Paleoproteomics, the study of ancient proteins, is a rapidly growing field at the intersection of
molecular biology, paleontology, archaeology, paleoecology, and history. Paleoproteomics …

The vocabulary of theoretical statistics can be difficult to embrace from the viewpoint of
computational proteomics research, even though the notions it conveys are essential to …

The annotation of small molecules in untargeted mass spectrometry relies on the matching
of fragment spectra to reference library spectra. While various spectrum-spectrum match …

Many of the novel ideas that drive today's proteomic technologies are focused essentially on
experimental or data-processing workflows. The latter are implemented and published in a …

Proteogenomics refers to the integrated analysis of the genome and proteome that
leverages mass-spectrometry (MS)-based proteomics data to improve genome annotations …

Background Proteogenomics aims to identify variant or unknown proteins in bottom-up
proteomics, by searching transcriptome-or genome-derived custom protein databases …

In bottom-up discovery proteomics, target–decoy competition (TDC) is the most popular
method for false discovery rate (FDR) control. Despite unquestionable statistical …

The analysis of shotgun proteomics data often involves generating lists of inferred peptide-
spectrum matches (PSMs) and/or of peptides. The canonical approach for generating these …

Shotgun proteomics workflows for database protein identification typically include a
combination of search engines and postsearch validation software based mostly on …

Proteome-wide analyses rely on tandem mass spectrometry and the extensive separation of
proteolytic mixtures. This imposes considerable instrumental time consumption, which is one …