Activity for ProteoWizard
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Novera Alam posted a comment on discussion Open Discussion (not monitored by pwiz developers; use support@proteowizard.org for that)
I have a waters cylic IMS file in mzML file format that I tried to convert to mgf format using the latest version of MSconvert. but it fails. the output is empty. could you please help with any suggestion for such file conversion. Or atleast sugges a way to export the list of deconvoluted mass with their corresponding abundances from the spectrum?
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Todd Creasy posted a comment on ticket #23
Just pinging about this. I am experiencing the same problem. Will there be support for M1 Macs in the near future or is there a way around this?
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David Jaffe created ticket #23
failure of msconvert through docker with chambm/pwiz-skyline... on Mac M1 Pro
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Triston Groff posted a comment on discussion Open Discussion (not monitored by pwiz developers; use support@proteowizard.org for that)
Use the peakPicking filter (must be the first filter). To centroid all MS level spectra, use 1- for the MS levels
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Hi Nathaniel, I work with a lot of .wiff files... Do you also have the wiff.scan files? There must be a .wiff and a .wiff.scan file with the same name in the directory for MSConvert to convert the files. Hope this helps.
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Eva Gorrochategui Matas posted a comment on discussion Open Discussion
I'm trying to convert a Sciex file (.wiff2) into an mzXML file using MSConvert from Proteowizard. Once I press the button "Start" it seems that the conversion starts and finishes almost immediately. Actually I get this message on the screen: Starting... Opening file "C:urinesample.wiff2" for read... Finished. However, at the end I don't obtain the output file. What can happen and what's the solution? Thanks!
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S Ray posted a comment on discussion Open Discussion
Hello All, We have some Thermo QExactive derived RAW files where the MS1 was acquired in PROFILE mode and the MS2 is centroided. I want to convert it to the MGF format in centroid mode> Can I choose peakPicking option to "Vendor MsLevel=1-" or do I've to specify "Vendor MsLevel=1-1" to convert the MS1 scans to profile mode explicitly? Thanks
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Brian Pratt posted a comment on ticket #22
I read that the peakpicking algorithm would be different (with my script using a local maxima algorithm and the application using either vendor of CWT methods) This is incorrect. MSConvertGUI and MSConvert offer exactly the same peakpicking options as they are both interfaces to the same underlying code. You should use SeeMS to try to understand why those files are not converting. Also note that your script seems inconsistent in which file types it's looking for - is it .d or .raw?
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Caoimhe FitzGibbon created ticket #22
Python MSConvert script not converting all files
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Michael Truell created ticket #21
Could not find configuration for IPerformanceMeasurementEvent
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Nathaniel Sherden posted a comment on discussion Open Discussion
UPDATE: Nope the file is fine, the person who supplied it to me showed me via a bunch of screen shots that there are indeed a bunch of perfectly good chromatograms in it via an officiall ABI/Sciex program. Is the problem that MS convert is having is that there are multiple chromatograms all compacted into the same .wiff file? Is there any way to get MSconvert to handle this? Do I need to find some way to break it into lots of little .wiff files before MSconvert will handle it? Any thoughts or help...
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As per the title but as I have never worked with .wiff files before or the instruments that create them I need a little bit of help figuring out the issue here even though I think it is human (more specifically: people sending me a garbage .wiff file.) MSconvert is producing the "errors" (again probably not errors, but correct analysis) in the attached picture. From what I can tell, basically the issue is this is a .wiff file, but it is not one that actually has any chromatograms in it, just a bunch...
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This is not the proper forum for support requests - you want https://sourceforge.net/p/proteowizard/mailman/proteowizard-support/ If your question is about a specific piece of ProteoWizard software, please indicate which one, what version you are using, what command line options used etc, On Sun, Mar 15, 2020 at 10:46 AM Aneel aneelapps@users.sourceforge.net wrote: The MS data converter tool is provided by sciex only all the related queries are belongs to how to convert the wiff to mgf/XML files...
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It appears that you have confused msconvert with some other software. You'll need to contact Sciex with these questions.
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Aneel posted a comment on ticket #23
The MS data converter tool is provided by sciex only all the related queries are belongs to how to convert the wiff to mgf/XML files On Sun, 15 Mar 2020, 22:44 Brian Pratt, pcbrefugee@users.sourceforge.net wrote: I appears that you have confused msconvert with some other software. You'll need to contact Sciex with these questions. On Sun, Mar 15, 2020 at 4:39 AM Aneel aneelapps@users.sourceforge.net wrote: [feature-requests:#23] https://sourceforge.net/p/proteowizard/feature-requests/23/ https://sourceforge.net/p/proteowizard/feature-requests/23/...
