Version 4.2.0 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. Let me know what other things would be useful to add here.
**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.
It is possible to build and run UniDec on Linux and Mac, but you will need to compile the binary from the C code and run the GUI with Python.
Note: We rely on help from the community to find issues and suggest improvements. If you encounter a bug, first try downloading the latest version if available. If that doesn't fix it, please send an email to mtmartyemail.arizona.edu. Thanks for your continued help.
**Change Log:**
v.4.2.0
**Added Smart Transform**. From the beginning, UniDec has asked users to decide how it should perform the nonlinear transform from m/z to mass (Integration or Interpolation). Now, the Smart Transform decides for the user based on the density of the data. Where the data is sparse relative to the mass sampling, it will use interpolation to fill in the gaps. Where data is dense relative to the mass sampling, it will use integration to ensure that all the data in-between is accounted for. Smart Transform is located under the Additional Deconvolution Parameters tab and has now been made the default. In some preliminary testing, the Smart Transform showed more robust peak areas that were less sensitive to the mass sampling. The peak heights may change some, but the peak areas should be a lot more reliable (remember Ctrl+I to integrate). Note: you may not notice much difference, but using the Smart Transform should avoid some glitches that are hard to spot. Let me know how it goes!
**Major improvements in 2D plotting speed** due to behind-the-scenes changes and optimzation of the plotting code.
**Sparse data support**. Improvements to the algorithm to support sparse data, including just peak centroids. This fundamentally changes the underlying algorithm in minor ways. You may notice minor differences but likely will not. Let me know if it causes any problems.
Better handling of click and zoom at the edges of the plot. Now, it will default to the edge if you go off the plot.
Added drag and drop for loading the state from a zip file.
Upgraded pymzml version for improved mzML compatibility and made mzML import more error tolerant.
Fixed issue with discrete plot and data that was non-uniformly sampled.
Fix to bug in calculating the error from the weighted standard deviation of charge state masses.
Fixed bug in Load and Save State with non-text files.
Fixed IM-MS plotting bugs.
Note: the the first binary from 200309 has been updated to 200311 to reflect further optimizations in plotting speed. I didn't feel like making a whole new version for a minor change though.
v.4.1.2
Version 4.1.2 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
**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.
It is possible to build and run UniDec on Linux and Mac, but you will need to compile the binary from the C code and run the GUI with Python.
Note: We rely on help from the community to find issues and suggest improvements. If you encounter a bug, first try downloading the latest version if available. If that doesn't fix it, please send an email to mtmartyemail.arizona.edu. Thanks for your continued help.
**Change Log:**
v.4.1.2
Added button in UniDec to turn off data normalization. Note: the beta values will be automatically scaled to match this.
Renamed the parameter ZScore in the UniScore calculation to CSScore. Added R squared to the UniScore calculation.
Added several experimental subtract and divide features. Tweaks to linear regression experimental feature.
Bug fixes and compatibility updates.
V.4.1.1
Version 4.1.1 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
**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.
It is possible to build and run UniDec on Linux and Mac, but you will need to compile the binary from the C code and run the GUI with Python.
Note: We rely on help from the community to find issues and suggest improvements. If you encounter a bug, first try downloading the latest version if available. If that doesn't fix it, please send an email to mtmartyemail.arizona.edu. Thanks for your continued help.
**Change Log:**
v.4.1.1
Added right click feature to color peaks by their scores.
Improvements to Data Collector module to fit protein oligomerization KDs and improve customization.
Added experimental Linear Regression features for analysis of repeating mass units.
Added experimental FPOP feature to print and copy average degree of oxidation.
Various syntax optimizations to address deprecation warnings and library updates.
v.4.1.0
Version 4.1.0 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
**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.
It is possible to build and run UniDec on Linux and Mac, but you will need to compile the binary from the C code and run the GUI with Python.
Note: We rely on help from the community to find issues and suggest improvements. If you encounter a bug, first try downloading the latest version if available. If that doesn't fix it, please send an email to mtmartyemail.arizona.edu. Thanks for your continued help.
**Change Log:**
Introduced **UniScore**. This will automatically score the quality of your peaks and the overall deconvolution. Various experimental features were also added with this to visualize and filter the scores. Some updates to the scoring algorithm from Version 4.0.2 to improve it.
A full description of the UniScore can be found in this preprint: https://doi.org/10.26434/chemrxiv.10278041
A good heuristic for UniScore and DScore values is:
80-100: A (Excellent)
60-80: B (Good)
40-60: C (Fair)
20-40: D (Poor)
0-20: F (Almost certainly noise)
Added Calculator for getting masses from Protein/Peptide or RNA sequences. This can be launched stand alone from the Experimental Menu or by right clicking on the Oligomer and Mass Tools Oligomer Builder box.
