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PeptideProphet

A software package for the statistical validation of peptide identifications made by tandem mass spectrometry (MS/MS) and database searching.
National Institutes of Health

Papers overview

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2013
2013
Unifying protein inference and peptide identification with feedback to update consistency between peptides
We first propose a new method to process peptide identification reports from databases search engines. Then via it we develop a… 
2012
2012
Learning score function parameters for improved spectrum identification in tandem mass spectrometry experiments.
The identification of proteins from spectra derived from a tandem mass spectrometry experiment involves several challenges… 
2012
2012
A feedback framework for protein inference with peptides identified from tandem mass spectra
Protein inference is an important computational step in proteomics. There exists a natural nest relationship between protein… 
2012
2012
Protein inference based on peptides identified from tandem mass spectra
Protein inference is a critical computational step in the study of proteomics. It lays the foundation for further structural and… 
2012
2012
Running PeptideProphet Separately on Replicates Improves Peptide Identification Results
Limited spectrum coverage is a problem in shotgun proteomics. Replicates are generated to improve the spectrum coverage. When… 
2011
2011
Importance of manual validation for the identification of phosphopeptides using a linear ion trap mass spectrometer.
Accurate determination of protein phosphorylation is challenging, particularly for researchers who lack access to a high-accuracy… 
2010
2010
A nested mixture model for protein identification using mass spectrometry
Mass spectrometry provides a high-throughput way to identify proteins in biological samples. In a typical experiment, proteins in… 
2009
2009
Oscore: a combined score to reduce false negative rates for peptide identification in tandem mass spectrometry analysis.
Tandem mass spectrometry (MS/MS) has been widely used in proteomics studies. Multiple algorithms have been developed for… 
2007
2007
Installation and use of the Computational Proteomics Analysis System (CPAS).
The community of proteomic researchers has been generating openly available software infrastructure for systematic proteomic data… 
2007
2007
The highway from genome to proteome
Following the sequencing of the human genome, the next step is the verification and functional annotation of all predicted genes… 
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