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This is under construction and more will be added in time. Feel free to contribute.
Some info on file types, installation, licensing, change logs, and usage is on the readme: https://github.com/michaelmarty/UniDec/
For a beginner video tutorial, check out: https://www.youtube.com/watch?v=e33JxgY6CJY
For more advanced tutorials check out our tutorial videos on:
- Importing Data into UniDec
- Intro to Data Processing
- Advanced Data Processing
- Intro to Deconvolution Parameters
- How UniDec works and Quick Controls
- UniDecCD: Deconvolution of CD-MS Data
- UniDecCD: Calibration
- UPP: UniDec Processing Pipeline
Other videos are coming, so please stay tuned and let us know if you have suggestions for future videos.
I'm working on a series of videos to teach Python programming. I'll post them here as they become available.
This series of lessons will cover how to set up Python from scratch and write a simple script to plot a mass spectrum.
- Lesson 0.0: Setting up Python from Scratch
- Lesson 0.1: Loading Data Into Python
- Lesson 0.2: Plotting a Spectrum
- Lesson 0.3: Too Fast, Go Back - Review and Background from Module 0
Check back for more videos, and let me know if you like these.
For those looking for a more extensive protocol, check out our article on ChemRxiv or Methods in Molecular Biology
These pages will describe the main features for UniDec. More are coming.
- Basic Deconvolution Parameters
- How does UniDec work?
- Quick Controls
- Advanced Deconvolution Parameters
Check out our pages on:
- What are those file outputs and how can I export my data?
- Installing the Source Code
- Hidden Features
- Advanced Analysis Tools
- Tips and Tricks
- Using MetaUniDec for Chromatograms
- Frequently Asked Questions
- Fitting KDs with the Data Collector
- How do I get the Error from a Deconvolution?
For those interested in learning programming from scratch, I'm going to try putting something together here:
These are the publications directly relevant to UniDec and will have additional details. Please cite these because citations are our best way to track usage and make the case for continued funding to support UniDec development.
- Original Paper: Please cite this on any paper using UniDec
Marty, M.T.; Baldwin A.J.; Marklund, E.G.; Hochberg, G.K.A.; Benesch, J.L.P.; Robinson C.V. “Bayesian Deconvolution of Mass and Ion Mobility Spectra: From Binary Interactions to Polydisperse Ensembles” Anal. Chem. 2015, 87, 4370-4376. Open Access Link
- General Protocol
Kostelic, M.M.; Marty, M.T.: Deconvolving Native and Intact Protein Mass Spectra with UniDec. In Proteoform Identification: Methods and Protocols; Sun, L., Liu, X., Eds.; Springer US: New York, NY, 2022; pp 159-180. Open Access Link
- MetaUniDec
Reid, D. J.; Diesing, J. M.; Miller, M. A.; Perry, S. M.; Wales, J. A.; Montfort, W. R.; Marty, M. T. "MetaUniDec: High-Throughput Deconvolution of Native Mass Spectra." J. Am. Soc. Mass. Spectrom. 2019, 30, 118-127. Open Access Link
- Softmax/Remove Artifacts/Beta Feature
Marty. M.T. “Eliminating Artifacts in Electrospray Deconvolution with a SoftMax Function.” J. Am. Soc. Mass Spectrom. 2019, 30, 2174-2177. Open Access Link
- DScore
Marty, M.T. “A Universal Score for Deconvolution of Intact Protein and Native Electrospray Mass Spectra.” Anal. Chem. 2020, 92, 4395-4401. Open Access Link
- Macromolecular Mass Defect Analysis
Marty, M.T.; Hoi, K.K.; Gault, J.; Robinson, C.V. “Probing the Lipid Annular Belt by Gas-phase Dissociation of Membrane Proteins in Nanodiscs” Angew. Chemie. Int. Ed. 2016, 55, 550-554. Open Access Link
- Point Smoothing
Kostelic, M.M.; Ryan, A.M.; Reid, D.J.; Noun, J.M.; Marty, M.T. "Expanding the Types of Lipids Amenable to Native Mass Spectrometry of Lipoprotein Complexes. J. Am. Soc. Mass Spectrom." 2019, 30, 1416-1425. Open Access Link
- DoubleDec
Norris, C.; Keener, J.E.; Perera, S.M.D.C.; Weerasinghe, N.; Fried, S.D.E.; Resager, W.C.; Rohrbough, J.G.; Brown, M.F.; Marty, M.T. “Native Mass Spectrometry Reveals the Simultaneous Binding of Lipids and Zinc to Rhodopsin” Int. J. Mass Spectrom. 2021. 460, 116477. Open Access Link
- UniDecCD
Kostelic, M.M.; Zak, C.K.; Liu, Y.; Chen, V.; Wu, Z.; Sivinski, J.; Chapman, E.; Marty, M.T. “UniDecCD: Deconvolution of Charge Detection-Mass Spectrometry Data.” Anal. Chem. 2021, DOI:10.1021/acs.analchem.1c03181. Open Access Link
- A Discussion of the Fundamentals in Error and Uncertainty Calculation
Marty, M.T. "Fundamentals: How Do We Calculate Mass, Error, and Uncertainty in Native Mass Spectrometry?" J. Am. Soc. Mass. Spectr. 2022, DOI: 10.1021/jasms.1022c00218. Open Access Link
- The UniDec Processing Pipeline (UPP)
Phung, W.; Bakalarski, C.; Hinkle, T.; Sandoval, W.; Marty, M.T. “The UniDec Processing Pipeline for Rapid Analysis of Biotherapeutic Mass Spectrometry Data.” Anal. Chem. 2023, Provisionally Accepted.