A Framework for Intelligent Data Acquisition and Real-Time Database Searching for Shotgun Proteomics

More than 100,000 Detectable Peptide Species Elute in Single Shotgun Proteomics Runs but the Majority is Inaccessible to Data-Dependent LC−MS/MS

(2011) Annette Michalski et al.   JOURNAL OF PROTEOME RESEARCH

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

(2011) Jürgen Cox et al.   JOURNAL OF PROTEOME RESEARCH

Software Lock Mass by Two-Dimensional Minimization of Peptide Mass Errors

(2011) Jürgen Cox et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Comprehensive proteomics

(2010) Martin Beck et al.   CURRENT OPINION IN BIOTECHNOLOGY

Mass spectrometry–based proteomics in cell biology

(2010) Tobias C. Walther et al.   JOURNAL OF CELL BIOLOGY

Directed mass spectrometry: towards hypothesis-driven proteomics

(2009) Alexander Schmidt et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Directed Sample Interrogation Utilizing anAccurateMassExclusion-Based Data-Dependent Acquisition Strategy (AMEx)

(2009) Emily L. Rudomin et al.   JOURNAL OF PROTEOME RESEARCH

Computational principles of determining and improving mass precision and accuracy for proteome measurements in an Orbitrap

(2009) Jürgen Cox et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Versatile Online−Offline Engine for Automated Acquisition of High-Resolution Tandem Mass Spectra

(2008) Craig D. Wenger et al.   ANALYTICAL CHEMISTRY

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

Decision tree–driven tandem mass spectrometry for shotgun proteomics

(2008) Danielle L Swaney et al.   NATURE METHODS