate a "gel image" (preferably nearly 1D) of an mzXML spectrum (MALDI collected on Bruker Microflex), but when I > attempt > > this either with or without mass ranges I get the error "vector::M_range_check" > > > > Please advise on what, if anything I can do to get mspicture working with this file. Thanks! > > > > Best regards, > > Charlie Sweet > |
From: Chambers, M. <mat...@gm...> - 2024-04-05 15:51:14
|
Hi Alexandre, You haven't really said what you mean by "obtain a good result" or what kind of results you've been able to obtain. Any time you're dealing with IMS though you need to pay extra attention to what the downstream software is expecting (and capable of dealing with). Without more information it's not possible to help. "--ignoreMissingZeroSamples" is a speed optimization if you plan to read profile data without applying your own centroiding (e.g. you have known m/z windows you want to extract intensities from). Also I think it only applies to Agilent data. -Matt On 4/2/2024 7:14 AM, Alexandre García Barrera via proteowizard-support wrote: > Hello, > > Thank you very much for your assistance. I'm trying to convert files from a Cyclic IMS acquired in HDMSe mode (Full SCan+AIF with > mobility) to mzML format. The data is acquired with Masslynx, the file has 3 functions (the 3rd one for leucine) in profile. I have tried > to convert them in different ways but I never manage to obtain a good result. > > I have consulted the forum, where someone had issues performing the conversion of this type of data but this problem was fixed: > https://github.com/ProteoWizard/pwiz/issues/1166 > https://github.com/ProteoWizard/pwiz/pull/1420 > > I can't find the filter/parameter --ignoreMissingZeroSamples and I'm not very familiar yet with data conversion. Could you please help me > choose appropriate parameters to convert this type of file to mzML format in profile and/or centroid? Thank you very much for your attention. > > Best regards, > > > -- > *Alexandre García* |
From: Chambers, M. <mat...@gm...> - 2024-04-05 15:47:00
|
Right, true will use vendor centroiding if possible and false will always use local maxima peak picking (which is terrible). On 4/5/2024 11:41 AM, Ronan Daly wrote: > That great Matthew, so can I take it that the old format (using true) will use the vendor centroiding? > > Many thanks, > > Ronan > > -- > Dr Rónán Daly > Head of AI/ML > MVLS Shared Research Facilities (SRF) > University of Glasgow > ron...@gl... > >> On 5 Apr 2024, at 16:39, Chambers, Matthew <mat...@gm...> wrote: >> >> Hi Ronan, >> >> You presume correctly. The format was updated when another non-vendor algorithm for centroiding was added (CWT/CantWaiT/Continuous >> Waveform Transform). Both formats are supported for backward compatibility. >> >> Hope this helps, >> -Matt >> >> >> On 4/5/2024 8:40 AM, Ronan Daly wrote: >>> Hi there, >>> >>> I'm looking at the documentation for the msconvert peakPicking filter and it says it should be in this format: >>> >>> peakPicking [<PickerType> [snr=<minimum signal-to-noise ratio>] [peakSpace=<minimum peak spacing>] [msLevel=<ms_levels>]] >>> >>> where PickerType should be vendor or cwt. So I would expect the filter to look like this: >>> >>> peakPicking vendor msLevel=1- >>> >>> >>> However, further down the documentation is gives examples that look like this >>> >>> peakPicking true 1- >>> >>> Can I ask what does true mean in this context? I'm presuming this might be some old syntax? >>> >>> Many thanks, >>> >>> Ronan > |
From: Ronan D. <Ron...@gl...> - 2024-04-05 15:41:14
|
That great Matthew, so can I take it that the old format (using true) will use the vendor centroiding? Many thanks, Ronan -- Dr Rónán Daly Head of AI/ML MVLS Shared Research Facilities (SRF) University of Glasgow ron...@gl... On 5 Apr 2024, at 16:39, Chambers, Matthew <mat...@gm...> wrote: Hi Ronan, You presume correctly. The format was updated when another non-vendor algorithm for centroiding was added (CWT/CantWaiT/Continuous Waveform Transform). Both formats are supported for backward compatibility. Hope this helps, -Matt On 4/5/2024 8:40 AM, Ronan Daly wrote: Hi there, I'm looking at the documentation for the msconvert peakPicking filter and it says it should be in this format: peakPicking [<PickerType> [snr=<minimum signal-to-noise ratio>] [peakSpace=<minimum peak spacing>] [msLevel=<ms_levels>]] where PickerType should be vendor or cwt. So I would expect the filter to look like this: peakPicking vendor msLevel=1- However, further down the documentation is gives examples that look like this peakPicking true 1- Can I ask what does true mean in this context? I'm presuming this might be some old syntax? Many thanks, Ronan |
From: Chambers, M. <mat...@gm...> - 2024-04-05 15:39:20
|
Hi Ronan, You presume correctly. The format was updated when another non-vendor algorithm for centroiding was added (CWT/CantWaiT/Continuous Waveform Transform). Both formats are supported for backward compatibility. Hope this helps, -Matt On 4/5/2024 8:40 AM, Ronan Daly wrote: > Hi there, > > I'm looking at the documentation for the msconvert peakPicking filter and it says it should be in this format: > > peakPicking [<PickerType> [snr=<minimum signal-to-noise ratio>] [peakSpace=<minimum peak spacing>] [msLevel=<ms_levels>]] > > where PickerType should be vendor or cwt. So I would expect the filter to look like this: > > peakPicking vendor msLevel=1- > > > However, further down the documentation is gives examples that look like this > > peakPicking true 1- > > Can I ask what does true mean in this context? I'm presuming this might be some old syntax? > > Many thanks, > > Ronan |
From: Ronan D. <Ron...@gl...> - 2024-04-05 12:41:11
|
Hi there, I'm looking at the documentation for the msconvert peakPicking filter and it says it should be in this format: peakPicking [<PickerType> [snr=<minimum signal-to-noise ratio>] [peakSpace=<minimum peak spacing>] [msLevel=<ms_levels>]] where PickerType should be vendor or cwt. So I would expect the filter to look like this: peakPicking vendor msLevel=1- However, further down the documentation is gives examples that look like this peakPicking true 1- Can I ask what does true mean in this context? I'm presuming this might be some old syntax? Many thanks, Ronan -- Dr Rónán Daly Head of AI/ML MVLS Shared Research Facilities (SRF) University of Glasgow ron...@gl... |
From: Chambers, M. <mat...@gm...> - 2024-04-03 16:58:56
