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Labs Using DCDT+ Publications List Revision History

What is DCDT+?

DCDT+ is a Windows® program for analysis of sedimentation velocity (SV) data that implements the dc/dt method originally developed by Walter Stafford, and also implements fitting of the derived g(s*) distributions as a mixture containing of up to 5 discrete (non-interacting) species.

The program is designed to be very easy to use, even for novices, yet it also offers many options for the 'power user' when they are needed. It uses multi-page analysis 'documents' and a familiar user interface with toolbars and buttons, making it similar to other Windows programs to reduce the learning curve. It also incorporates a number of intelligent 'wizards' that automatically accomplish tasks such as locating the meniscus position, removal of systematic noise ("jitter") and fringe jumps from interference scans, and even selection of which scans should be used for analysis.

This is not a package that tries to do everything---its purpose is to implement one particular approach, do that very well and very easily, and do it in a highly reproducible and well-documented manner.

The success of this approach is demonstrated by its use in 200+ publications. More significantly, many of these are from intermittent or casual users of AUC, proving you don't have to devote years to learning data analysis to successfully answer important research questions with SV.

The program is now distributed as "freeware" and requires no registration. The only restriction is that it cannot be sold or packaged with other commercial software. The author asks only that you cite it properly when publishing your analyzed results.

Unique features:

bulletModern multi-document, Explorer-style user interface
bulletmultiple analyses can be open simultaneously, and their g(s*) distributions are automatically incorporated into an overlay graph [example below]

bulletExplorer-like navigation tree to move to specific analysis pages (analysis steps) and between analysis documents
bulletclick-and-drag setting of meniscus marker, data limits, peak limits etc. [see image below]

bulletNew algorithm for fitting of g(s*) distributions or dc/dt curves as mixtures gives s, D, and M values for each species with theoretical accuracy of better than 0.1%, independent of the number of scans used in the analysis
bulletLoad the entire run and then use scroll bars to select the subset of scans to be analyzed (or just let the program wizard do it for you) [see image below]

bulletOptionally normalizes g(s*) distributions to allow easy comparisons of samples at different concentrations (a great diagnostic to distinguish interacting systems from mixtures, as in example shown 3 pictures above)
bullet'Standard' program mode alters user interface to hide options you probably don't need; 'Advanced' mode provides more options to power users
bulletProgram wizards automatically accomplish many tasks
bulletOnce scans are loaded, you can can calculate the g(s*) distribution and go all the way to a completed fit as a single species simply by repeatedly hitting the Enter key to accept the wizards' default choices
bulletNew! Generates a log file that records every step of the data analysis, every option selected, every intermediate fitting result (including a table and graph), when it was done, and by whom (for computers with authenticated log-in servers)
bulletEvaluates fitted parameter confidence intervals using any of three orthogonal approaches: F statistics, the bootstrap method, or a Monte Carlo algorithm that puts the random noise in the theoretical scans [to eliminate any concerns about effects of the transformation to g(s*)]
bulletTrue local Help file to give context-sensitive Help for each dialog box or control, with extensive tutorials and a searchable index. (A PDF file to print a user manual is also available to registered users)
bulletGenerates nicely formatted printed reports with tables, and which document every factor that influences the results. These reports (with graphs) can be pasted into your word processor or electronic lab notebook
bulletSaved analysis documents record every parameter, including the raw data, in a single file so you can re-load your analysis back to exactly the same state
bulletAnalysis documents appear in your 'My Recent Documents' folder, just like your other documents
bulletCreates 9 types of publication-quality graphs of fit results

DCDT+ is used by more than 100 laboratories around the world (partial list here).

 

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Jump to: Download it Now! | System Requirements | Revision history | User List | Publications 

How does DCDT+ differ from the ORIGIN® version of DCDT supplied by Beckman Coulter?

