Abstract 1575 Evaluating Various Quantitative Proteomics Approaches: DDA, DIA, TMT, and PRM

Quantitative proteomics is a strong pillar in utilizing analyses such as post-transitional modification, expression, and interaction of proteins.The technique examines proteins and peptides through metabolic and chemical marking techniques or through techniques that function independently from labeling using stable isotopes.Data-dependent acquisition (DDA) is a technique that identifies quality proteins and peptides in a sample but has limitations in accuracy and sensitivity.Data-independent acquisition (DIA), a developing technique, has been crafted to address the limitations of accuracy and sensitivity in DDA.Targeted qualifications are detectable by developing the data-independent acquisition method to suppress the data-dependent method within data analysis.The project seeks to assess how various quantification techniques are effective in uncovering and locating samples that have been introduced to low-abundance desired proteins among the presence of the proteins found in the proteome of human cells, more specifically from HeLa cells.These procedures enable the simulation of qualifying low abundance marked proteins among the several thousands of proteins done through various Liquid Chromatography and Mass Spectrometry experiments.Ultimately, various experiments were designed to demonstrate the various analytical technique capabilities and limitations unveiled to evaluate which is effective in a given scenario.