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 has extensive expertise in bioinformatics and we are consistently looking to utilize new software and methods to enhacne our capabilities. 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.


We primarily use Thermo Proteome Discoverer software for data analysis but also have access to the following, which we use when suited to the analysis:

  • CPFP
  • MaxQuant
  • Matrix Science Mascot Server
  • GPM X! Tandem
  • ISB Trans-Proteomic Pipeline
  • Byonic

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

MS Proteomics Services