|
I doubt it: they seem to be empty. Only way to be sure is to try it and see though. :) On 4/3/2024 12:57 PM, Liang, George C wrote: > Hi Matt, > > Thank you. That solved the problem. Would moving those files cause issues for other softwares (e.g. GRITS toolbox) when reading the .mzML > files. > > Best Regards, > George > > -------------------------------------------------------------------------------------------------------------------------------------------- > *From:* Chambers, Matthew <mat...@gm...> > *Sent:* Wednesday, April 3, 2024 11:31 AM > *To:* su...@pr... <su...@pr...>; Liang, George C <Geo...@st...> > *Cc:* Brian Pratt <bs...@pr...> > *Subject:* Re: [proteowizard-support] Problem with Water file conversion > > > Thanks for providing an example raw file. It's getting an error reading the analog channels, a feature which was added recently. I'll add > error handling for that to skip the channels with a warning message. In the meantime I think you can skip those channels by moving the > CHRO*.* files to a subdir in your .raw folder. > > Hope this helps, > -Matt > > > On 4/2/2024 2:05 PM, Brian Pratt wrote: > > It's possible that the file is damaged. Can you open it in any other software? > > > On Tue, Apr 2, 2024 at 8:38 AM Liang, George C <Geo...@st... <mailto:Geo...@st...>> wrote: > > Hello, > > I am trying to convert a Waters qtof MRM raw file. The file is attached (04022024_Glycan_1.raw 1.zip > <https://urldefense.com/v3/__https://studentuml-my.sharepoint.com/:u:/g/personal/george_liang_student_uml_edu/EYhcJGPtYZtPuFz1LJ4oIPEB1oSwbqJt5jg2lZB2_ATknQ__;!!NcNAlj2UIVkjDA!9xW43XAtnBjNlUdfB3i0OWJXtvA47QFp5J2t5esEBm2tV0T8OrlQFTsVNHXL8llAUK8WHNbvDFsuqwqnKGEqMCHxuOWWsLog85A$>). > But when I try to use the Proteowizard to convert to .mzML, I get the following errors: > > C:\Users\Administrator\OneDrive\Desktop\George\Water Raw\04022024_Glycan_1.raw > ------------------------------ > Starting...Opening file "C:\Users\Administrator\OneDrive\Desktop\George\Water Raw\04022024_Glycan_1.raw" for read... > Failed - System.Exception: [pwiz::CLI::msdata::ReaderList::read] Unhandled exception: Generic Error > at pwiz.CLI.msdata.ReaderList.read(String filename, MSDataList results, ReaderConfig config) > at MSConvertGUI.MainLogic.processFile(String filename, Config config, ReaderList readers, Map`2 usedOutputFilenames) > at MSConvertGUI.MainLogic.Go(Config config, Map`2 usedOutputFilenames) > > What is the issue? I was able to convert other files with MRM raw files before but only when there was no signal detected. Is the > file too big? Thank you for your time and help. > > Best Regards, > George > |
From: Liang, G. C <Geo...@st...> - 2024-04-03 16:57:48
|
Hi Matt, Thank you. That solved the problem. Would moving those files cause issues for other softwares (e.g. GRITS toolbox) when reading the .mzML files. Best Regards, George ________________________________ From: Chambers, Matthew <mat...@gm...> Sent: Wednesday, April 3, 2024 11:31 AM To: su...@pr... <su...@pr...>; Liang, George C <Geo...@st...> Cc: Brian Pratt <bs...@pr...> Subject: Re: [proteowizard-support] Problem with Water file conversion This Message Is From an Untrusted Sender You have not previously corresponded with this sender. Report Suspicious<https://us-phishalarm-ewt.proofpoint.com/EWT/v1/NcNAlj2UIVkjDA!6UAdK76An3tM-E88Wt4pPgQEiCGPJe5m0q9dOzDvpCaqnVahtPaGBDyswKzNoHTkFggG3OYwu96drOvoC45gpC0flk_FFSVocqkvIpoBhh4$> Hi George, Thanks for providing an example raw file. It's getting an error reading the analog channels, a feature which was added recently. I'll add error handling for that to skip the channels with a warning message. In the meantime I think you can skip those channels by moving the CHRO*.* files to a subdir in your .raw folder. Hope this helps, -Matt On 4/2/2024 2:05 PM, Brian Pratt wrote: It's possible that the file is damaged. Can you open it in any other software? On Tue, Apr 2, 2024 at 8:38 AM Liang, George C <Geo...@st...<mailto:Geo...@st...>> wrote: Hello, I am trying to convert a Waters qtof MRM raw file. The file is attached ([https://res.cdn.office.net/assets/mail/file-icon/png/zip_16x16.png]04022024_Glycan_1.raw 1.zip<https://urldefense.com/v3/__https://studentuml-my.sharepoint.com/:u:/g/personal/george_liang_student_uml_edu/EYhcJGPtYZtPuFz1LJ4oIPEB1oSwbqJt5jg2lZB2_ATknQ__;!!NcNAlj2UIVkjDA!9xW43XAtnBjNlUdfB3i0OWJXtvA47QFp5J2t5esEBm2tV0T8OrlQFTsVNHXL8llAUK8WHNbvDFsuqwqnKGEqMCHxuOWWsLog85A$>). But when I try to use the Proteowizard to convert to .mzML, I get the following errors: C:\Users\Administrator\OneDrive\Desktop\George\Water Raw\04022024_Glycan_1.raw ------------------------------ Starting...Opening file "C:\Users\Administrator\OneDrive\Desktop\George\Water Raw\04022024_Glycan_1.raw" for read... Failed - System.Exception: [pwiz::CLI::msdata::ReaderList::read] Unhandled exception: Generic Error at pwiz.CLI.msdata.ReaderList.read(String filename, MSDataList results, ReaderConfig config) at MSConvertGUI.MainLogic.processFile(String filename, Config config, ReaderList readers, Map`2 usedOutputFilenames) at MSConvertGUI.MainLogic.Go(Config config, Map`2 usedOutputFilenames) What is the issue? I was able to convert other files with MRM raw files before but only when there was no signal detected. Is the file too big? Thank you for your time and help. Best Regards, George |
From: Chambers, M. <mat...@gm...> - 2024-04-03 16:03:23
|
Hi George, Thanks for providing an example raw file. It's getting an error reading the analog channels, a feature which was added recently. I'll add error handling for that to skip the channels with a warning message. In the meantime I think you can skip those channels by moving the CHRO*.* files to a subdir in your .raw folder. Hope this helps, -Matt On 4/2/2024 2:05 PM, Brian Pratt wrote: > It's possible that the file is damaged. Can you open it in any other software? > > > On Tue, Apr 2, 2024 at 8:38 AM Liang, George C <Geo...@st...> wrote: > > Hello, > > I am trying to convert a Waters qtof MRM raw file. The file is attached (04022024_Glycan_1.raw 1.zip > <https://studentuml-my.sharepoint.com/:u:/g/personal/george_liang_student_uml_edu/EYhcJGPtYZtPuFz1LJ4oIPEB1oSwbqJt5jg2lZB2_ATknQ>). > But when I try to use the Proteowizard to convert to .mzML, I get the following errors: > > C:\Users\Administrator\OneDrive\Desktop\George\Water Raw\04022024_Glycan_1.raw > ------------------------------ > Starting...Opening file "C:\Users\Administrator\OneDrive\Desktop\George\Water Raw\04022024_Glycan_1.raw" for read... > Failed - System.Exception: [pwiz::CLI::msdata::ReaderList::read] Unhandled exception: Generic Error > at pwiz.CLI.msdata.ReaderList.read(String filename, MSDataList results, ReaderConfig config) > at MSConvertGUI.MainLogic.processFile(String filename, Config config, ReaderList readers, Map`2 usedOutputFilenames) > at MSConvertGUI.MainLogic.Go(Config config, Map`2 usedOutputFilenames) > > What is the issue? I was able to convert other files with MRM raw files before but only when there was no signal detected. Is the file > too big? Thank you for your time and help. > > Best Regards, > George > |
