Computing & Data Analysis

Continuous improvement in mass-spectrometry instrumentation means that proteomics facilities are generating a growing amount of data, and tackling increasingly complex datasets. The rise of quantitative proteomics in particular demands robust data analysis techniques to ensure high quality results are generated for users. The UTSW Proteomics Core is embracing the need for high quality proteomics data analysis by using the best free and commerical software, and developing in house data analysis platforms.

Bioinformatics Expertise and Resources

The core staff includes a dedicated computational proteomics expert, actively involved in the analysis of customers results as well as research in state-of-the-art analysis algorithms and tools. We maintain servers for data processing and an enterprise-grade SAN solution for data storage, housed in UT Southwestern’s on-site data center. Modern virtual-machine technology ensures our computing¬†resources¬†are used efficiently, and minimizes time spent on maintenance. We take data security seriously, ensuring results are backed-up nightly and that multiple copies are kept of all original MS raw data acquired in the core.

 

Software

We regularly use the following software for data analysis:

  • CPFP
  • Matrix Science Mascot Server
  • MaxQuant
  • Thermo Proteome Discoverer
  • GPM X! Tandem
  • NCBI OMSSA
  • ISB Trans-Proteomic Pipeline

We are always seeking new and improved software to ensure that customers’ data is analyzed to the best of our ability.

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