Alexis T. Chang

Carafe2 enables high quality in silico spectral library generation for timsTOF data-independent acquisition proteomics

Carafe2 generates high-quality in silico spectral libraries for timsTOF DIA proteomics by fine-tuning deep learning models on DIA data, outperforming DDA-trained models in multiple applications.

Mistranslating tRNA variants impact the proteome and phosphoproteome of Saccharomyces cerevisiae

The paper profiles the proteome and phosphoproteome of yeast expressing three mistranslating tRNA variants, showing varied growth defects and impacts on cellular processes.

Carafe enables high quality in silico spectral library generation for data-independent acquisition proteomics

Carafe generates high-quality in silico spectral libraries for DIA proteomics by training deep learning models directly on DIA data, improving fragment ion intensity prediction and peptide detection.

R2HaPpY: Rapid-robust phosphotyrosine peptide enrichment using HaloTag-Src SH2 pY superbinder

The paper introduces a rapid and cost-effective method for phosphotyrosine peptide enrichment, enabling sensitive detection of phosphotyrosine sites in biological samples.

The fitness cost of spurious phosphorylation

The paper quantifies the fitness cost of spurious phosphorylation in yeast by expressing tyrosine kinases and analyzing phosphoproteomes, finding a strong correlation between spurious phosphorylation and decreased growth.

Multiplex, multimodal mapping of variant effects in secreted proteins

The paper introduces MultiSTEP, a method to assess variant effects in secreted proteins, and applies it to coagulation factor IX, identifying functional variants and reclassifying uncertain ones.

Automated Enrichment of Phosphotyrosine Peptides for High-Throughput Proteomics

The paper introduces R2-pY, a robotic method for phosphotyrosine enrichment in proteomics, achieving high efficiency and reproducibility with 96 samples processed in parallel.