HOWTO - Overview


Welcome to UltraScan! The purpose of this HOWTO manual is to provide step-by-step instructions for a successful implementation of UltraScan and to guide you through the use of the software. You can use it as a study guide to help you learn all the functions of UltraScan and to master AUC analysis.

This manual is subdivided into several chapters, each dealing with a different topic. Each topic can be studied independently from the previous topic. You should be able to obtain a comprehensive introduction to AUC data analysis by completing all chapters in this manual.

In addition to this study guide, UltraScan comes with a complete online help manual, whose pages will be cross-referenced in this study guide.

UltraScan Design:

UltraScan is designed to provide an efficient, robust and intuitive user interface to accomplish two goals: 1) minimal learning time and 2) efficient and fast execution of all analysis steps with a minimum number of mouseclicks. UltraScan is programmed using efficient C++ code which guarantees a fast performning analysis.

Relational Database Interface:

In order to accommodate facility operators who may have to analyze a large number of experiments from multiple investigators, UltraScan comes with an SQL database interface that allows the user to interface with a relational database for data management. This way experimental data and data analysis results can be efficiently stored and quickly searched and accessed.

Experimental Data Handling:

To speed up execution, UltraScan requires that the user first edits the experimental data before it is used for analysis. During editing, UltraScan will generate a binary copy of the experimental data which is then used with all analysis methods in UltraScan, and no additional editing is required after the initial edit. The binary data also loads much faster than ASCII data, which is important for large datasets found in interference experiments. So before you can analyze any data, the raw experimental data needs to be edited with UltraScan and saved as a binary copy.

Data Analysis:

Edited data can be analyzed with multiple methods, depending on the type of experiment performed. For velocity experiment, the following analysis options exist:

Equilibrium experiments can be analyzed by direct curvefitting to predefined fitting models. In addition, the data can be analyzed with a fixed molecular weight distribution algorithm, which uses either generalized least squares or non-negativelAy constrained least squared to identify composition of the sample.

Accessory Data Files:

Buffer density and viscosity values are used in UltraScan to automatically correct molecular weights, sedimentation and diffusion coefficients, as well as frictional coefficients. Hydrodynamic corrections are derived from the experimental temperature as well as buffer composition, which are stored in buffer files that contain partial concentration and polynomial fits to viscosity and density data. Partial specific volume and extinction coefficients for 280 nm (for the calculation of association constants in molar units) are derived from peptide sequence information, which can be downloaded from the NCBI or Genbank databases and imported into UltraScan. These files can be stored on the harddrive or in the SQL database, where they are automatically associated with the analyzed data to obtain temperature and buffer corrections during analysis.

HTML Reports:

All experimental data as well as analysis results can be easily compiled into HTML reports, which will organize the data into charts, graphs, platform independent spreadsheets and analysis reports easily accessible from a web page for easy viewing.

Experimental Simulations:

UltraScan provides several modules that facilitate the simulation of experiments as well as molecular structure to obtain optimal parameters for the execution of the experiments before the experiment is carried out. This minimizes time and sample loss and assists in an efficient use of instrument time. The educational modules can also be used in a teaching environment to demonstrate sedimentation processes.