Version 7.0.2 UniDec.

Please cite Marty et al. Anal. Chem. 2015. DOI: 10.1021/acs.analchem.5b00140 if you use UniDec in publications.

Check out a video tutorial: https://www.youtube.com/watch?v=e33JxgY6CJY. For more user help and additional video tutorials, see the Wiki page: https://github.com/michaelmarty/UniDec/wiki.

Installation Instructions: Download the zip file and extract it to a convenient location. Click on "GUI_UniDec.exe". The software should then run with no additional installation. It is a self-contained package. Note, this compiled version will only run on Windows.

Important Note: If you are having issues where it crashes when opening Thermo files, it may be because the security settings are blocking parts of the software. To fix this, delete the unzipped folder, right click on the zip file, select Properties, and click unblock. You can then unzip the file again, and it should work.

If you need to use Windows 7 or earlier, I would recommend installing a Win 7 compatible Python version and using and <python -m unidec.Launcher> to run UniDec from the source code.

We rely on help from the community to find issues and suggest improvements. Please send comments via email to [email protected]. Thanks for your continued help!

Change Log:

v.7.0.2

Improvements to UPP outputs. Fixed issue with reports getting overwritten if the same file is used in multiple rows with UPP.

Added new options in MetaUniDec for Average Charge State Plotting. Added exports of text files for fits and fitdata.

Added new pre-import intensity filter for UCD, which should help with memory crashes on large data files.

Fixed bug opening mzML files with new build.

Fixed bug with smashflag on UPP.

Fixed a few display and interface bugs on UCCD and UCD.

Fixed Waters Data Conversion Wizard issue with Trapping Collision Energy (eV). Stopped it from closing by default when the conversion is initiated.

Fixed bug with KD fitting on DataCollector. Fixed bug with UltraMeta.

Fixed bugs with UCD Thermo imports and with Thermo header information for resolution.

Version 7.0.1 UniDec.

Please cite Marty et al. Anal. Chem. 2015. DOI: 10.1021/acs.analchem.5b00140 if you use UniDec in publications.

Check out a video tutorial: https://www.youtube.com/watch?v=e33JxgY6CJY. For more user help and additional video tutorials, see the Wiki page: https://github.com/michaelmarty/UniDec/wiki.

Installation Instructions: Download the zip file and extract it to a convenient location. Click on "GUI_UniDec.exe". The software should then run with no additional installation. It is a self-contained package. Note, this compiled version will only run on Windows.

Important Note: If you are having issues where it crashes when opening Thermo files, it may be because the security settings are blocking parts of the software. To fix this, delete the unzipped folder, right click on the zip file, select Properties, and click unblock. You can then unzip the file again, and it should work.

If you need to use Windows 7 or earlier, I would recommend installing a Win 7 compatible Python version and using and <python -m unidec.Launcher> to run UniDec from the source code.

We rely on help from the community to find issues and suggest improvements. Please send comments via email to [email protected]. Thanks for your continued help!

Change Log:

v.7.0.1

Continued development and tweaks to UniChromCD. Bug fixes and GUI improvements. Added multiplex spectrum cropping. New HT sequences.

Switched default font to Arial after years of fighting Illustrator on Deja Vu Sans.

Bug fixes for file opening on Agilent and mzML.

v.7.0.0

Added new module for time domain CD-MS data analysis, UniChromCD. This includes some cool new plotting and analysis features. Most importantly, it also includes our new method for Hadamard Transform analysis of CD-MS spectra. You can use the tools for regular LC-CD-MS or go crazy with HT-LC-CD-MS. More info coming soon on this front...:)

UPP added NumPeaks output on all to help with catching bad files in the results. Also, fixed bugs to allow files with bad data to proceed relatively unscathed. It should be more error tolerant now for large runs.

Added Ctrl+0 as shortcut to open the most recent file.

Added experimental feature for check box on main UniDec panel for whether to normalize the peak threshold. When on, it will behave as previously where the peak thershold is a ratio of the max intensity. When off, it will be a fixed intensity. Try switching off "Publication Mode" to view the plot with intensity axes. Note, this interacts with the Peak Normalization parameter directly above it. Max will normalize everything to 100. Total can get weird. None is the safest bet.

