Analytical Utility of Mass Spectral Binning in Proteomic Experiments by SPectral Immonium Ion Detection (SPIID)

Advances in characterizing ubiquitylation sites by mass spectrometry

(2013) Kathrine B Sylvestersen et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Pyteomics—a Python Framework for Exploratory Data Analysis and Rapid Software Prototyping in Proteomics

(2013) Anton A. Goloborodko et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Functional Proteomics Defines the Molecular Switch Underlying FGF Receptor Trafficking and Cellular Outputs

(2013) Chiara Francavilla et al.   MOLECULAR CELL

Proteome-wide Identification of Poly(ADP-Ribosyl)ation Targets in Different Genotoxic Stress Responses

(2013) Stephanie Jungmichel et al.   MOLECULAR CELL

Reduction in Database Search Space by Utilization of Amino Acid Composition Information from Electron Transfer Dissociation and Higher-Energy Collisional Dissociation Mass Spectra

(2012) Thomas A. Hansen et al.   ANALYTICAL CHEMISTRY

A Systematic Investigation into the Nature of Tryptic HCD Spectra

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

Optimized Fast and Sensitive Acquisition Methods for Shotgun Proteomics on a Quadrupole Orbitrap Mass Spectrometer

(2012) Christian D. Kelstrup et al.   JOURNAL OF PROTEOME RESEARCH

File Formats Commonly Used in Mass Spectrometry Proteomics

(2012) Eric W. Deutsch   MOLECULAR & CELLULAR PROTEOMICS

Proteomic Analysis of Lysine Acetylation Sites in Rat Tissues Reveals Organ Specificity and Subcellular Patterns

(2012) Alicia Lundby et al.   Cell Reports

Pinpointing Phosphorylation Sites: Quantitative Filtering and a Novel Site-specific x-Ion Fragment

(2011) Christian D. Kelstrup 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

Improved Peptide Identification by Targeted Fragmentation Using CID, HCD and ETD on an LTQ-Orbitrap Velos

(2011) Christian K. Frese et al.   JOURNAL OF PROTEOME RESEARCH

Characterization and Diagnostic Value of Amino Acid Side Chain Neutral Losses Following Electron-Transfer Dissociation

(2011) Qiangwei Xia et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Mass Spectrometry-based Proteomics Using Q Exactive, a High-performance Benchtop Quadrupole Orbitrap Mass Spectrometer

(2011) Annette Michalski et al.   MOLECULAR & CELLULAR PROTEOMICS

A Proteome-wide, Quantitative Survey of In Vivo Ubiquitylation Sites Reveals Widespread Regulatory Roles

(2011) Sebastian A. Wagner et al.   MOLECULAR & CELLULAR PROTEOMICS

Proteome-Wide Mapping of the Drosophila Acetylome Demonstrates a High Degree of Conservation of Lysine Acetylation

(2011) B. T. Weinert et al.   Science Signaling

Comprehensive Profiling of Phosphopeptides Based on Anion Exchange Followed by Flow-Through Enrichment with Titanium Dioxide (AFET)

(2010) Song Nie et al.   JOURNAL OF PROTEOME RESEARCH

pNovo:De novoPeptide Sequencing and Identification Using HCD Spectra

(2010) Hao Chi et al.   JOURNAL OF PROTEOME RESEARCH

A Novel Proteomics Approach to Identify SUMOylated Proteins and Their Modification Sites in Human Cells

(2010) Frederic Galisson et al.   MOLECULAR & CELLULAR PROTEOMICS

Mass Spectrometric Analysis of Lysine Ubiquitylation Reveals Promiscuity at Site Level

(2010) Jannie M. R. Danielsen et al.   MOLECULAR & CELLULAR PROTEOMICS

Decoding signalling networks by mass spectrometry-based proteomics

(2010) Chunaram Choudhary et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Quantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis

(2010) J. V. Olsen et al.   Science Signaling

Proteomics by Mass Spectrometry: Approaches, Advances, and Applications

(2009) John R. Yates et al.   Annual Review of Biomedical Engineering

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

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

MassMatrix: A database search program for rapid characterization of proteins and peptides from tandem mass spectrometry data

(2009) Hua Xu et al.   PROTEOMICS

Lysine Acetylation Targets Protein Complexes and Co-Regulates Major Cellular Functions

(2009) C. Choudhary et al.   SCIENCE

Utility of Immonium Ions for Assignment of ε-N-Acetyllysine-Containing Peptides by Tandem Mass Spectrometry

(2008) Morten B. Trelle et al.   ANALYTICAL CHEMISTRY

Analytical Utility of Small Neutral Losses from Reduced Species in Electron Capture Dissociation Studied Using SwedECD Database

(2008) Maria Fälth et al.   ANALYTICAL CHEMISTRY

ProteoWizard: open source software for rapid proteomics tools development

(2008) Darren Kessner et al.   BIOINFORMATICS

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

Iodoacetamide-induced artifact mimics ubiquitination in mass spectrometry

(2008) Michael L Nielsen et al.   NATURE METHODS