The analysis of the large amount of data generated in mass spectrometry–based proteomics
experiments represents a significant challenge and is currently a bottleneck in many …

Proteogenomics is an area of research at the interface of proteomics and genomics. In this
approach, customized protein sequence databases generated using genomic and …

Protein glycosylation involves the co-translational or post-translational addition of glycans to
proteins and is a crucial protein modification in health and disease. The aim of …

We present a statistical model to estimate the accuracy of peptide assignments to tandem
mass (MS/MS) spectra made by database search applications such as SEQUEST. Employing …

Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer with poor patient
survival. Toward understanding the underlying molecular alterations that drive PDAC …

Circular RNAs (circRNAs) are an intriguing class of RNA due to their covalently closed structure,
high stability, and implicated roles in gene regulation. Here, we used an exome capture …

There is a need to better understand and handle the 'dark matter' of proteomics—the vast
diversity of post-translational and chemical modifications that are unaccounted in a typical …

The shotgun proteomic strategy based on digesting proteins into peptides and sequencing
them using tandem mass spectrometry and automated database searching has become the …

To explore the biology of lung adenocarcinoma (LUAD) and identify new therapeutic
opportunities, we performed comprehensive proteogenomic characterization of 110 tumors and …

We present 'significance analysis of interactome' (SAINT), a computational tool that assigns
confidence scores to protein-protein interaction data generated using affinity purification–…