Blocked mouse wheel events on drop down selections. This should fix a lot of accidental switches to parameters.

Removed or made optional some dependencies to streamline installation. Removed special report type. Updates for Python 3.12 and general library updates.

Fixed deep bug with integration transforms. Improvements and refactoring to support UniChromCD. Fixed execution bug on servers. Fixed other bugs.

v.6.0.5

Merged into v.7

Minor fixes to update compatibility for Python 3.11 and 3.12.

Fixed common crash bug when isotope mode is on. Added warnings for if isotope mode is on.

Version 7.0.0 Beta 1 UniDec.

Please cite Marty et al. Anal. Chem. 2015. DOI: 10.1021/acs.analchem.5b00140 if you use UniDec in publications.

Check out a video tutorial: https://www.youtube.com/watch?v=e33JxgY6CJY. For more user help and additional video tutorials, see the Wiki page: https://github.com/michaelmarty/UniDec/wiki.

Installation Instructions: Download the zip file and extract it to a convenient location. Click on "GUI_UniDec.exe". The software should then run with no additional installation. It is a self-contained package. Note, this compiled version will only run on Windows.

Important Note: If you are having issues where it crashes when opening Thermo files, it may be because the security settings are blocking parts of the software. To fix this, delete the unzipped folder, right click on the zip file, select Properties, and click unblock. You can then unzip the file again, and it should work.

If you need to use Windows 7 or earlier, I would recommend installing a Win 7 compatible Python version and using and <python -m unidec.Launcher> to run UniDec from the source code.

We rely on help from the community to find issues and suggest improvements. Please send comments via email to [email protected]. Thanks for your continued help!

Change Log:

v.7.0.0

Added new module for time domain CD-MS data analysis, UniChromCD. This includes some cool new plotting and analysis features. Most importantly, it also includes our new method for Hadamard Transform analysis of CD-MS spectra. You can use the tools for regular LC-CD-MS or go crazy with HT-LC-CD-MS. More info coming soon on this front...:)

UPP added NumPeaks output on all to help with catching bad files in the results. Also, fixed bugs to allow files with bad data to proceed relatively unscathed. It should be more error tolerant now for large runs.

Added Ctrl+0 as shortcut to open the most recent file.

Added experimental feature for check box on main UniDec panel for whether to normalize the peak threshold. When on, it will behave as previously where the peak thershold is a ratio of the max intensity. When off, it will be a fixed intensity. Try switching off "Publication Mode" to view the plot with intensity axes. Note, this interacts with the Peak Normalization parameter directly above it. Max will normalize everything to 100. Total can get weird. None is the safest bet.

Blocked mouse wheel events on drop down selections. This should fix a lot of accidental switches to parameters.

Removed or made optional some dependencies to streamline installation. Removed special report type. Updates for Python 3.12 and general library updates.

Fixed deep bug with integration transforms. Improvements and refactoring to support UniChromCD. Fixed execution bug on servers. Fixed other bugs.

v.6.0.5

Merged into v.7

Minor fixes to update compatibility for Python 3.11 and 3.12.

Fixed common crash bug when isotope mode is on. Added warnings for if isotope mode is on.

Version 6.0.4 UniDec.

Please cite Marty et al. Anal. Chem. 2015. DOI: 10.1021/acs.analchem.5b00140 if you use UniDec in publications.

Check out a video tutorial: https://www.youtube.com/watch?v=e33JxgY6CJY. For more user help and additional video tutorials, see the Wiki page: https://github.com/michaelmarty/UniDec/wiki.

For a video tutorial on how to use the new UPP module, check out: https://youtu.be/dVoG6Gew27g.

Installation Instructions: Download the zip file and extract it to a convenient location. Click on "GUI_UniDec.exe". The software should then run with no additional installation. It is a self-contained package. Note, this compiled version will only run on Windows.

Important Note: If you are having issues where it crashes when opening Thermo files, it may be because the security settings are blocking parts of the software. To fix this, delete the unzipped folder, right click on the zip file, select Properties, and click unblock. You can then unzip the file again, and it should work.

If you need to use Windows 7 or earlier, I would recommend installing a Win 7 compatible Python version and using and <python -m unidec.Launcher> to run UniDec from the source code.

