A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics
AI Nesvizhskii - Journal of proteomics, 2010 - Elsevier
This manuscript provides a comprehensive review of the peptide and protein identification
process using tandem mass spectrometry (MS/MS) data generated in shotgun proteomic …
process using tandem mass spectrometry (MS/MS) data generated in shotgun proteomic …
Assigning significance to peptides identified by tandem mass spectrometry using decoy databases
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 …
a list of peptide− spectrum matches, ranked according to an arbitrary score. In this article, we …
Analysis and validation of proteomic data generated by tandem mass spectrometry
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 …
experiments represents a significant challenge and is currently a bottleneck in many …
Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry
Comprehensive characterization of a proteome is a fundamental goal in proteomics. To
achieve saturation coverage of a proteome or specific subproteome via tandem mass …
achieve saturation coverage of a proteome or specific subproteome via tandem mass …
Deciphering the human platelet sheddome
KP Fong, C Barry, AN Tran, EA Traxler… - Blood, The Journal …, 2011 - ashpublications.org
Activated platelets shed surface proteins, potentially modifying platelet function as well as
providing a source of bioactive fragments. Previous studies have identified several …
providing a source of bioactive fragments. Previous studies have identified several …
Improving sensitivity by probabilistically combining results from multiple MS/MS search methodologies
BC Searle, M Turner, AI Nesvizhskii - The Journal of Proteome …, 2008 - ACS Publications
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 …
standard LC/MS/MS study of digested proteins. Subtle variations in database-searching …
Protein inference: a review
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 …
as protein inference, is a critical step in proteomics research. Due to the existence of …
Deterministic protein inference for shotgun proteomics data provides new insights into Arabidopsis pollen development and function
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 …
study developmental processes, such as cell polarity, tip growth, and morphogenesis. Upon …
Efficient marginalization to compute protein posterior probabilities from shotgun mass spectrometry data
O Serang, MJ MacCoss, WS Noble - Journal of proteome research, 2010 - ACS Publications
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 …
definitively solved. Identifying the proteins in a sample requires ranking them, ideally with …
Analysis of the zebrafish proteome during embryonic development
The model organism zebrafish (Danio rerio) is particularly amenable to studies deciphering
regulatory genetic networks in vertebrate development, biology, and pharmacology …
regulatory genetic networks in vertebrate development, biology, and pharmacology …