py_diAID

py_diAID optimizes data-independent acquisition (DIA) window placement for dia-PASEF on Bruker trapped ion mobility (IM)-separated quadrupole time-of-flight mass spectrometers to improve proteome and phosphoproteome coverage.

Key Features:

• Optimal Window Design: Uses variable isolation windows positioned based on precursor density in both the m/z and ion mobility (IM) planes to maximize data completeness and depth of coverage.
• Automated Isolation Design: Automates the design of isolation windows to generate reproducible DIA window schemes for dia-PASEF experiments.
• Integration with Evosep LC: Supports workflows using Evosep liquid chromatography and enables reproducible identification of >7,700 proteins in a human cancer cell line with 44-minute quadruplicate single-shot injections.
• High Sensitivity and Throughput: Enables consistent identification of >6,000 proteins in mammalian cell lysates at 100 samples per day throughput using 11-minute LC gradients with four replicates per sample.
• Phosphoproteomics Capability: Facilitates high-sensitivity phosphoproteomics, enabling quantification of >35,000 phosphosites in a human cancer cell line stimulated with epidermal growth factor within 21-minute runs.

Scientific Applications:

• Deep proteome profiling: Achieves extensive proteome coverage in mammalian and human cancer cell line samples for comparative and quantitative studies.
• Phosphoproteome mapping: Enables large-scale quantification of phosphorylation sites, including stimulus-responsive phosphosites following epidermal growth factor stimulation.
• High-throughput studies: Supports large-scale, high-throughput proteomic and phosphoproteomic experiments requiring short LC gradients and multiple replicates per sample.

Methodology:

Employs variable isolation windows positioned according to precursor density across the m/z and ion mobility (IM) planes and automates isolation window design for dia-PASEF.