We rely on help from the community to find issues and suggest improvements. Please send comments via email to [email protected]. Thanks for your continued help!

Change Log:

v.6.0.4

Added "Notes" option to UPP to add notes to the bottom of the report. Added peak and data normalization options to UPP spreadsheet inputs. See help file.

Added "PyroGlu" option in UPP to automatically account for pyroglutamate formation on sequences that could have it. See help file for more information.

Printing HTML reports to PDF now looks better, with page breaks and background colors.

Command line now runs DScore with peak picking, so DScores will now appear in UPP.

Added del_columns custom field in batch.py for those that want to edit the report fields.

Fixed bug with CDCReader path in ImportWizard. Fixed weird bug with compressed mzML files. Fixed bug with save figure as and color bars.

Checksums:

MD5: a67326bac045b60ec365e27d5686d6da
SHA256: d2088e2b7735f8a5f3aabaa495d75477fff2862ca485b4a631ec57ee22845943

Version 6.0.3 UniDec.

Please cite Marty et al. Anal. Chem. 2015. DOI: 10.1021/acs.analchem.5b00140 if you use UniDec in publications.

Check out a video tutorial: https://www.youtube.com/watch?v=e33JxgY6CJY. For more user help and additional video tutorials, see the Wiki page: https://github.com/michaelmarty/UniDec/wiki.

For a video tutorial on how to use the new UPP module, check out: https://youtu.be/dVoG6Gew27g.

Installation Instructions: Download the zip file and extract it to a convenient location. Click on "GUI_UniDec.exe". The software should then run with no additional installation. It is a self-contained package. Note, this compiled version will only run on Windows.

Important Note: If you are having issues where it crashes when opening Thermo files, it may be because the security settings are blocking parts of the software. To fix this, delete the unzipped folder, right click on the zip file, select Properties, and click unblock. You can then unzip the file again, and it should work.

If you need to use Windows 7 or earlier, I would recommend installing a Win 7 compatible Python version and using and <python -m unidec.Launcher> to run UniDec from the source code.

We rely on help from the community to find issues and suggest improvements. Please send comments via email to [email protected]. Thanks for your continued help!

Change Log:

v.6.0.3

Added global peak output to UPP. Updated documentation and help for UPP to show how to write your own workflows.

Added cosine similarity to Image Plotter.

Added "Config Smash File" input to UPP.

Added DScore to peakparam.dat output.

Fixed bug with Waters time range on file open.

Fixed bug with peaks shapes not registering. Note, this fix will break compatiblity for the charge peak shape
parameter on older config files for UCD. Just change zpsfun to zpsfn on the config file to rescue.

Fixed bug with PDF saving not working.

Version 6.0.2 UniDec.

Please cite Marty et al. Anal. Chem. 2015. DOI: 10.1021/acs.analchem.5b00140 if you use UniDec in publications.

Check out a video tutorial: https://www.youtube.com/watch?v=e33JxgY6CJY. For more user help and additional video tutorials, see the Wiki page: https://github.com/michaelmarty/UniDec/wiki.

For a video tutorial on how to use the new UPP module, check out: https://youtu.be/dVoG6Gew27g.

Installation Instructions: Download the zip file and extract it to a convenient location. Click on "GUI_UniDec.exe". The software should then run with no additional installation. It is a self-contained package. Note, this compiled version will only run on Windows.

Important Note: If you are having issues where it crashes when opening Thermo files, it may be because the security settings are blocking parts of the software. To fix this, delete the unzipped folder, right click on the zip file, select Properties, and click unblock. You can then unzip the file again, and it should work.

Also, I recently learned that this version of UniDec is not compatible with Windows 7 because the newer versions of Python are no longer compatible. If you need to use Windows 7, I would recommend installing a Win 7 compatible Python version and using and <python -m unidec.Launcher> to run UniDec from the source code.

We rely on help from the community to find issues and suggest improvements. Please send comments via email to [email protected]. Thanks for your continued help!

Change Log:

v.6.0.2

Added a new Drug-to-Antibody Ratio (DAR) calculation mode for UPP. See help file for the new keywords.

