As part of the Proteomics Section of the Biomolecular Resource Facility and consistent with its mission, the goal of the Proteomics Bioinformatics Core is to assist researchers at UTMB in their analyses of gels and other proteomicsseparation technologies.
The core utilizes Nonlinear Dynamics software, which quantifies stained protein images and calculates relative levels of expression in comparative studies. The software generates suggested spot picking lists as well as statistical analyses for estimating the significance of expression levels. After discussion with investigators, promising protein spots are then processed using robotic devices with identification accomplished utilizing the resources of the Mass Spectrometry Core of the Proteomics Section and database interrogation. In order to provide investigators with sample tracking, powerful data management capability, and facile data access, GenoLogics Proteus LIMS (Laboratory Information Management System) is also in place.
- The Protein Bioinformatics Core provides informatics tools, including statistical tools, for the analysis of 1D and 2D electrophoresis gels utilizing a software suite from Nonlinear Dynamics (Progenesis) and sample tracking, data management and access tools, using software from GenoLogics (Proteus LIMS). The BRF is a major Nonlinear and GenoLogics partner and collaborates with these manufacturers in the development of their software.
- The Bioinformatics Core interacts extensively with other BRF Cores, and UTMB Centers and Departments and has integrated the Progenesis software into high-end user groups. For example, the BRF has installed the Editor Progenesis software at a number of sites across the UTMB campus.
- Group training sessions are scheduled as needed, typically every six months.
- Analysis of gel images and quantification of protein expression utilizing Nonlinear Dynamics Progenesis Discovery Software
- Validation of data utilizing statistical analysis
- Student’s t-test: Hypothesis and significance testing
- Multiple Hypothesis testing corrections
- Hierarchical clustering: Control vs. Treated
- Analysis of Variance (ANOVA): Time course/dosage dependence of expression
- Nonlinear 1D gel analysis software suite
- Nonlinear Progenesis SameSpots with Statistical Package software suite for 2D gel analysis (16 floating licenses)
- Nonlinear Progenesis LC-MS for label-free LC-MS data analysis
- Genologics LIMS for data management and access