An automated interface for sedimentation velocity analysis in SEDFIT

Sedimentation velocity analytical ultracentrifugation (SV-AUC) is an indispensable tool for the study of particle size distributions in biopharmaceutical industry, for example, to characterize protein therapeutics and vaccine products. In particular, the diffusion-deconvoluted sedimentation coefficient distribution analysis, in the software SEDFIT, has found widespread applications due to its relatively high resolution and sensitivity. However, a lack of suitable software compatible with Good Manufacturing Practices (GMP) has hampered the use of SV-AUC in this regulatory environment. To address this, we have created an interface for SEDFIT so that it can serve as an automatically spawned module with controlled data input through command line parameters and output of key results in files. The interface can be integrated in custom GMP compatible software, and in scripts that provide documentation and meta-analyses for replicate or related samples, for example, to streamline analysis of large families of experimental data, such as binding isotherm analyses in the study of protein interactions. To test and demonstrate this approach we provide a MATLAB script mlSEDFIT.Author summary: Sedimentation velocity analytical ultracentrifugation (SV-AUC), a classical first-principles based method to study size-distributions of macromolecules and particles in solution, has become a popular technique in a variety of disciplines, such as physical biochemistry, structural biology, supramolecular chemistry, and nanoparticles due to its high resolution, wide size-range, and label-free detection. It has also assumed an important role in pharmaceutical development of therapeutics and vaccines. One factor complicating the implementation of SV-AUC in biotechnology is the lack of compatibility of the most widely used software, SEDFIT, with regulatory requirements in the good manufacturing practices (GMP) environment. In this paper we present a solution to this problem, by introducing a command line interface that permits automated configuration of SEDFIT, data loading, and retrieval of results. In this way, SEDFIT may be used as a computational module integrated in GMP-compliant software. We demonstrate the validity of the results from this approach. In addition, this automation facilitates meta-analyses of families of SV-AUC experiments, for example, in binding isotherm analysis of interacting macromolecules.