From: Brian P. <bs...@pr...> - 2024-04-02 21:33:33
|
It's possible that the file is damaged. Can you open it in any other software? On Tue, Apr 2, 2024 at 8:38 AM Liang, George C <Geo...@st...> wrote: > Hello, > > I am trying to convert a Waters qtof MRM raw file. The file is attached (04022024_Glycan_1.raw > 1.zip > <https://studentuml-my.sharepoint.com/:u:/g/personal/george_liang_student_uml_edu/EYhcJGPtYZtPuFz1LJ4oIPEB1oSwbqJt5jg2lZB2_ATknQ>). > But when I try to use the Proteowizard to convert to .mzML, I get the > following errors: > > C:\Users\Administrator\OneDrive\Desktop\George\Water > Raw\04022024_Glycan_1.raw > ------------------------------ > Starting...Opening file > "C:\Users\Administrator\OneDrive\Desktop\George\Water > Raw\04022024_Glycan_1.raw" for read... > Failed - System.Exception: [pwiz::CLI::msdata::ReaderList::read] Unhandled > exception: Generic Error > at pwiz.CLI.msdata.ReaderList.read(String filename, MSDataList results, > ReaderConfig config) > at MSConvertGUI.MainLogic.processFile(String filename, Config config, > ReaderList readers, Map`2 usedOutputFilenames) > at MSConvertGUI.MainLogic.Go(Config config, Map`2 usedOutputFilenames) > > What is the issue? I was able to convert other files with MRM raw files > before but only when there was no signal detected. Is the file too big? > Thank you for your time and help. > > Best Regards, > George > _______________________________________________ > proteowizard-support mailing list > pro...@li... > https://lists.sourceforge.net/lists/listinfo/proteowizard-support > |
From: Liang, G. C <Geo...@st...> - 2024-04-02 15:38:20
|
Hello, I am trying to convert a Waters qtof MRM raw file. The file is attached ([https://res.cdn.office.net/assets/mail/file-icon/png/zip_16x16.png]04022024_Glycan_1.raw 1.zip<https://studentuml-my.sharepoint.com/:u:/g/personal/george_liang_student_uml_edu/EYhcJGPtYZtPuFz1LJ4oIPEB1oSwbqJt5jg2lZB2_ATknQ>). But when I try to use the Proteowizard to convert to .mzML, I get the following errors: C:\Users\Administrator\OneDrive\Desktop\George\Water Raw\04022024_Glycan_1.raw ------------------------------ Starting...Opening file "C:\Users\Administrator\OneDrive\Desktop\George\Water Raw\04022024_Glycan_1.raw" for read... Failed - System.Exception: [pwiz::CLI::msdata::ReaderList::read] Unhandled exception: Generic Error at pwiz.CLI.msdata.ReaderList.read(String filename, MSDataList results, ReaderConfig config) at MSConvertGUI.MainLogic.processFile(String filename, Config config, ReaderList readers, Map`2 usedOutputFilenames) at MSConvertGUI.MainLogic.Go(Config config, Map`2 usedOutputFilenames) What is the issue? I was able to convert other files with MRM raw files before but only when there was no signal detected. Is the file too big? Thank you for your time and help. Best Regards, George |
From: Alexandre G. B. <ale...@ci...> - 2024-04-02 11:14:54
|
Hello, Thank you very much for your assistance. I'm trying to convert files from a Cyclic IMS acquired in HDMSe mode (Full SCan+AIF with mobility) to mzML format. The data is acquired with Masslynx, the file has 3 functions (the 3rd one for leucine) in profile. I have tried to convert them in different ways but I never manage to obtain a good result. I have consulted the forum, where someone had issues performing the conversion of this type of data but this problem was fixed: https://github.com/ProteoWizard/pwiz/issues/1166 https://github.com/ProteoWizard/pwiz/pull/1420 I can't find the filter/parameter --ignoreMissingZeroSamples and I'm not very familiar yet with data conversion. Could you please help me choose appropriate parameters to convert this type of file to mzML format in profile and/or centroid? Thank you very much for your attention. Best regards, -- Alexandre García Laboratory technician | Mass spectrometry - special techniques service Institute of Environmental Assessment and Water Research (IDAEA-CSIC) e: ale...@ci... p: +34 932 557 669 | 437 882 a: c/ Jordi Girona, 18-26. 08034 | Barcelona w: https://www.idaea.csic.es |
From: Charles S. <sw...@us...> - 2024-03-27 16:37:56
|
Hi Matt, Thanks for the followup. A sample of the mzXML files I'm using is attached, and the command's I've tried are: mspicture test.mzXML mspicture --mzLow=1200 --mzHigh=2000 test.mzXML Both return the following: [Pseudo2DGel::Impl::update] unknown mass analyzer type, assuming ion trap vector::_M_range_check Is it possible that this is due to it being a MALDI spectrum and not LC-MS? I was hoping to adapt the tool go generate gel-view versions of simple MALDI spectra but perhaps this is not possible. Best. Charlie -------------------------------------------------------------------------------------------------------- Charles R. Sweet, Ph.D. Associate Professor of Biochemistry and Biology Chemistry Department United States Naval Academy Annapolis, MD 21402 sw...@us... https://sites.google.com/usna.edu/sweetlab/home/ (410) 293-6643 (office) (410) 293-2218 (fax) ** For use by intended recipient only. If you are not the intended recipient, delete this email and notify the sender. ** -------------------------------------------------------------------------------------------------------- On Wed, Mar 27, 2024 at 11:05 AM Chambers, Matthew < mat...@gm...> wrote: > Hi Charlie, > > This usually indicates that mspicture is making an assumption about the > input data that isn't holding true. If you provide an example file > and command-line triggering the error I can look into fixing it or at > least giving a better error message. > > Thanks, > -Matt > > > On 3/25/2024 6:03 PM, Charles Sweet via proteowizard-support wrote: > > Dear Proteowizard support, > > I am using mspicture in linux command line with Proteowizard > installed through Bioconda. (conda v. 23.5, Proteowizard v.3.0.9992). I > > would like to generate a "gel image" (preferably nearly 1D) of an mzXML > spectrum (MALDI collected on Bruker Microflex), but when I attempt > > this either with or without mass ranges I get the error > "vector::M_range_check" > > > > Please advise on what, if anything I can do to get mspicture working > with this file. Thanks! > > > > Best regards, > > Charlie Sweet > |
