In this project, I conducted extensive research into TMT (Tandem Mass Tag) and iTRAQ (Isobaric Tags for Relative and Absolute Quantitation) quantitative proteomics, focusing on their application in high-throughput protein identification and quantification workflows. These isobaric labeling techniques allow researchers to multiplex samples for mass spectrometry analysis, enabling the detection of subtle yet biologically meaningful differences in protein expression. I explored the full experimental pipeline — from protein extraction and enzymatic digestion, to peptide labeling, LC-MS/MS analysis, and automated data processing using tools like Proteome Discoverer. A key part of this work involved understanding how these platforms quantify mass-to-charge ratios and identify differential protein expression across biological samples.

As part of the project, I investigated how TMT/iTRAQ methods can be applied to study molecular mechanisms underlying diseases such as congenital heart defects. Specifically, I examined the role of miRNA-21 in valvulogenesis using zebrafish as a model organism. This work included bioinformatic and luciferase validation of differentially expressed proteins regulated by miR-21, identifying over 250 affected proteins through TMT-MS and revealing new regulatory targets. The experience deepened my knowledge of proteomics, mass spectrometry, and the use of systems biology tools to uncover protein-level changes driving developmental and disease-related processes.

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