Fixed bug to now allow protein-protein oligomerization KD values to be measured with the Data Collector. Find out more on the UniDec Wiki Page.
v.4.0.2
Version 4.0.2 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
**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.
It is possible to build and run UniDec on Linux and Mac, but you will need to compile the binary from the C code and run the GUI with Python.
**Note:** We rely on help from the community to find issues and suggest improvements. If you encounter a bug, first try downloading the latest version if available. If that doesn't fix it, please send an email to mtmartyemail.arizona.edu. Thanks for your continued help.
**Change Log:**
Switched UniDec to load processed data if it already exists.
Added Copy All Basic to the peak panel, which copies the peak mass, height, and area to a format you can paste into excel. I can add additional copy modes easily now, so let me know what you would like to be able to copy out.
Added control of spectra color map on MetaUniDec.
Added Waterfall Plots on Experimental Menu in MetaUniDec.
Many Bug Fixes: Sped up quick control responses by only doing auto peak width when needed. Fixed memory leak with HDF5 files. Fixed bugs slowing down file imports. Fixed bug with PDF Report Generator. Fix bug with isolate/ignore/repopulate/reorder in MetaUniDec.
Experimental features for peak scoring. More to come in future releases.
v.4.0.1
Version 4.0.1 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
Note: We rely on help from the community to find issues and suggest improvements. If you encounter a bug, first try downloading the latest version if available. If that doesn't fix it, please send an email to mtmartyemail.arizona.edu. Thanks for your continued help.
Change Log:
v.4.0.1
Improved the peak panel by switching to white text when the background gets dark, adding commas to the masses (hopefully it will be easier to read), and **adding new right click features to label masses**. Also fixed text colors on MetaUniDec spectrum panel.
Moved the Bin Every and Background Subtraction parameters from the main Data Processing tab to the Advanced Data Processing Parameters tab. **Added a Backround Subtraction check box** to turn on background subtraction with a curved background set to 100.
Added experimental support for **Agilent .D** files. Please test it and let me know how it works. You may need to run UniDec as an administrator first to get it to register all the DLLs correctly.
Added peak centroids, FWHM, and error between charge states to the _peakparams.dat output.
Added a check box to ignore zero values in UltraMeta and fixed the bar charts on UltraMeta to have the same colors as the main window.
Added the ability in UltraMeta to right click on a file and open it in MetaUniDec.
Added the ability to reorder spectra in MetaUniDec by editing the indexes.
Added new extraction choices for area of peaks above a threshold in UltraMeta and MetaUniDec.
UltraMeta will now be tolerant of different files having different x values when creating error bars. It will only plot and average consensus data points.
Mass Defect plots will now switch to kDa from Da if appropriate.
When adding data to HDF5 files, having CID_n or SID_n in the file name will import n as the collision voltage.
Fixed several bugs/issues to make everything run more smoothly.
V.4.0.0.beta1
Version 4.0.0 Beta 1 of UniDec. Includes MetaUniDec and other tools.
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
Note: We rely on help from the community to find issues and suggest improvements. If you encounter a bug, first try downloading the latest version if available. If that doesn't fix it, please send an email to mtmartyemail.arizona.edu. Thanks for your continued help.
Note: I have switched to the Waters MassLynxSDK version 4.5 from our custom converters. You may need to download new MassLynxRaw.dll files from Waters. I am working with Waters to get approval to distribute the DLL files bundled with UniDec, but it isn't final yet. Because I used the Waters API, I am not releasing the source code for the Waters Importer until I have that agreement in place. I will do this as soon as I can. In the mean time, Waters import features will work on the compiled binary version but not from the Python source code. You can keep using v.3.2 in the Master Branch in the mean time. Stay tuned...
Change Log:
v.4.0.0 Beta 1
Added Quick Controls to the main panel. This should allow you to turn on and off features quickly without those pesky numbers. The advanced controls are still available as before.
A new experimental feature has been added based to use a SoftMax function (controlled by the parameter beta) to suppress deconvolution artifacts. The higher beta is, the more the algorithm with seek a single charge state assignment for each data point. Setting beta to zero will turn this off. This seems to work best when combined with other assumptions, such as peak width, point smoothing, and charge and mass smoothing. It also seems to work best when combined with background subtraction. Play around with it and let me know what you think. A minus flag applies the SoftMax to the entire data set rather than just a single column of the m/z vs charge matrix at once.