From: Chambers, M. <mat...@gm...> - 2024-03-27 15:31:58
|
Hi Gaia, Of course we are open to feedback (and also pull requests on our GitHub :) ). I'm aware of the freezing issue with the file open dialog: I think that's usually due to slow/unresponsive attached network drives - is that your case as well? It could definitely be handled more gracefully though (it's trying to load the root drive/folder tree on the UI thread). It is indeed annoying and should be fixed. The main window being frozen when the conversion is in progress is working as designed. I suppose I could keep that window able to change, and just disable the "Run" button while the conversion is in progress, but this is the first time I've heard anyone comment on it. What do you intend to do on the main window after starting conversion? Can you just start another MSConvertGUI instance? Since you mention MSConvert as a bottleneck in your workflow, I wonder if you've considered automating the conversion as part of your workflow, i.e. running the command-line msconvert.exe as part of the workflow rather than a manual step. It's also possible to set up an automatic file monitor that will run an msconvert.exe job whenever a new RAW file shows up in a directory. That way the files are already converted when you want to start the workflow. Thanks, -Matt On 3/27/2024 8:01 AM, Gaia Burgio wrote: > Hi there, > > I often use MSconvert from ProteoWizard to handle my MS data, convert files, and centroid my data. I am wondering if you take in > suggestions for fixing bugs such as continuous freezing of the window when navigating folders, and freezing of the main window when the > conversion progress window is open. I understand the software handles heavy files and some issues are to be expected, however this ends up > often representing a bottleneck at the very beginning of an already long and laborious workflow which doesn't seem to be fixed when using > more powerful computers. > > Hope to hear back from you soon and thank you very much for your time, > > Gaia Burgio, Ph.D. |
From: Chambers, M. <mat...@gm...> - 2024-03-27 15:05:32
|
Hi Charlie, This usually indicates that mspicture is making an assumption about the input data that isn't holding true. If you provide an example file and command-line triggering the error I can look into fixing it or at least giving a better error message. Thanks, -Matt On 3/25/2024 6:03 PM, Charles Sweet via proteowizard-support wrote: > Dear Proteowizard support, > I am using mspicture in linux command line with Proteowizard installed through Bioconda. (conda v. 23.5, Proteowizard v.3.0.9992). I > would like to generate a "gel image" (preferably nearly 1D) of an mzXML spectrum (MALDI collected on Bruker Microflex), but when I attempt > this either with or without mass ranges I get the error "vector::M_range_check" > > Please advise on what, if anything I can do to get mspicture working with this file. Thanks! > > Best regards, > Charlie Sweet |
From: Gaia B. <Gai...@gl...> - 2024-03-27 12:29:02
|
Hi there, I often use MSconvert from ProteoWizard to handle my MS data, convert files, and centroid my data. I am wondering if you take in suggestions for fixing bugs such as continuous freezing of the window when navigating folders, and freezing of the main window when the conversion progress window is open. I understand the software handles heavy files and some issues are to be expected, however this ends up often representing a bottleneck at the very beginning of an already long and laborious workflow which doesn't seem to be fixed when using more powerful computers. Hope to hear back from you soon and thank you very much for your time, Gaia Burgio, Ph.D. Research Associate, Chemistry of Natural Products Advanced Research Centre, University of Glasgow 11 Chapel Lane G11 6EW |
From: Helwig, V. <v.h...@hw...> - 2024-03-27 08:56:22
|
Dear Sir or Madam Unfortunately, I have not yet received an answer to my problem with the ID Picker. Could you tell me who to contact for the ID Picker? Do you need any further information or are there any problems with the files I have uploaded to Skyline? Many thanks in advance and best regards Veronika Helwig Veronika Helwig - Trainee Laboratory Services - HWI pharma services GmbH Rheinzaberner Strasse 8 76761 Ruelzheim Germany Phone: +49 7272 7767-2395 Fax: Email: v.h...@hw...<mailto:v.h...@hw...> Web: www.hwi-group.de<http://www.hwi-group.de> Innovative Technologies and Services for Pharma & Biotech [cid:image001_neu_93011670-5570-4e8f-9412-8beff6609697.png]<https://www.hwi-group.de/home.html> [cid:01-Arial-LinkedIn_2f24b964-1c47-46d0-bd9f-2608291d2353.png]<https://de.linkedin.com/company/hwi-pharma-services-gmbh>[cid:01-Arial-YouTube_cb8449f2-53f5-4af0-93b1-d8285769b785.png]<https://www.youtube.com/@hwigroup4045> Managing Directors: Dr. Stefan Wissel, Dr. Frank Böttcher Registered Office: Ruelzheim Municipal Court of Landau, registration number: 21388 For information on personal data processing please visit: https://www.hwi-group.de/unternehmen/infocenter.html The contents of this email are confidential. If you are not the named addressee or if this transmission has been addressed to you in error, please notify the sender immediately and then delete this email. Any unauthorized copying and transmission is forbidden. Email transmission cannot be guaranteed to be secure. If verification is required, please request a hard copy version. Von: Helwig, Veronika Gesendet: Dienstag, 12. März 2024 10:26 An: Nick Shulman <nicksh@u.washington.edu> Cc: su...@pr...; Schelder, Malgorzata <m.s...@hw...> Betreff: AW: [proteowizard-support] ID Picker Error Hello Mr Shulman, I wanted to ask again whether you have already had the opportunity to look at my problem and my uploaded data. Or if you could give me the e-mail address of your ID Picker expert? Many thanks in advance and best regards Veronika Helwig Von: Helwig, Veronika Gesendet: Donnerstag, 29. Februar 2024 09:25 An: Nick Shulman <nicksh@u.washington.edu<mailto:nicksh@u.washington.edu>> Cc: su...