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.
Banyan Biomarkers, Inc., 13400 Progress Boulevard, Alachua, FL 32615, USA.
Joy D
JD
Guingab-Cagmat
Banyan Biomarkers, Inc., 13400 Progress Boulevard, Alachua, FL 32615, USA.
Emilio B
EB
Cagmat
Department of Psychiatry, University of Florida, McKnight Brain Institute, Gainesville, FL 32601, USA.
Firas H
FH
Kobeissy
Banyan Biomarkers, Inc., 13400 Progress Boulevard, Alachua, FL 32615, USA.
John
J
Anagli
D000465:Algorithms; D000818:Animals; D001921:Brain / Q000378:metabolism*; D001930:Brain Injuries / Q000378:metabolism*; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D010449:Peptide Mapping / Q000379:methods*; D020543:Proteome / Q000378:metabolism*; D040901:Proteomics / Q000379:methods*; D012984:Software
D020543:Proteome
bioinformatics; biomarkers; data mining; mass spectrometry; proteomic brain perturbation; proteomics; traumatic brain injury