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ProteinProphet

A software model that has as input the list of peptides assigned to MS/MS spectra and corresponding probabilities that those peptide assignments are… 
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
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… 
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… 
2010
2010
Nogo-A modulates growth cone motility via Rho-GTP / LIMK 1 / cofilin in the unlesioned adult nervous system
Nogo-A has been extensively studied as a myelin-associated neurite outgrowth inhibitor in the lesioned adult central nervous… 
2009
2009
MaXIC-Q Web: a fully automated web service using statistical and computational methods for protein quantitation based on stable isotope labeling and LC–MS
Isotope labeling combined with liquid chromatography–mass spectrometry (LC–MS) provides a robust platform for analyzing… 
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… 
2006
2006
Proteome Analysis of Halobacterium sp. NRC-1 Facilitated by the Biomodule Analysis Tool BMSorter*S
To better understand the extremely halophilic archaeon Halobacterium species NRC-1, we analyzed its soluble proteome by two… 
2006
2006
Protein probabilities in shotgun proteomics: Evaluating different estimation methods using a semi‐random sampling model
The calculation of protein probabilities is one of the most intractable problems in large‐scale proteomic research. Current… 
2005
2005
Analysis of phosphatase and tensin homolog tumor suppressor interacting proteins by in vitro and in silico proteomics
The phosphatase and tensin homolog (PTEN) tumor suppressor is a multifunctional protein deregulated in many types of cancer. To… 
Review
2005
Review
2005
Annotated proteome of a human T-cell lymphoma.
As the reliable identification of proteins by tandem mass spectrometry becomes increasingly common, the full characterization of… 
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