@pr...<mailto:su...@pr...> Betreff: AW: [proteowizard-support] ID Picker Error Hello Nick, I have uploaded the files to Skyline: [cid:ima...@01...93B370] Best regards Veronika Helwig Von: Nick Shulman <nicksh@u.washington.edu<mailto:nicksh@u.washington.edu>> Gesendet: Montag, 26. Februar 2024 22:37 An: Helwig, Veronika <v.h...@hw...<mailto:v.h...@hw...>> Cc: su...@pr...<mailto:su...@pr...>; Schelder, Malgorzata <m.s...@hw...<mailto:m.s...@hw...>> Betreff: Re: [proteowizard-support] ID Picker Error I believe our ID Picker expert is on vacation until tomorrow. If you would like, you could send us your files. We might be able to figure out what is going on from looking at your files, or they might be helpful tomorrow. I am not sure which files we would need. You could send the files to us via Google Drive or DropBox etc. Alternatively you could create a free account on the skyline.ms<http://skyline.ms> website and upload them here: https://skyline.ms/files.url -- Nick On Mon, Feb 26, 2024 at 3:45 AM Helwig, Veronika <v.h...@hw...<mailto:v.h...@hw...>> wrote: Dear Sir or Madam, as I have not received an answer to my support enquiry after 1 week, I wanted to ask again whether you can help me with this problem: I have repeated my search in Mascot, this time also with a Decoy database. Then the search worked, but the following error message appeared: [Ein Bild, das Text, Elektronik, Screenshot, Display enthält. Automatisch generierte Beschreibung] Many thanks in advance and best regards Veronika Helwig Veronika Helwig - Trainee Laboratory Services - HWI pharma services GmbH Rheinzaberner Strasse 8 76761 Ruelzheim Germany Phone: +49 7272 7767-2395 Fax: Email: v.h...@hw...<mailto:v.h...@hw...> Web: www.hwi-group.de<http://www.hwi-group.de> Innovative Technologies and Services for Pharma & Biotech [cid:ima...@01...93B370]<https://www.hwi-group.de/home.html> [cid:ima...@01...93B370]<https://de.linkedin.com/company/hwi-pharma-services-gmbh>[cid:ima...@01...93B370]<https://www.youtube.com/@hwigroup4045> Managing Directors: Dr. Stefan Wissel, Dr. Frank Böttcher Registered Office: Ruelzheim Municipal Court of Landau, registration number: 21388 For information on personal data processing please visit: https://www.hwi-group.de/unternehmen/infocenter.html The contents of this email are confidential. If you are not the named addressee or if this transmission has been addressed to you in error, please notify the sender immediately and then delete this email. Any unauthorized copying and transmission is forbidden. Email transmission cannot be guaranteed to be secure. If verification is required, please request a hard copy version. _______________________________________________ proteowizard-support mailing list pro...@li...<mailto:pro...@li...> https://lists.sourceforge.net/lists/listinfo/proteowizard-support |
From: Charles S. <sw...@us...> - 2024-03-25 22:27:43
|
Dear Proteowizard support, I am using mspicture in linux command line with Proteowizard installed through Bioconda. (conda v. 23.5, Proteowizard v.3.0.9992). I would like to generate a "gel image" (preferably nearly 1D) of an mzXML spectrum (MALDI collected on Bruker Microflex), but when I attempt this either with or without mass ranges I get the error "vector::M_range_check" Please advise on what, if anything I can do to get mspicture working with this file. Thanks! Best regards, Charlie Sweet -------------------------------------------------------------------------------------------------------- Charles R. Sweet, Ph.D. Associate Professor of Biochemistry and Biology Chemistry Department United States Naval Academy Annapolis, MD 21402 sw...@us... https://sites.google.com/usna.edu/sweetlab/home/ (410) 293-6643 (office) (410) 293-2218 (fax) ** For use by intended recipient only. If you are not the intended recipient, delete this email and notify the sender. ** -------------------------------------------------------------------------------------------------------- |
From: Chambers, M. <mat...@gm...> - 2024-03-14 17:26:01
|
Yes, the TIC chromatogram is composed of all spectra of any type, so that's not a bug. That's usually only useful if you filter it some way, usually one trace per ms level or spectrum type (or in Waters' case, per function). That's why the 3rd array with the function number is provided. For Waters, only SRM chromatograms are currently created as separate chromatograms. The mzML spec is very loose for chromatograms so you pretty much have to look at the data and decide what you want to get out of it. A ProteoWizard PR that added extra chromatograms for non-MS functions would be welcome. On 3/14/2024 12:19 PM, Gerd Rheinwald wrote: > > Hi Matt, > > I am trying to understand the strategy and format of how the DAD trace is stored in the mzML file. There is no separation between the DAD > trace and the TIC trace. > > MS and MSn spectra are stored in an array of spectra, followed by an array of UV spectra (labelled electromagnetic radiation spectra in mzML). > > It seems that the TIC stored in the trace array at the end of the file is composed of all MS/MSn and UV spectra. > > I can of course use the /msLevel 0-0/ to "filter out" only the spectra related to the DAD data, but this is not really useful as I lose > all the MS/MSn information. > > There is more details in the attached response to Brian, I sent earlier today. > > @Brian <mailto:bs...@pr...> – the customer also allowed me to share that the files are from the research site from F. > Hoffmann-La Roche Ltd in Switzerland. > > They classify the non-existent separation between DAD and MS traces as a bug in MSConvert. > > I think it’s more a format specification issue. > > In the meantime, our programmers have confirmed that they have a solution in mind. > > When importing the file, they will recreate the TIC from the MS/MSn array and the DAD chromatogram from the UV spectra array. > > Regards, > > Gerd > > *Von:*Chambers, Matthew <mat...@gm...> > *Gesendet:* Donnerstag, 14. März 2024 16:09 > *An:* Gerd Rheinwald <ger...@ac...> > *Cc:* support <su...@pr...>; Jan Stanstrup <sta...@gm...