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I appears that you have confused msconvert with some other software. You'll need to contact Sciex with these questions. On Sun, Mar 15, 2020 at 4:39 AM Aneel aneelapps@users.sourceforge.net wrote: [feature-requests:#23] https://sourceforge.net/p/proteowizard/feature-requests/23/ Checksum enable electronic signature in analyst software audit trail manager* Status: open Group: Next_Release_(example) Created: Sun Mar 15, 2020 11:39 AM UTC by Aneel Last Updated: Sun Mar 15, 2020 11:39 AM UTC Owner: nobody...
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I appears that you have confused msconvert with some other software. You'll need to contact Sciex with these questions. On Sun, Mar 15, 2020 at 4:20 AM Aneel aneelapps@users.sourceforge.net wrote: [feature-requests:#21] https://sourceforge.net/p/proteowizard/feature-requests/21/ wiff to mgf convrt using MS Data converter* Status: open Group: Next_Release_(example) Created: Sun Mar 15, 2020 11:20 AM UTC by Aneel Last Updated: Sun Mar 15, 2020 11:20 AM UTC Owner: nobody converting .WIFF file to MGF...
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Checksum enable electronic signature in analyst software audit trail manager
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Wiff files corrupted [Analyst software]
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wiff to mgf convrt using MS Data converter
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Sapna Tras posted a comment on discussion Open Discussion
Hi All, The MSCONVERT app crashes when I try to import .Raw files and convert to mzml. below attached is a screen shot of the error.
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Kamila Schmidt posted a comment on discussion Open Discussion
Hi all, I am trying to convert Thermo raw files into mzML files using MSConvert in ProteoWizard 3.0.19326 and getting the folowing error: Failed - System.Exception: [pwiz::CLI::msdata::MSDataFile::write] Unhandled exception: managed and native storage have different sizes at pwiz.CLI.msdata.MSDataFile.write(MSData msd, String filename, WriteConfig config, IterationListenerRegistry iterationListenerRegistry) at MSConvertGUI.MainLogic.processFile(String filename, Config config, ReaderList readers,...
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Hi All, The MSCONVERT app crashes when I try to import .Raw files and convert to mzml. below attached is a screen shot of the error.
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Jie Hu created ticket #20
Build problem
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Eleonora Amante posted a comment on discussion Open Discussion
Hello I need to convert my .wiff files into a centroided .mzXML. I have seen in other discussions that it is possible, but I cannot find the right option. Can someone help me? Thank you!
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逄雪超 created ticket #20
convert wiff2 obtained from SCIEX X500R to mzML
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Gautam Saxena posted a comment on discussion Open Discussion
(CrossPosted here: https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/proteomicsqa/a4MUEZrzCBo/d2rDoVXrBwAJ ) Hi ProteoWizard Engineers, So, I've been trying to read Sciex wiff file from Java by using SWIG + ProteoWizard's WiffFile.cpp file. I haven't quite got it working, but I'm 99% sure that's because I don't know C/C++ (and more importantly, boost), so I get all these compilation issues. I read in an old paper that ProteoWizard folks were thinking about using SWIG for the...
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Matt Chambers committed [r11906]
* testing read only
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* testing read only
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* testing read only
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Archie Cobbs posted a comment on ticket #19
OK. I've worked around it by ignoring all characters prior to the first '<'. If you have any contacts with the Bruker team (perhaps Daniel Kruegler?), they might be interested to see this issue. Thanks.
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Hi Archie, Thanks for the report. Unfortunately that log message is coming from the Bruker reader DLL, and we can't readily control that behavior. (MSConvert already directs informational messages to stderr when stdout is the output stream.) You'll have to work out a solution that doesn't involve stdout, or possibly run the conversion twice to provoke the creation of that sqlite file when needed. Brian On Fri, Apr 6, 2018 at 5:32 PM, Archie Cobbs archiecobbs@users.sourceforge.net wrote: I suppose...
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I suppose it's obvious, but the proper fix is to send all log messages to standard error, not standard output.
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Output to stdout broken (invalid XML) due to log message
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Nicholas Shulman committed [r11903]
Calibration curve fixes (reported by Will):
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More detail about precursor and fragment isotope distributions.
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Fix all forms that don't currently inherit from either FormEx, CommonFormEx, or DockableFormEx (so that they properly stay hidden when running tests offscreen).
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Tobias Rohde committed [r11900]
Skyline (audit log branch) - improved log messages, audit log form and undo-redo list
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Skyline: handle small molecule transition lists such as this one, where the product columns are left empty to imp[y that the precursor is the ion of interest for this row
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BOUTASKIOUINE MUSTAPHA modified a comment on discussion Open Discussion
Hello, I have ran quickbuild.bat and it has completed without error and generated exe files but i did not find WiffFileTest. My question, how to compile/run WiffFileTest.cpp ? Best regards,
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Hello, I have ran quickbuild.bat and it has completed without error and generated exe files but i did not find WiffFileTest. My question, how to compile WiffFileTest.cpp ? Best regards,
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Hello, I have imported the project on Visual studio but i can not run WiffFileTest because i am getting error : Error 153 error D8045: cannot compile C file 'build-nt-x86\ext\hdf5\hdf5\msvc-12.0\release\asynch-exceptions-on\link-static\threading-multi\H5lib_settings.c' with the /clr option ..\pwiz-src-3_0_11885.tar\pwiz-src\cl Best regards,
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How to run WiffFileTest.cpp?
