This manuscript provides a comprehensive review of the peptide and protein identification
process using tandem mass spectrometry (MS/MS) data generated in shotgun proteomic …

Automated methods for assigning peptides to observed tandem mass spectra typically return
a list of peptide− spectrum matches, ranked according to an arbitrary score. In this article, we …

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 …

Comprehensive characterization of a proteome is a fundamental goal in proteomics. To
achieve saturation coverage of a proteome or specific subproteome via tandem mass …

Activated platelets shed surface proteins, potentially modifying platelet function as well as
providing a source of bioactive fragments. Previous studies have identified several …

Database-searching programs generally identify only a fraction of the spectra acquired in a
standard LC/MS/MS study of digested proteins. Subtle variations in database-searching …

Assembling peptides identified from tandem mass spectra into a list of proteins, referred to
as protein inference, is a critical step in proteomics research. Due to the existence of …

Pollen, the male gametophyte of flowering plants, represents an ideal biological system to
study developmental processes, such as cell polarity, tip growth, and morphogenesis. Upon …

The problem of identifying proteins from a shotgun proteomics experiment has not been
definitively solved. Identifying the proteins in a sample requires ranking them, ideally with …

The model organism zebrafish (Danio rerio) is particularly amenable to studies deciphering
regulatory genetic networks in vertebrate development, biology, and pharmacology …