Adriaan Sticker

The paper introduces TargetDecoy, a Bioconductor package to assess and control the quality of the target-decoy approach for peptide identification in proteomics.

This paper introduces MSqRob-Sum, a novel summarization strategy for proteome-wide label-free quantification that maintains the performance of MSqRob while enabling protein-level analysis and reducing computational demands.

The paper introduces a hurdle model to address missing values in proteomics by combining binomial count and intensity-based components, showing improved performance over existing methods.

The paper argues that searching all expected peptides and removing irrelevant ones before FDR calculation improves reliability compared to discarding irrelevant peptides before or after FDR calculation.