plexDIA

plexDIA performs multiplexed Data Independent Acquisition (DIA) analysis to increase the depth and throughput of quantitative proteomics for sensitive and accurate protein quantification across large sample sets.

Key Features:

• Multiplexed DIA Implementation: Implements multiplexed Data Independent Acquisition (DIA) to parallelize the analysis of precursors and samples for increased throughput.
• Improved Retention Time Precision: Provides enhanced precision in retention time estimates to reduce variability in protein quantification.
• Multiplicative Gains in Throughput: Combines optimized multiplexing reagents, data acquisition processes, and analytical interpretation to increase throughput and handle larger datasets.
• Future Directions for Advancement: Includes optimized mass-tags, isotopologous carriers, and algorithm development that exploit the regular structures in plexDIA data to improve sensitivity, proteome coverage, and quantitative accuracy.

Scientific Applications:

• Functional Proteomics: Enables analysis of protein conformations, turnover dynamics, post-translational modification states, and protein activities in functional proteomic assays.
• Single-Cell Proteomics: Extends sensitivity to support single-cell protein analysis and investigation of cellular heterogeneity.

Methodology:

Computational methods explicitly include multiplexed DIA data acquisition and analysis, parallel processing of precursors and samples, retention-time estimation, and algorithmic approaches that exploit regular data structures for analytical interpretation.