Other improvements to UPP:

• Added color to the columns on UPP.
• Added ability to do peak integration.
• Added low and high charge config options.
• Added buttons to open results in Excel or other spreadsheet software.
• Added global HTML report.
• Improved file naming of outputs.
• Added progress bar on the bottom.

Fixed bug with HTML float sorting as text. Fixed major bugs with file imports.

Version 6.0.1 UniDec.

Please cite Marty et al. Anal. Chem. 2015. DOI: 10.1021/acs.analchem.5b00140 if you use UniDec in publications.

Check out a video tutorial: https://www.youtube.com/watch?v=e33JxgY6CJY. For more user help and additional video tutorials, see the Wiki page: https://github.com/michaelmarty/UniDec/wiki.

For a video tutorial on how to use the new UPP module, check out: https://youtu.be/dVoG6Gew27g.

Installation Instructions: Download the zip file and extract it to a convenient location. Click on "GUI_UniDec.exe". The software should then run with no additional installation. It is a self-contained package. Note, this compiled version will only run on Windows.

Important Note: If you are having issues where it crashes when opening Thermo files, it may be because the security settings are blocking parts of the software. To fix this, delete the unzipped folder, right click on the zip file, select Properties, and click unblock. You can then unzip the file again, and it should work.

Also, I recently learned that this version of UniDec is not compatible with Windows 7 because the newer versions of Python are no longer compatible. If you need to use Windows 7, I would recommend installing a Win 7 compatible Python version and using and <python -m unidec.Launcher> to run UniDec from the source code.

We rely on help from the community to find issues and suggest improvements. Please send comments via email to [email protected]. Thanks for your continued help!

Change Log:

v.6.0.1

Added Noise Removal Tool to UniDec and UniDecCD. This allows you to select specific noise regions (common in UHMR data) and set them to 0. Try Tools > Select Noise Peaks and the checking "Remove Noise Peaks" in the Advanced Data Processing Parameters.

UPP Changes:

• Added "Config m/z Peak FWHM", "Config m/z Peak Shape", and "Config Sample Mass Every" parameters. If "Config m/z Peak FWHM" is specified as a float or integer, it will use that and skip the automatic peak width determination.
• Enabled relative paths.
• Added "All" or "None" keywords on "Apply Fixed Mods" and "Disulfides Oxidized."
• Added "Config File" keyword to load a specific config file.
• More tolerant of nans and different file extensions
• Added ability to select files to load to UPP.
• Added "Global Fixed Mod" to apply the same float value to each pair.
• Special Bispecific Antibody Pairing Calculations (see Help File)
• Fixed issues bugs with use_converted, clear all, and resetting the config.

Fixed major bugs with 2D zooming and plotting.

v.6.0.0

Major changes to code structure to enable PyPI distribution. Changed to more conventional Python package structure with unidec top directory. Renamed unidec_modules to modules, unidec_src to src, and unidec_bin to bin. Renamed some top level windows and moved all to main folder. For example, unidectools.py has been moved from modules to the top level and renamed as tools.py, and unidec.py has been renamed as engine.py. The good news is that you can now do pip install unidec and python -m unidec.Launcher to run UniDec from the command line.

Improved command line tools. Added -o option for file output in unidec. Included new entry points and smoothed out command line interface. Now you can use unidec to lanuch python -m unidec in the scripts folder. Similarly, gunidec will launch python -m unidec.Launcher. If you have Python and the scripts folder configured in your system path, command line tools will be much easier to use.

Added a new mode to the Oligomer and Mass Tools, Site Mode. Here, you can specify specific binding sites and which potential species could be bound in that site. Any number of rows (species) or columns (sites) can be added as long as your memory can handle the possible combinations. Use 0s and 1s to incidate whether each species can be bound at each site. You can copy/paste from excel or open a CSV or XLSX file.

Added the first build of the UniDec Processing Pipeline tool to help with batch processing and analysis for large sample sets. More details to come.

Added new experimental HTML report generator. Found in File > Save Figure Presets. Test this out and let me know what you'd like to see in it.

Added a color plot option to the right click of the peak panel. Check it out!

Added FWHM and error to the Copy All Full right click option in the peak panel.

Changed default behavior for zooming such that it does not zoom out when plots are replotted. This is a major change that I think will be more intuitive. If you want to zoom out, you can still click once on the plot as usual.