Changed the Waters MS import from rawreader.exe to the MassLynxSDK 4.5. Waters DLLs will soon be included. Stay tuned...
Added Ctrl+C to copy out images from plots. You should be able to paste these into other applications.
Added Example Data, which can be quickly loaded from the File menu. You can also add data to this by dropping your own files in the Example Data folder. It works in the same was as the custom presets.
Added Data Reduction data processing feature in UniDec for removing noise from large data sets. Basically, you set a percentage of the data you want to remove. UniDec then finds what intensity threshold is required to remove that much and takes out all data below that threshold.
Added UniChrom for quick viewing of chromatogram TICs. You can open mzML or Thermo .Raw files directly. Waters .Raw files can be opened by dragging and dropping it in the main window.
Added more functionality for UltraMeta.
Added drag and drop for _conf.dat files to UniDec to more easily import settings.
Adjustments to the algorithm to improve speed and reliability. Switched build to Visual Studio 2019 and Intel Parallel Studio 19.
Changes to the Gaussian blur functions for charge and mass, which are activated by negative flags for mass and charge smooth width.
Removed cross validation feature because I'm pretty sure no one was using it.
v.3.2.0
Version 3.2.0 of UniDec. Includes MetaUniDec and other tools.
Please cite Marty et al. Anal. Chem. 2015. DOI: 10.1021/acs.analchem.5b00140 if you use UniDec in publications.
Note: With V.3.1.0, several background changes to the algorithm (MS-only) have allowed the use of more general settings, such as a peak width of 0 (v.2.7.3) and a point smooth width of 1, which adds an additional smooth of +/- 1 data point. We hope that these defaults and changes to the layout will allow new users to more easily access the software. Users will still have access to these parameters in the advanced settings windows.
More info on installation can be found here: https://github.com/michaelmarty/UniDec
If you would like to receive updates when new versions are released, please email mtmartyemail.arizona.edu to get added to the mailing list.
Note: We rely on help from the community to find issues and suggest improvements. If you encounter a bug, first try downloading the latest version if available. If that doesn't fix it, please send an email to mtmartyemail.arizona.edu. Thanks for your continued help.
Note: some Waters users are having problems with the data converter. Waters has changed their DLL files so that they are no longer compatible with our converter. Please see: https://github.com/michaelmarty/UniDec for more info on the specific DLL files that are required or contact me to get the appropriate DLLs.
V.3.1.0.1
Version 3.1.0 of UniDec. Includes MetaUniDec and other tools.
Please cite Marty et al. Anal. Chem. 2015. DOI: 10.1021/acs.analchem.5b00140 if you use UniDec in publications.
This version adds a new parameter for Point Width Smooth. It also changes the right control panels to streamline the key parameters and updates the default parameters to make them more universal.
Note: Several background changes to the algorithm (MS-only) have allowed the use of more general settings, such as a peak width of 0 (v.2.7.3) and a point smooth width of 1, which adds an additional smooth of +/- 1 data point. We hope that these defaults and changes to the layout will allow new users to more easily access the software. Users will still have access to these parameters in the advanced settings windows.
More info on installation can be found here: https://github.com/michaelmarty/UniDec
If you would like to receive updates when new versions are released, please email mtmartyemail.arizona.edu to get added to the mailing list.
Note: We rely on help from the community to find issues and suggest improvements. If you encounter a bug, first try downloading the latest version if available. If that doesn't fix it, please send an email to mtmartyemail.arizona.edu. Thanks for your continued help.
Note: some Waters users are having problems with the data converter. Waters has changed their DLL files so that they are no longer compatible with our converter. Please see: https://github.com/michaelmarty/UniDec for more info on the specific DLL files that are required or contact me to get the appropriate DLLs.
v.3.0.0
Version 3.0.0 of UniDec. Includes MetaUniDec and other tools. Version 3 is largely the same feature set as version 2.7.3, but it has been ported to Python 3.6. The largest noticeable change will be significantly improved speed for plotting. There were a number of changes behind the scenes, so please report any bugs that you encounter.
More info on installation can be found here: https://github.com/michaelmarty/UniDec
If you would like to receive updates when new versions are released, please email mtmartyemail.arizona.edu to get added to the mailing list.
Note: We rely on help from the community to find issues and suggest improvements. If you encounter a bug, first try downloading the latest version if available. If that doesn't fix it, please send an email to mtmartyemail.arizona.edu. Thanks for your continued help.
Note: some Waters users are having problems with the data converter. Waters has changed their DLL files so that they are no longer compatible with our converter. Please see: https://github.com/michaelmarty/UniDec for more info on the specific DLL files that are required or contact me to get the appropriate DLLs.