Bioinformatics

To discover proteins, peptide sequences resolved by mass spectrometry need to be computationally reassembled. This is not an easy problem to solve, but it is a necessary hurdle to overcome in order to use advanced proteomics technology in any applied setting, especially agriculture. Cooper developed a probability-based model that solved this problem. His software was further developed to evaluate phosphorylation of peptides, as well as perform statistically reliable relative quantitation of proteins between samples. This work was complemented by research on improving the certainty of mass spectrometry protein identification.

Cooper’s bioinformatics work has greatly enabled systems biology research in agriculture and has raised scientific awareness of the need to improve proteomics data quality community standards across scientific disciplines.

Papers:

Proteomic Identification and Meta-Analysis in Salvia hispanica RNA-Seq de novo Assemblies (2021). Ashwil Klein, Lizex H. H. Husselmann, Achmat Williams, Liam Bell, Bret Cooper, Brent Ragar, and David L. Tabb. Plants 10, 765.

Doubling down on phosphorylation as a variable peptide modification (2016). Bret Cooper. Proteomics 16, 2444–2447.

The Problem with Peptide Presumption and the Downfall of Target-Decoy False Discovery Rates (2012). Bret Cooper. Analytical Chemistry, 84, 9663-9667. Published on-line before print Oct. 29, 2012.

A Parallelized Binary Search Tree. (2011). Jian Feng, Daniel Q. Naiman, and Bret Cooper. Journal of Information Technology & Software Engineering, 1, e103.

The Problem with Peptide Presumption and Low Mascot Scoring (2011). Bret Cooper. Journal of Proteome Research 10, 1432-1435. Published on-line before print Jan. 13, 2011.

Relative, Label-free Protein Quantitation: Spectral Counting Error Statistics from Nine Replicate MudPIT Samples (2010). Bret Cooper, Jian Feng, Wesley M. Garrett. Journal of the American Society for Mass Spectrometry 21, 1534-1546. Published on-line before print May 6, 2010.

Correlation of Multiple Peptide Mass Spectra for Phosphoprotein Identification (2009). Jian Feng, Wesley M. Garrett, Daniel Q. Naiman, and Bret Cooper. Journal of Proteome Research 8, 5396-5405. Published on-line before print Sept. 18, 2009.

Combined Dynamic Arrays for Storing and Searching Semi-Ordered Tandem Mass Spectrometry Data (2008). Jian Feng, Daniel Q. Naiman, and Bret Cooper. Journal of Computational Biology 15, 457-468.

Tandem Mass Spectrometry for the Detection of Plant Pathogenic Fungi and the Effects of Database Composition on Protein Inferences (2007). Neerav D. Padliya, Wesley M. Garrett, Kimberly B. Campbell, David L. Tabb, and Bret Cooper. Proteomics 7, 3932-3942.

Probability-Based Pattern Recognition and Statistical Framework for Randomization: Modeling Tandem Mass Spectrum/Peptide Sequence False Match Frequencies (2007). Jian Feng, Daniel Q. Naiman and Bret Cooper. Bioinformatics 23, 2210-2217. Published on line before print May 17, 2007; DOI: 10.1093/bioinformatics/btm267.

A Probability Model for Assessing Proteins Assembled from Peptide Sequences Inferred from Tandem Mass Spectrometry Data (2007). Jian Feng, Daniel Q. Naiman and Bret Cooper. Analytical Chemistry 79, 3901-3911. Published on line before print April 19, 2007. DOI: 10.1021/ac070202e.