Uses and challenges of bioinformatic tools in mass spectrometric-based proteomic brain perturbation studies

Mass spectrometry (MS) has become the method of choice to study the proteome of brain injury. The high throughput nature of MS-based proteomic experiments generates massive amount of mass spectral data presenting great challenges in downstream interpretation. Currently, different bioinformatics platforms are available for functional analysis and data mining of MS-generated proteomic data. These tools provide a way to convert data sets to biologically interpretable results and functional outcomes. In this review, a brief overview of the currently available bioinformatics strategies applied to neuroproteomic studies is presented. Application of commercially available bioinformatics software to different brain injury studies demonstrates integration of the data mining and analysis applications into neuroproteomic workflows that can identify major protein markers as well as highlight the biological processes and molecular functions involved.