Enhanced Peptide Identification by Electron Transfer Dissociation Using an Improved Mascot Percolator

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

COMPASS: A suite of pre- and post-search proteomics software tools for OMSSA

(2011) Craig D. Wenger et al.   PROTEOMICS

An FDA bioinformatics tool for microbial genomics research on molecular characterization of bacterial foodborne pathogens using microarrays

(2010) Hong Fang et al.   BMC BIOINFORMATICS

Feasibility of Large-Scale Phosphoproteomics with Higher Energy Collisional Dissociation Fragmentation

(2010) Nagarjuna Nagaraj et al.   JOURNAL OF PROTEOME RESEARCH

Improving Software Performance for Peptide Electron Transfer Dissociation Data Analysis by Implementation of Charge State- and Sequence-Dependent Scoring

(2010) Peter R. Baker et al.   MOLECULAR & CELLULAR PROTEOMICS

Trans-Proteomic Pipeline supports and improves analysis of electron transfer dissociation data sets

(2010) Eric W. Deutsch et al.   PROTEOMICS

Evaluation of Several MS/MS Search Algorithms for Analysis of Spectra Derived from Electron Transfer Dissociation Experiments

(2009) Kumaran Kandasamy et al.   ANALYTICAL CHEMISTRY

Database Search Strategies for Proteomic Data Sets Generated by Electron Capture Dissociation Mass Spectrometry

(2009) Steve M. M. Sweet et al.   JOURNAL OF PROTEOME RESEARCH

Electron Transfer Dissociation in Conjunction with Collision Activation To Investigate theDrosophila melanogasterPhosphoproteome

(2009) Bruno Domon et al.   JOURNAL OF PROTEOME RESEARCH

A New Probabilistic Database Search Algorithm for ETD Spectra

(2009) Rovshan G. Sadygov et al.   JOURNAL OF PROTEOME RESEARCH

False Discovery Rates of Protein Identifications: A Strike against the Two-Peptide Rule

(2009) Nitin Gupta et al.   JOURNAL OF PROTEOME RESEARCH

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

A guide to the Proteomics Identifications Database proteomics data repository

(2009) Juan Antonio Vizcaíno et al.   PROTEOMICS

The effect of interfering ions on search algorithm performance for electron-transfer dissociation data

(2009) David M. Good et al.   PROTEOMICS

Comprehensive Comparison of Collision Induced Dissociation and Electron Transfer Dissociation

(2008) Henrik Molina et al.   ANALYTICAL CHEMISTRY

A Proteomics Grade Electron Transfer Dissociation-Enabled Hybrid Linear Ion Trap-Orbitrap Mass Spectrometer

(2008) Graeme C. McAlister et al.   JOURNAL OF PROTEOME RESEARCH

In-depth Analysis of Tandem Mass Spectrometry Data from Disparate Instrument Types

(2008) Robert J. Chalkley et al.   MOLECULAR & CELLULAR PROTEOMICS

Decision tree–driven tandem mass spectrometry for shotgun proteomics

(2008) Danielle L Swaney et al.   NATURE METHODS

Application of electron transfer dissociation (ETD) for the analysis of posttranslational modifications

(2008) Julia Wiesner et al.   PROTEOMICS

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

Posterior Error Probabilities and False Discovery Rates: Two Sides of the Same Coin

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