Expanding Proteome Coverage with Orthogonal-specificity α-Lytic Proteases

Sequencing-Grade De novo Analysis of MS/MS Triplets (CID/HCD/ETD) From Overlapping Peptides

(2013) Adrian Guthals et al.   JOURNAL OF PROTEOME RESEARCH

Consecutive Proteolytic Digestion in an Enzyme Reactor Increases Depth of Proteomic and Phosphoproteomic Analysis

(2012) Jacek R. Wiśniewski et al.   ANALYTICAL CHEMISTRY

A Systematic Investigation into the Nature of Tryptic HCD Spectra

(2012) Annette Michalski et al.   JOURNAL OF PROTEOME RESEARCH

Charge State Coalescence During Electrospray Ionization Improves Peptide Identification by Tandem Mass Spectrometry

(2012) Jesse G. Meyer et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Peptide Identification by Tandem Mass Spectrometry with Alternate Fragmentation Modes

(2012) Adrian Guthals et al.   MOLECULAR & CELLULAR PROTEOMICS

Modification Site Localization Scoring: Strategies and Performance

(2012) Robert J. Chalkley et al.   MOLECULAR & CELLULAR PROTEOMICS

Proteomic workflow for analysis of archival formalin-fixed and paraffin-embedded clinical samples to a depth of 10 000 proteins

(2012) Jacek R. Wiśniewski et al.   Proteomics Clinical Applications

Effectiveness of CID, HCD, and ETD with FT MS/MS for Degradomic-Peptidomic Analysis: Comparison of Peptide Identification Methods

(2011) Yufeng Shen et al.   JOURNAL OF PROTEOME RESEARCH

Target-Decoy Approach and False Discovery Rate: When Things May Go Wrong

(2011) Nitin Gupta et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

System-wide Perturbation Analysis with Nearly Complete Coverage of the Yeast Proteome by Single-shot Ultra HPLC Runs on a Bench Top Orbitrap

(2011) Nagarjuna Nagaraj et al.   MOLECULAR & CELLULAR PROTEOMICS

Reversed-phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells

(2011) Yuexi Wang et al.   PROTEOMICS

Mass spectrometry–based proteomics in cell biology

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

Value of Using Multiple Proteases for Large-Scale Mass Spectrometry-Based Proteomics

(2010) Danielle L. Swaney et al.   JOURNAL OF PROTEOME RESEARCH

The Generating Function of CID, ETD, and CID/ETD Pairs of Tandem Mass Spectra: Applications to Database Search

(2010) Sangtae Kim et al.   MOLECULAR & CELLULAR PROTEOMICS

Unbiased Quantitation of Escherichia coli Membrane Proteome Using Phase Transfer Surfactants

(2009) Takeshi Masuda et al.   MOLECULAR & CELLULAR PROTEOMICS

A Dual Pressure Linear Ion Trap Orbitrap Instrument with Very High Sequencing Speed

(2009) Jesper V. Olsen et al.   MOLECULAR & CELLULAR PROTEOMICS

Improved visualization of protein consensus sequences by iceLogo

(2009) Niklaas Colaert et al.   NATURE METHODS

Evaluation of the Low-Specificity Protease Elastase for Large-Scale Phosphoproteome Analysis

(2008) Bin Wang et al.   ANALYTICAL CHEMISTRY

ProteoWizard: open source software for rapid proteomics tools development

(2008) Darren Kessner et al.   BIOINFORMATICS

Phase Transfer Surfactant-Aided Trypsin Digestion for Membrane Proteome Analysis

(2008) Takeshi Masuda et al.   JOURNAL OF PROTEOME RESEARCH

Spectral Probabilities and Generating Functions of Tandem Mass Spectra: A Strike against Decoy Databases

(2008) Sangtae Kim et al.   JOURNAL OF PROTEOME RESEARCH

Elastase Digests

(2008) Benjamin Rietschel et al.   MOLECULAR & CELLULAR PROTEOMICS

Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast

(2008) Lyris M. F. de Godoy et al.   NATURE

Decision tree–driven tandem mass spectrometry for shotgun proteomics

(2008) Danielle L Swaney et al.   NATURE METHODS