Proteomics

Proteomics is the comprehensive analysis of all proteins present in a biological sample, encompassing their identity, quantity, modifications, and interactions ¹.

How It Works

Shotgun proteomics, the most common approach, begins with protein extraction and enzymatic digestion (typically with trypsin) into peptides. The peptide mixture is separated by liquid chromatography and analyzed by tandem mass spectrometry (LC-MS/MS). Each peptide generates a fragmentation spectrum that serves as a fingerprint for identification.

Quantitative proteomics employs label-free methods (spectral counting, ion intensity) to compare protein abundances across conditions. Chemical labeling (TMT, iTRAQ) and metabolic labeling (SILAC) serve the same purpose. Data-independent acquisition (DIA) methods provide comprehensive and reproducible quantification of thousands of proteins in a single run.

In synthetic biology, proteomics reveals the global impact of engineered circuits on host protein expression. It also quantifies the burden imposed by heterologous protein production and identifies protease-mediated degradation of circuit components. It complements transcriptomics by capturing post-transcriptional regulation effects.

Computational Considerations

Analysis platforms such as MaxQuant perform peptide identification via database searching with false discovery rate control, and extract quantitative information from chromatographic peak areas ². Downstream statistical tools (Perseus, MSstats) normalize data, impute missing values, and identify differentially abundant proteins. Functional enrichment analysis maps protein-level changes onto Gene Ontology terms and pathway databases, providing mechanistic insight into cellular responses to genetic engineering.