Removed the ability to manually integrate peaks. Now, only auto integration is allowed. If you want to have this added back in, let me know, but it seemed to be causing more trouble than it was worth.

Various bug fixes including fixing EPS export and bugs on Export2D. Fixed import of tab delimited files. Resized manual file menu. Improved window stretching in oligomer and mass tools. Broken plot peaks on UniDecCD. Bug on selecting alternative matches not propagating. Updated background color to blue on alternative matches to avoid confusion with RYG scheme. Fixed labeling bug with isolated match names.

Version 6.0.0 UniDec.

Please cite Marty et al. Anal. Chem. 2015. DOI: 10.1021/acs.analchem.5b00140 if you use UniDec in publications.

Check out a video tutorial: https://www.youtube.com/watch?v=e33JxgY6CJY. For more user help and additional video tutorials, see the Wiki page: https://github.com/michaelmarty/UniDec/wiki.

Installation Instructions: Download the zip file and extract it to a convenient location. Click on "GUI_UniDec.exe". The software should then run with no additional installation. It is a self-contained package. Note, this compiled version will only run on Windows.

Important Note: If you are having issues where it crashes when opening Thermo files, it may be because the security settings are blocking parts of the software. To fix this, delete the unzipped folder, right click on the zip file, select Properties, and click unblock. You can then unzip the file again, and it should work.

Also, I recently learned that this version of UniDec is not compatible with Windows 7 because the newer versions of Python are no longer compatible. If you need to use Windows 7, I would recommend installing a Win 7 compatible Python version and using and <python -m unidec.Launcher> to run UniDec from the source code.

We rely on help from the community to find issues and suggest improvements. Please send comments via email to [email protected]. Thanks for your continued help!

Change Log:

v.6.0.0

Major changes to code structure to enable PyPI distribution. Changed to more conventional Python package structure with unidec top directory. Renamed unidec_modules to modules, unidec_src to src, and unidec_bin to bin. Renamed some top level windows and moved all to main folder. For example, unidectools.py has been moved from modules to the top level and renamed as tools.py, and unidec.py has been renamed as engine.py. The good news is that you can now do pip install unidec and python -m unidec.Launcher to run UniDec from the command line.

Improved command line tools. Added -o option for file output in unidec. Included new entry points and smoothed out command line interface. Now you can use unidec to lanuch python -m unidec in the scripts folder. Similarly, gunidec will launch python -m unidec.Launcher. If you have Python and the scripts folder configured in your system path, command line tools will be much easier to use.

Added a new mode to the Oligomer and Mass Tools, Site Mode. Here, you can specify specific binding sites and which potential species could be bound in that site. Any number of rows (species) or columns (sites) can be added as long as your memory can handle the possible combinations. Use 0s and 1s to incidate whether each species can be bound at each site. You can copy/paste from excel or open a CSV or XLSX file.

Added the first build of the UniDec Processing Pipeline tool to help with batch processing and analysis for large sample sets. More details to come.

Added new experimental HTML report generator. Found in File > Save Figure Presets. Test this out and let me know what you'd like to see in it.

Added a color plot option to the right click of the peak panel. Check it out!

Added FWHM and error to the Copy All Full right click option in the peak panel.

Changed default behavior for zooming such that it does not zoom out when plots are replotted. This is a major change that I think will be more intuitive. If you want to zoom out, you can still click once on the plot as usual.

Removed the ability to manually integrate peaks. Now, only auto integration is allowed. If you want to have this added back in, let me know, but it seemed to be causing more trouble than it was worth.

Various bug fixes including fixing EPS export and bugs on Export2D. Fixed import of tab delimited files. Resized manual file menu. Improved window stretching in oligomer and mass tools. Broken plot peaks on UniDecCD. Bug on selecting alternative matches not propagating. Updated background color to blue on alternative matches to avoid confusion with RYG scheme. Fixed labeling bug with isolated match names.

Version 5.2.1 UniDec.

Please cite Marty et al. Anal. Chem. 2015. DOI: 10.1021/acs.analchem.5b00140 if you use UniDec in publications.