> > *Betreff:* Re: [proteowizard-support] DAD traces in mzML > > *CAUTION:* This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender > and know the content is safe. > > Hi Gerd, > > Are you referring to the TIC chromatogram by "single MS trace"? Pwiz will include all kinds of spectra in the TIC chromatogram. But there > is a 3rd array in that chromatogram that, for Waters, stores the function that each value in the chromatogram came from. You can thus > filter those values by function pretty easily. Most other vendors have 3rd arrays for ms level instead, but it's a similar concept. > > Hope this helps, > -Matt > > On 3/13/2024 9:22 AM, Jan Stanstrup wrote: > > When I did the same the dad trace was labeled as mslevel 0. > > On Wed, Mar 13, 2024, 14:09 Gerd Rheinwald via proteowizard-support <pro...@li...> wrote: > > Hello! > > I have a question regarding the conversion of original instrument Raw Data to mzML. > > I got mzML data created with ProteoWizard from one of our customers using Waters and MassHunter instruments. > > It seems that the DAD/PDA detector is not interpreted as separate analyzer and that the UV spectra from the DAD trace and the MS > spectra from the MS1 are merged into a single MS trace. > > Is this understanding correct or are we missing a setting in the ProteoWizard? > > Regards, > > Gerd Rheinwald > > -------------------------------------------------------------------------------------------------------------------------------------------- > > Dr. Gerd Rheinwald > > Team Leader, Sr. Application Scientist > > > > Advanced Chemistry Development > > Germany GmbH > > Hahnstraße 70 > > D-60528 Frankfurt,Germany > > -------------------------------------------------------------------------------------------------------------------------------------------- > > Direkt/direct: > > Tel: > > > > +49 (0) 6326 700 468 > > Zentrale/switch board Frankfurt: > > Tel: > > > > +49 (0) 69 58 99 67 94 > > Fax: > > > > +49 (0) 6109 7009322 > > Email > > > > ger...@ac... <mailto:ger...@ac...> > > Web > > > > www.acdlabs.com <http://../../../../Documents/ACDLabs/www.acdlabs.com> > > -------------------------------------------------------------------------------------------------------------------------------------------- > > *Analytica 2024* > > Join us at Analytica in Messe München, Hall A1 / Stand 229.Read more > <https://exhibitors.analytica.de/exhibitor-portal/2024/list-of-exhibitors/exhibitordetails/?elb=277.1100.1604.1.111> > > A purple and white logo Description automatically generated > <https://exhibitors.analytica.de/ausstellerportal/2024/hallenplaene/hallenplan/a1/?elb=277.1100.1604.1.111&clb=277.1200.1696.1.111&lid=A1> > > ** > > CONFIDENTIALITY NOTICE : Unless expressly stated otherwise, this message is confidential and is intended for the addressee(s) > only. If you are not an addressee, please inform the sender immediately or contact in...@ac... > > ACD/LABS’ PRIVACY POLICY: we are committed to protecting your personal data and remain compliant with privacy legislation in all > our customer locales. Opt-in or change your preferences <https://www.acdlabs.com/newsletters/opt-in/> about the information you’d > like to receive about ACD/Labs products (you can unsubscribe at any time). Read our Privacy Policy for more details > <https://www.acdlabs.com/company/privacypolicy.php>. > > Amtsgericht Frankfurt am Main HRB 85 756 > > Geschäftsführerin: Catherine Commins > > _______________________________________________ > 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: Chambers, M. <mat...@gm...> - 2024-03-14 15:09:22
|
Hi Gerd, Are you referring to the TIC chromatogram by "single MS trace"? Pwiz will include all kinds of spectra in the TIC chromatogram. But there is a 3rd array in that chromatogram that, for Waters, stores the function that each value in the chromatogram came from. You can thus filter those values by function pretty easily. Most other vendors have 3rd arrays for ms level instead, but it's a similar concept. Hope this helps, -Matt On 3/13/2024 9:22 AM, Jan Stanstrup wrote: > When I did the same the dad trace was labeled as mslevel 0. > > On Wed, Mar 13, 2024, 14:09 Gerd Rheinwald via proteowizard-support <pro...@li...> wrote: > > Hello! > > I have a question regarding the conversion of original instrument Raw Data to mzML. > > I got mzML data created with ProteoWizard from one of our customers using Waters and MassHunter instruments. > > It seems that the DAD/PDA detector is not interpreted as separate analyzer and that the UV spectra from the DAD trace and the MS > spectra from the MS1 are merged into a single MS trace. > > Is this understanding correct or are we missing a setting in the ProteoWizard? > > Regards, > > Gerd Rheinwald > > -------------------------------------------------------------------------------------------------------------------------------------------- > > Dr. Gerd Rheinwald > > Team Leader, Sr. Application Scientist > > > > Advanced Chemistry Development > > Germany GmbH > > Hahnstraße 70 > > D-60528 Frankfurt,Germany > > -------------------------------------------------------------------------------------------------------------------------------------------- > > Direkt/direct: > > Tel: > > > > +49 (0) 6326 700 468 > > Zentrale/switch board Frankfurt: > > Tel: > > > > +49 (0) 69 58 99 67 94 > > Fax: > > > > +49 (0) 6109 7009322 > > Email > > > > ger...@ac... <mailto:ger...@ac...> > > Web > > > > www.acdlabs.com <http://../../../../Documents/ACDLabs/www.acdlabs.com> > > -------------------------------------------------------------------------------------------------------------------------------------------- > > *Analytica 2024* > > Join us at Analytica in Messe München, Hall A1 / Stand 229.Read more > <https://exhibitors.analytica.de/exhibitor-portal/2024/list-of-exhibitors/exhibitordetails/?elb=277.1100.1604.1.111> > > A purple and white logo Description automatically generated > <https://exhibitors.analytica.de/ausstellerportal/2024/hallenplaene/hallenplan/a1/?elb=277.1100.1604.1.111&clb=277.1200.1696.1.111&lid=A1>__ > > ** > > CONFIDENTIALITY NOTICE : Unless expressly stated otherwise, this message is confidential and is intended for the addressee(s) only. If > you are not an addressee, please inform the sender immediately or contact in...@ac... <mailto:in...@ac...> > > ACD/LABS’ PRIVACY POLICY: we are committed to protecting your personal data and remain compliant with privacy legislation in all our > customer locales. Opt-in or change your preferences <https://www.acdlabs.com/newsletters/opt-in/> about the information you’d like to > receive about ACD/Labs products (you can unsubscribe at any time). Read our Privacy Policy for more details > <https://www.acdlabs.com/company/privacypolicy.php>. > > Amtsgericht Frankfurt am Main HRB 85 756 > > Geschäftsführerin: Catherine Commins > > _______________________________________________ > 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: Brian P. <bs...@pr...> - 2024-03-13 20:10:40
