Theses and Dissertations

Issuing Body

Mississippi State University


Bridges, M. Susan

Committee Member

Hansen, A. Eric

Committee Member

Boyle, A. John

Committee Member

Willeford, O. Kenneth

Committee Member

Burgess, C. Shane

Date of Degree


Document Type

Dissertation - Open Access


Molecular Biology

Degree Name

Doctor of Philosophy


College of Agriculture and Life Sciences


Department of Biochemistry and Molecular Biology


Proteins provide evidence that a given gene is expressed, and machine learning algorithms can be applied to various proteomics problems in order to gain information about the underlying biology. This dissertation applies machine learning algorithms to proteomics data in order to predict whether or not a given peptide is observable by mass spectrometry, whether a given peptide can serve as a cell penetrating peptide, and then utilizes the peptides observed through mass spectrometry to aid in the structural annotation of the chicken genome. Peptides observed by mass spectrometry are used to identify proteins, and being able to accurately predict which peptides will be seen can allow researchers to analyze to what extent a given protein is observable. Cell penetrating peptides can possibly be utilized to allow targeted small molecule delivery across cellular membranes and possibly serve a role as drug delivery peptides. Peptides and proteins identified through mass spectrometry can help refine computational gene models and improve structural genome annotations.



machine learning||proteomics||mapping algorithms||cell penetrating peptides||peptide observability||proteogenomic mapping||chicken