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UniDec Version 6.0.1
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@michaelmarty michaelmarty released this 13 Mar 21:42
· 181 commits to master since this release
v.6.0.1
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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.

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