|
Can you provide example files (input and output) and a screenshot of the settings you used? That will help us arrive at a solution most quickly. Best regards, Brian Pratt On Wed, Mar 13, 2024 at 6:22 AM Jan Stanstrup <sta...@gm...> wrote: > When I did the same the dad trace was labeled as mslevel 0. > > On Wed, Mar 13, 2024, 14:09 Gerd Rheinwald via proteowizard-support < > pro...@li...> wrote: > >> Hello! >> >> >> >> I have a question regarding the conversion of original instrument Raw >> Data to mzML. >> >> >> >> I got mzML data created with ProteoWizard from one of our customers using >> Waters and MassHunter instruments. >> >> >> >> It seems that the DAD/PDA detector is not interpreted as separate >> analyzer and that the UV spectra from the DAD trace and the MS spectra from >> the MS1 are merged into a single MS trace. >> >> >> >> Is this understanding correct or are we missing a setting in the >> ProteoWizard? >> >> >> >> Regards, >> >> >> >> Gerd Rheinwald >> >> >> ------------------------------ >> >> Dr. Gerd Rheinwald >> >> Team Leader, Sr. Application Scientist >> >> >> >> Advanced Chemistry Development >> >> Germany GmbH >> >> Hahnstraße 70 >> >> D-60528 Frankfurt,Germany >> ------------------------------ >> >> Direkt/direct: >> >> Tel: >> >> +49 (0) 6326 700 468 >> >> Zentrale/switch board Frankfurt: >> >> Tel: >> >> +49 (0) 69 58 99 67 94 >> >> Fax: >> >> +49 (0) 6109 7009322 >> >> Email >> >> ger...@ac... >> >> Web >> >> www.acdlabs.com <http://../../../../Documents/ACDLabs/www.acdlabs.com> >> ------------------------------ >> >> *Analytica 2024* >> >> Join us at Analytica in Messe München, Hall A1 / Stand 229. Read more >> <https://exhibitors.analytica.de/exhibitor-portal/2024/list-of-exhibitors/exhibitordetails/?elb=277.1100.1604.1.111> >> >> [image: A purple and white logo Description automatically generated] >> <https://exhibitors.analytica.de/ausstellerportal/2024/hallenplaene/hallenplan/a1/?elb=277.1100.1604.1.111&clb=277.1200.1696.1.111&lid=A1> >> >> >> >> CONFIDENTIALITY NOTICE : Unless expressly stated otherwise, this message >> is confidential and is intended for the addressee(s) only. If you are not >> an addressee, please inform the sender immediately or contact >> in...@ac... >> >> >> >> ACD/LABS’ PRIVACY POLICY: we are committed to protecting your personal >> data and remain compliant with privacy legislation in all our customer >> locales. Opt-in or change your preferences >> <https://www.acdlabs.com/newsletters/opt-in/> about the information >> you’d like to receive about ACD/Labs products (you can unsubscribe at any >> time). Read our Privacy Policy for more details >> <https://www.acdlabs.com/company/privacypolicy.php>. >> >> >> >> Amtsgericht Frankfurt am Main HRB 85 756 >> >> Geschäftsführerin: Catherine Commins >> _______________________________________________ >> 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: Jan S. <sta...@gm...> - 2024-03-13 13:22:52
|
When I did the same the dad trace was labeled as mslevel 0. On Wed, Mar 13, 2024, 14:09 Gerd Rheinwald via proteowizard-support < pro...@li...> wrote: > Hello! > > > > I have a question regarding the conversion of original instrument Raw Data > to mzML. > > > > I got mzML data created with ProteoWizard from one of our customers using > Waters and MassHunter instruments. > > > > It seems that the DAD/PDA detector is not interpreted as separate analyzer > and that the UV spectra from the DAD trace and the MS spectra from the MS1 > are merged into a single MS trace. > > > > Is this understanding correct or are we missing a setting in the > ProteoWizard? > > > > Regards, > > > > Gerd Rheinwald > > > ------------------------------ > > Dr. Gerd Rheinwald > > Team Leader, Sr. Application Scientist > > > > Advanced Chemistry Development > > Germany GmbH > > Hahnstraße 70 > > D-60528 Frankfurt,Germany > ------------------------------ > > Direkt/direct: > > Tel: > > +49 (0) 6326 700 468 > > Zentrale/switch board Frankfurt: > > Tel: > > +49 (0) 69 58 99 67 94 > > Fax: > > +49 (0) 6109 7009322 > > Email > > ger...@ac... > > Web > > www.acdlabs.com <http://../../../../Documents/ACDLabs/www.acdlabs.com> > ------------------------------ > > *Analytica 2024* > > Join us at Analytica in Messe München, Hall A1 / Stand 229. Read more > <https://exhibitors.analytica.de/exhibitor-portal/2024/list-of-exhibitors/exhibitordetails/?elb=277.1100.1604.1.111> > > [image: A purple and white logo Description automatically generated] > <https://exhibitors.analytica.de/ausstellerportal/2024/hallenplaene/hallenplan/a1/?elb=277.1100.1604.1.111&clb=277.1200.1696.1.111&lid=A1> > > > > CONFIDENTIALITY NOTICE : Unless expressly stated otherwise, this message > is confidential and is intended for the addressee(s) only. If you are not > an addressee, please inform the sender immediately or contact > in...@ac... > > > > ACD/LABS’ PRIVACY POLICY: we are committed to protecting your personal > data and remain compliant with privacy legislation in all our customer > locales. Opt-in or change your preferences > <https://www.acdlabs.com/newsletters/opt-in/> about the information you’d > like to receive about ACD/Labs products (you can unsubscribe at any time). Read > our Privacy Policy for more details > <https://www.acdlabs.com/company/privacypolicy.php>. > > > > Amtsgericht Frankfurt am Main HRB 85 756 > > Geschäftsführerin: Catherine Commins > _______________________________________________ > proteowizard-support mailing list > pro...@li... > https://lists.sourceforge.net/lists/listinfo/proteowizard-support > |
From: Gerd R. <ger...@ac...> - 2024-03-13 13:09:41
