H. Lee Moffitt Cancer Center & Research Institute

Proteomics was established to address the needs of MCC investigators in examining protein identification, expression, and post-translational modification as part of broader initiatives to determine the molecular basis of cancer development and treatment. The characterization of proteins and protein expression patterns is going to play a central role in the future diagnosis and treatment of disease. Proteomics combines several emerging technologies including separations, mass spectrometry and bioinformatics. The strength of protein sequence analysis has been developed using liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS); this technique can be adapted to proteome-wide cataloging and quantitative profiling experiments.

Proteomics provides collaborative support for investigators with experiment design, instrumentation, and data analysis to address a broad range of biological or clinical problems. Most of the experiments proceed from “bottom up” approaches. Proteins are first enzymatically digested; the resulting peptides are sequenced to identify the protein and localize any post-translational modifications. The peptide information is coalesced to develop an understanding of the protein-protein interactions, protein function, and the molecular controls that are used in signaling. Quantitative experiments can be developed and translated into clinical samples using the results of the “bottom up” sequencing experiments. Just as antibody based assays rely on a peptide epitope, each peptide detected in proteomic analysis can be quantified by using multiple reaction monitoring. The intact mass of the peptide and specific fragments can be used to isolate the signal for that peptide from other components in complex mixtures like tumor tissue, blood, or urine. Quantitative mass spectrometry assays provide the versatility and flexibility to verify the utility of many biomarkers simultaneously (10s-100s); the molecules with the greatest value can be monitored with MS or antibody based methods in clinical labs.

Descriptions of experimental workflows are presented at this website; examples of how proteomics can contribute to clinical practice are described in the following review article:

Koomen JM, Haura EB, Bepler G, Sutphen R, Remily-Wood ER, Benson K, Hussein M, Hazlehurst LA, Yeatman TJ, Hildreth LT, Sellers TA, Jacobsen PB, Fenstermacher DA, Dalton WS

Proteomic contributions to personalized cancer care.
Mol Cell Proteomics. 2008 Oct;7(10):1780-94. Epub 2008 Jul 29.
PMID: 18664563 [PubMed - in process]

Workflow Descriptions:

1. Protein Identification
2. Posttranslational Modification Analysis
3. Serine / Threonine Phosphoproteomics
4. Absolute Protein Quantitation Using Multiple Reaction Monitoring
5. Relative Protein Quantification Using iTRAQ
6. Two-Dimensional Liquid Chromatography