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Fix problem where bilinear calibration curve would not look right if you zoomed in too much.
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Skyline: Drift time predictor derived from "Use Results" wasn't being retained (or used, as result) properly with small molecule data. A number of changes along the way to fixing this:
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Merge from trunk
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Merge from trunk
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Skyline: implemented ToString() in TransitionIsotopeDistInfo for debugging convenience. No behavioral change.
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Import/Export annotations menu items.
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Skyline: small molecule transition list reader wasn't working properly when Transition Settings precursor and fragment mass types were different. This could lead to confusing messages about calculated mz values not matching, even if no explicit mz value was provided. Also, displayed mz value for precursor and precursor transition in Targets tree would not match.
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Merge from trunk.
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Disable Chorus.
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Some fixes: allow removing annotations while importing.
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Fix calculation of Limit of Quantification with respect to "Max LOQ Bias".
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Kaipo committed [r11887]
BiblioSpec: add score column to RetentionTimes table in filtered blib files
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Skyline: add CV column for Thermo transition list export
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Checking in MattC's patch to allow simultaneous use of Waters vendor peak picking and lockmass correction. Formerly both demanded to be first, lockmass correction is now able to wrap Waters native peak picking.
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Skyline: small update to our CSV reader to make it possible to read a small molecule transition list with isotopic formulas like CO""2 (meaning CO"2, the double " is an escape). N.B. the notion of proper quote handling (as currently implemented by Excel and Google Sheets) has moved on since our CSV parser was originally implemented, and this may be revisited soon. It really ought to be possible to just say CO"2 as that works fine in other parsers. Currently we just drop the " in CO"2, which w...
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Issue 553: Support Contains filter for report column that looks like text
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Merge from trunk
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Steffen Neumann created ticket #18
mzML writer created files don't validate
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Merge from trunk.
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When exporting annotations, use a big wide grid instead of one annotation per row.
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Add comments and localize strings.
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Command line import of annotations
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Skyline (audit log branch) - property name localization
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Import annotations
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Skyline: offer a more helpful error message in the thrown exception when we hit "Win32 Error 5", which is actually about write permissions.
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Skyline: tweak this script to remove spurious warning when PrtocolBuffers has already been cleaned
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Brendan MacLean committed [r11871]
Skyline: Merged revision(s) 11869 from branches/skyline_4_1:
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Skyline: Revert unintended changes to Skyline.csproj
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Skyline: Fix PeptideSettingsUI handling for Sonar settings
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Skyline: Fix recent DLL dependency changes (VC14 and SQLite)
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New branch for "element locator" which identifies every node in a Skyline document.
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Fix parent window of LongWaitDlg that comes up when reimporting chromatograms.
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Show error message when creating background proteome if any protein sequence contains invalid characters.
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Fix problem where SpectraST libraries would always think they were changed and Skyline would update library info on every docnode.
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Skyline (audit log branch) - improved log messages, added new mode
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Skyline: fix an L10N omission (changed a resx string used in two places but only updated one of them to use the new resource string)
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Merge from 4.1 branch.
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Fix bug where libraries were disregarding modifications when returning retention times.
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Skyline: Improved backward compatibility for older Skyline small mol documents.
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Skyline: correct a failure to completely populate some tables in File>Export>SpectralLibrary .blib files, especially around Collisional Cross Section values. This corrects two issues:
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Skyline: support negative CoV
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- added VC14 CRT merge modules to pwiz and IDPicker installers
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Skyline (audit log branch) - better log messages, improved audit log form, fixed bugs
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Add a text file to "pwiz_tools/Skyline/ProtocolBuffers/GeneratedCode" in case other source control systems cannot handle empty folders.
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Skyline: move this tutorial test to the TestPerf workspace due to its use of a large download
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Skyline: Rename ion mobility tutorial to be more obviously appealing to researchers interested in ion mobility
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Fix intermittent failure in TestSmallMoleculesTutorial: consistent ChromGroupHeaderInfo sort order
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Enable ratio to heavy in small molecule documents, even if there are no peptide modifications associated with the label type.
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Skyline: Fix names of new tutorials (second try - without renaming)
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Updated tutorial from NatBr.
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Reduce amount of memory used when building background proteome.
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Fix Topograph unit test. Add all VC140 .dll's to testrunconfig
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* added VC14 CRT for Topograph to be able to use TIMS SDK 2.2 DLLs
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BiblioSpec: add .osw support
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Skyline: Fix file names for new small molecule tutorials
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