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Hello! I have a question regarding the conversion of original instrument Raw Data to mzML. I got mzML data created with ProteoWizard from one of our customers using Waters and MassHunter instruments. It seems that the DAD/PDA detector is not interpreted as separate analyzer and that the UV spectra from the DAD trace and the MS spectra from the MS1 are merged into a single MS trace. Is this understanding correct or are we missing a setting in the ProteoWizard? Regards, Gerd Rheinwald ________________________________ Dr. Gerd Rheinwald Team Leader, Sr. Application Scientist [cid:image001.png@01DA754D.9245F200] Advanced Chemistry Development Germany GmbH Hahnstraße 70 D-60528 Frankfurt,Germany ________________________________ Direkt/direct: Tel: +49 (0) 6326 700 468 Zentrale/switch board Frankfurt: Tel: +49 (0) 69 58 99 67 94 Fax: +49 (0) 6109 7009322 Email ger...@ac...<mailto:ger...@ac...> Web www.acdlabs.com<../../../../Documents/ACDLabs/www.acdlabs.com> ________________________________ Analytica 2024 Join us at Analytica in Messe München, Hall A1 / Stand 229. Read more<https://exhibitors.analytica.de/exhibitor-portal/2024/list-of-exhibitors/exhibitordetails/?elb=277.1100.1604.1.111> [A purple and white logo Description automatically generated]<https://exhibitors.analytica.de/ausstellerportal/2024/hallenplaene/hallenplan/a1/?elb=277.1100.1604.1.111&clb=277.1200.1696.1.111&lid=A1> CONFIDENTIALITY NOTICE : Unless expressly stated otherwise, this message is confidential and is intended for the addressee(s) only. If you are not an addressee, please inform the sender immediately or contact in...@ac...<mailto:in...@ac...> ACD/LABS' PRIVACY POLICY: we are committed to protecting your personal data and remain compliant with privacy legislation in all our customer locales. Opt-in or change your preferences<https://www.acdlabs.com/newsletters/opt-in/> about the information you'd like to receive about ACD/Labs products (you can unsubscribe at any time). Read our Privacy Policy for more details<https://www.acdlabs.com/company/privacypolicy.php>. Amtsgericht Frankfurt am Main HRB 85 756 Geschäftsführerin: Catherine Commins |
From: Chambers, M. <mat...@gm...> - 2024-03-12 15:07:19
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Hi Veronika Download the latest IDPicker now. The issues with Mascot import should be fixed. -Matt On 3/12/2024 5:25 AM, Helwig, Veronika wrote: > > Hello Mr Shulman, > > I wanted to ask again whether you have already had the opportunity to look at my problem and my uploaded data. Or if you could give me the > e-mail address of your ID Picker expert? > > Many thanks in advance and best regards > > Veronika Helwig > > Veronika Helwig > - Trainee Laboratory Services - > > *HWI pharma services GmbH* > Rheinzaberner Strasse 8 > 76761 Ruelzheim > Germany > Phone: +49 7272 7767-2395 > Fax: > Email: v.h...@hw...<mailto:v.h...@hw...> > Web: www.hwi-group.de <http://www.hwi-group.de> > > *Innovative Technologies and Services for Pharma & Biotech * > > *<https://www.hwi-group.de/home.html> > <https://de.linkedin.com/company/hwi-pharma-services-gmbh><https://www.youtube.com/@hwigroup4045> > * > > Managing Directors: Dr. Stefan Wissel, Dr. Frank Böttcher > Registered Office: Ruelzheim > Municipal Court of Landau, registration number: 21388 > > For information on personal data processing please visit: https://www.hwi-group.de/unternehmen/infocenter.html > > The contents of this email are confidential. If you are not the named addressee or if this transmission has been addressed to you in > error, please notify the sender immediately and then delete this email. Any unauthorized copying and transmission is forbidden. Email > transmission cannot be guaranteed to be secure. If verification is required, please request a hard copy version. > > *Von:* Helwig, Veronika > *Gesendet:* Donnerstag, 29. Februar 2024 09:25 > *An:* Nick Shulman <nicksh@u.washington.edu> > *Cc:* su...@pr... > *Betreff:* AW: [proteowizard-support] ID Picker Error > > Hello Nick, > > I have uploaded the files to Skyline: > > Best regards > > Veronika Helwig > > *Von:* Nick Shulman <nicksh@u.washington.edu> > *Gesendet:* Montag, 26. Februar 2024 22:37 > *An:* Helwig, Veronika <v.h...@hw...> > *Cc:* su...@pr...; Schelder, Malgorzata <m.s...@hw...> > *Betreff:* Re: [proteowizard-support] ID Picker Error > > I believe our ID Picker expert is on vacation until tomorrow. > > If you would like, you could send us your files. We might be able to figure out what is going on from looking at your files, or they might > be helpful tomorrow. > > I am not sure which files we would need. > > You could send the files to us via Google Drive or DropBox etc. > > Alternatively you could create a free account on the skyline.ms <http://skyline.ms> website and upload them here: > > https://skyline.ms/files.url > > -- Nick > > On Mon, Feb 26, 2024 at 3:45 AM Helwig, Veronika <v.h...@hw...> wrote: > > Dear Sir or Madam, > > as I have not received an answer to my support enquiry after 1 week, I wanted to ask again whether you can help me with this problem: > > I have repeated my search in Mascot, this time also with a Decoy database. Then the search worked, but the following error message > appeared: > > Ein Bild, das Text, Elektronik, Screenshot, Display enthält. Automatisch generierte Beschreibung > > Many thanks in advance and best regards > > Veronika Helwig > > Veronika Helwig > - Trainee Laboratory Services - > > *HWI pharma services GmbH* > Rheinzaberner Strasse 8 > 76761 Ruelzheim > Germany > Phone: +49 7272 7767-2395 > Fax: > Email: v.h...@hw... <mailto:v.h...@hw...> > Web: www.hwi-group.de <http://www.hwi-group.de> > > *Innovative Technologies and Services for Pharma & Biotech * > > ** <https://www.hwi-group.de/home.html>* > *** <https://de.linkedin.com/company/hwi-pharma-services-gmbh>** <https://www.youtube.com/@hwigroup4045> > > Managing Directors: Dr. Stefan Wissel, Dr. Frank Böttcher > Registered Office: Ruelzheim > Municipal Court of Landau, registration number: 21388 > > For information on personal data processing please visit: https://www.hwi-group.de/unternehmen/infocenter.html > <https://www.hwi-group.de/unternehmen/infocenter.html> > > The contents of this email are confidential. If you are not the named addressee or if this transmission has been addressed to you in > error, please notify the sender immediately and then delete this email. Any unauthorized copying and transmission is forbidden. Email > transmission cannot be guaranteed to be secure. If verification is required, please request a hard copy version. > > _______________________________________________ > 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 |