Check out a video tutorial: https://www.youtube.com/watch?v=e33JxgY6CJY. For more user help and additional video tutorials, see the Wiki page: https://github.com/michaelmarty/UniDec/wiki.

Installation Instructions: Download the zip file and extract it to a convenient location. Click on "GUI_UniDec.exe". The software should then run with no additional installation. It is a self-contained package. Note, this compiled version will only run on Windows.

Important Note: If you are having issues where it crashes when opening Thermo files, it may be because the security settings are blocking parts of the software. To fix this, delete the unzipped folder, right click on the zip file, select Properties, and click unblock. You can then unzip the file again, and it should work.

Also, I recently learned that this version of UniDec is not compatible with Windows 7 because the newer versions of Python are no longer compatible. If you need to use Windows 7, I would recommend installing a Win 7 compatible Python version and using and <python -m unidec.Launcher> to run UniDec from the source code.

We rely on help from the community to find issues and suggest improvements. Please send comments via email to [email protected]. Thanks for your continued help!

Change Log:
v.5.2.1

UniDec and UniChrom now try to read the polarity from the data and set the adduct appropriately for some file types. Check that this is working!

Added right click for zoom on UniChrom TIC.

Added ability to label names from peak panel.

Added drag and drop for batch processing in UniChrom.

Significantly faster reading of some mzML files.

Fixes to reading in Agilent Files. May no longer need adminstrator access but not sure. Also, may work with Bruker TIMS data, but also not sure about this. Let me know how it goes if anyone has the guts to try it...

Fixes with reading some config files. Fixes with npz file reading.

Version 5.2.0 UniDec.

Please cite Marty et al. Anal. Chem. 2015. DOI: 10.1021/acs.analchem.5b00140 if you use UniDec in publications.

Check out a video tutorial: https://www.youtube.com/watch?v=e33JxgY6CJY. For more user help and additional video tutorials, see the Wiki page: https://github.com/michaelmarty/UniDec/wiki.

Installation Instructions: Download the zip file and extract it to a convenient location. Click on "GUI_UniDec.exe". The software should then run with no additional installation. It is a self-contained package. Note, this compiled version will only run on Windows.

Important Note: If you are having issues where it crashes when opening Thermo files, it may be because the security settings are blocking parts of the software. To fix this, delete the unzipped folder, right click on the zip file, select Properties, and click unblock. You can then unzip the file again, and it should work.

We rely on help from the community to find issues and suggest improvements. Please send comments via email to [email protected]. Thanks for your continued help!

Change Log:
v.5.2.0

Major speed up to Plot Peaks command that simulates the isolated charge state distributions! This function is now built into the same C code used by UniDec, and is called by the UniDec.exe _conf.dat -conv. It produces a binary file output that is read in and plotted.

Improvements to matching speed and API. Added right click option to send item from oligomer list to common matches list. Added a bunch of glycans and stuff to the common masses table.

Improvements to MetaUniDec. Create a merged template rather than just using the first spectrum. Improvements to speed by keeping file open for the whole session. Reduction in print outputs.

Improvements to Imaging viewer, including bug fixes.

Added ability to calculate consecutive differences in peak masses.

Added continuous plot button for UCD m/z vs. mass. Also, fixed bug to improve plotting.

Improved copy/paste from peak list.

Added ability to read text file exported from Chromeleon that have a bunch of commas in the numbers.

Added mzXML support courtesy of pyteomics (please cite: Goloborodko, A.A.; Levitsky, L.I.; Ivanov, M.V.; and Gorshkov, M.V. (2013) “Pyteomics - a Python Framework for Exploratory Data Analysis and Rapid Software Prototyping in Proteomics”, Journal of The American Society for Mass Spectrometry, 24(2), 301–304. DOI: 10.1007/s13361-012-0516-6 and Levitsky, L.I.; Klein, J.; Ivanov, M.V.; and Gorshkov, M.V. (2018) “Pyteomics 4.0: five years of development of a Python proteomics framework”, Journal of Proteome Research. DOI: 10.1021/acs.jproteome.8b00717)

Added Docker container and updated for command line usage of unidec.py. (NOTE: Still experimental. Reach out if interested)

Fixed bug with the Peak Width Tools in UCD. Fixed labeling issue on UniChrom. Added UCD as command launch item.