Andrew Collins

The paper reanalyzes public DIA proteomics datasets to provide a baseline view of human protein expression across tissues and compares it with previous DDA results.

The paper reanalyzes public pig proteomics data to map baseline protein expression across 14 organs and compares it with human orthologs.

The paper introduces a pipeline to improve phosphosite identification confidence by combining multiple data sets and using decoy amino acids to estimate false localisation rates, resulting in more confident identifications.

The paper reanalyzes 24 public proteomics datasets to assess baseline protein abundance in 31 human organs and integrates the results into the Expression Atlas for combined proteomics and transcriptomics analysis.

The paper reanalyzes proteomics datasets from mouse and rat tissues to compare baseline protein expression across species and organs, finding high correlation among orthologs in brain, kidney, heart, and liver.

The paper introduces PEFF, a new format for proteomics data that enhances FASTA with metadata for sequence variants and PTMs, enabling better analysis in proteogenomics and top-down proteomics.