bulletDCDT+ provides correct values of D and M from fitting the g(s*) distributions
bullet the Beckman implementations (even the newest Origin 6 versions) contain an error in converting the width of the fitted Gaussians to diffusion coefficients; the returned D and M values are never accurate
bulletJust load the entire run in one operation and then select which scans to analyze using slider controls
bullet no more struggling to figure out which scans to load and analyze
bulletDCDT+ provides a quick test for whether you are broadening the curves by including too many scans
bullet get the best signal/noise possible without hoping and guessing about when you are averaging too many scans or struggling with cumbersome manual calculations
bullet standard errors or confidence intervals are calculated for all fitted parameters
bullet what good are fitting results if you don't know the uncertainty in the values returned?
bulletDCDT+ comes with a comprehensive, local context-sensitive Help file and optional printed manual
bullet includes step-by-step tutorials, tips, "how-to" guides, frequently-asked questions, a searchable index, and images of all forms
bulletfull reports of analyses are provided for documented, reproducible results
bullet sedimentation coefficients can be internally converted to s20,w values
bulletDCDT+ provides a unique option of fitting to dc/dt curves, giving improved accuracy and improved resolution of multiple species in some cases
bulletDCDT+ shows you the dc/dt curves for every individual scan pair so you can identify abnormal interference scans (outliers) before you unknowingly include them in your analyses
bullet bad scans can be removed from the analysis without starting over and reloading all the scans
bulletreproducible setting of the meniscus position
bullet no more struggling with the Origin® data marker and a tiny graph
bulletresults from fits give true molecular masses for any value of v-bar and density
bullet no more cumbersome manual calculations
bulletwhen the zero of the dc/dt curves is manually adjusted, that fact and the amount of the adjustment is documented in fit reports
bullet what good are results that can't be documented or reproduced?
bulletduring multi-species fits the masses and/or sedimentation coefficients can be constrained to ratios appropriate for small oligomers
bulletincludes a Claverie finite-element velocity experiment simulator for "what-if" testing and self-teaching
bullet unique option of using an alternative algorithm for calculating g(s*) distributions that works better than the standard Stafford algorithm when the time span of the scans grows long
bulletcomputes the number-, weight-, z-, and z+1-average sedimentation coefficients and total concentration from both the g(s*) and g^(s*) distributions, with error bars for all these values
bullethandles an unlimited number scans (up to available memory), not just 40
bulletcomputes and displays g^(s*) (g-hat), the distribution that should be used when studying interacting systems, as well as g(s*)
 
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How does DCDT+ differ from the ls-g(s) or c(s) methods in Peter Schuck's SEDFIT?

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The ls-g(s) distributions derived by SEDFIT are equivalent to the g(s*) distributions derived via the DCDT method only when the time span of the scans used in either method is small (a small number of scans). As the time span grows larger they become non-equivalent, and for ls-g(s) there is no longer any direct theoretical relationship between the width of a peak and the diffusion coefficient (or mass) of that species as there is for g(s*).

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For g(s*) derived via the DCDT method the removal of baseline noise (time-independent noise) and interference 'jitter' (radially-independent noise) is done via simple arithmetic and is model-independent. For ls-g(s) and c(s) the removal of this systematic noise is model-dependent.

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For c(s) distributions the diffusion information is essentially removed, which enhances the resolution for mixtures. The peak widths in c(s) are a function of signal/noise ratio and regularization parameters; they have no physical meaning.

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False peaks are often generated if the ls-g(s) method is applied to scans encompassing a large fraction of the run, especially for samples where diffusion is significant (conditions where it does not provide a good fit of the raw data). The c(s) method also generates false peaks if not used very carefully or whenever it cannot generate a good fit of the raw data. The dc/dt method never generates false peaks.

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Fitting of ls-g(s) distributions to one or more peaks is not implemented in SEDFIT; peak fitting makes no sense for c(s) distributions

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Neither ls-g(s) nor c(s) provides error bars for the distributions or properties of individual peaks

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SEDFIT does not provide reports, and does not store the analysis in a file so it can be re-opened

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SEDFIT cannot have multiple analyses open at the same time, and cannot overlay ls-g(s) or c(s) distributions from different samples

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SEDFIT does not have a local context-sensitive Help file with searchable index, or offer a printed manual

 

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System Requirements

DCDT+ version 2 will run under Windows 98, NT, 2000, XP, Vista, or Windows 7. Use via Windows dual-boot configurations on MacIntosh systems is neither supported nor guaranteed.

This program also requires the Microsoft .NET framework to be present on the computer. This is often already true for newer computers. If it is not already present, this is detected during installation and a link is given so it can be downloaded from Microsoft and installed.

Although DCDT+ will run correctly at a 640x480 (VGA) video resolution, a resolution of 1024 x 768 or higher is highly recommended. 

The program requires approximately 8 MBytes of disk space (most of which is for the comprehensive Help file). 

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How should I cite this program?

  1. The primary citation for this program is
    bulletPhilo, J. S. (2006). Improved methods for fitting sedimentation coefficient distributions derived by time-derivative techniques. Anal. Biochem. 354, 238-246.
  2. Because the original development of the dc/dt method was by Walter Stafford, please always also cite Walter Stafford's original paper:
    bulletStafford, W.F., III. 1992. Boundary analysis in sedimentation transport experiments: A procedure for obtaining sedimentation coefficient distributions using the time derivative of the concentration profile. Analytical Biochemistry 203:295-301.
  3. The program itself should be mentioned in your Methods section as DCDT+ by John Philo, with the version number.

Specialized method citations

The reference for the special multi-segment dc/dt calculations is

bulletPhilo, J. S. (2011). Limiting the sedimentation coefficient range for sedimentation velocity data analysis: Partial boundary modeling and g(s*) approaches revisited. Anal. Biochem. 412, 189-202.

The reference for fitting to dc/dt data rather than g(s*), and for the Use true mean time button (the 'broad algorithm')  is:

bulletPhilo, J.S. (2000) A method for directly fitting the time derivative of sedimentation velocity data and an alternative algorithm for calculating sedimentation coefficient distribution functions. Analytical Biochemistry, 279, 151-163.