Learning from Decoys to Improve the Sensitivity and Specificity of Proteomics Database Search Results

MassWiz: A Novel Scoring Algorithm with Target-Decoy Based Analysis Pipeline for Tandem Mass Spectrometry

(2011) Amit Kumar Yadav et al.   JOURNAL OF PROTEOME RESEARCH

On Using Samples of Known Protein Content to Assess the Statistical Calibration of Scores Assigned to Peptide-Spectrum Matches in Shotgun Proteomics

(2011) Viktor Granholm et al.   JOURNAL OF PROTEOME RESEARCH

Systematic evaluation of alternating CID and ETD fragmentation for phosphorylated peptides

(2011) Min-Sik Kim et al.   PROTEOMICS

Peptide identification quality control

(2011) Marc Vaudel et al.   PROTEOMICS

Improvements to the Percolator Algorithm for Peptide Identification from Shotgun Proteomics Data Sets

(2009) Marina Spivak et al.   JOURNAL OF PROTEOME RESEARCH

Accurate and Sensitive Peptide Identification with Mascot Percolator

(2009) Markus Brosch et al.   JOURNAL OF PROTEOME RESEARCH

Target-Decoy with Mass Binning: A Simple and Effective Validation Method for Shotgun Proteomics Using High Resolution Mass Spectrometry

(2009) Jong Wha J. Joo et al.   JOURNAL OF PROTEOME RESEARCH

Filtering strategies for improving protein identification in high-throughput MS/MS studies

(2009) Jussi Salmi et al.   PROTEOMICS

Adaptive Discriminant Function Analysis and Reranking of MS/MS Database Search Results for Improved Peptide Identification in Shotgun Proteomics

(2008) Ying Ding et al.   JOURNAL OF PROTEOME RESEARCH

Nonlinear Fitting Method for Determining Local False Discovery Rates from Decoy Database Searches

(2008) Wilfred H. Tang et al.   JOURNAL OF PROTEOME RESEARCH

Semisupervised Model-Based Validation of Peptide Identifications in Mass Spectrometry-Based Proteomics

(2007) Hyungwon Choi et al.   JOURNAL OF PROTEOME RESEARCH

The Standard Protein Mix Database: A Diverse Data Set To Assist in the Production of Improved Peptide and Protein Identification Software Tools

(2007) John Klimek et al.   JOURNAL OF PROTEOME RESEARCH

Assigning Significance to Peptides Identified by Tandem Mass Spectrometry Using Decoy Databases

(2007) Lukas Käll et al.   JOURNAL OF PROTEOME RESEARCH