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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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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
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… 
2008
2008
iProphet: A new tool for combining PeptideProphet results from multiple search engines improves spectrum validation
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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