Characterization of a high field Orbitrap mass spectrometer for proteome analysis

Segmentation of Precursor Mass Range Using “Tiling” Approach Increases Peptide Identifications for MS1-Based Label-Free Quantification

(2013) Catherine E. Vincent et al.   ANALYTICAL CHEMISTRY

Evaluation and Optimization of Mass Spectrometric Settings during Data-dependent Acquisition Mode: Focus on LTQ-Orbitrap Mass Analyzers

(2013) Anastasia Kalli et al.   JOURNAL OF PROTEOME RESEARCH

Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present

(2012) Marcus Bantscheff et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

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

(2012) Nagarjuna Nagaraj 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

Evaluation of the Compact High-Field Orbitrap for Top-Down Proteomics of Human Cells

(2012) Dorothy R. Ahlf et al.   JOURNAL OF PROTEOME RESEARCH

Effects of Column and Gradient Lengths on Peak Capacity and Peptide Identification in Nanoflow LC-MS/MS of Complex Proteomic Samples

(2012) Edward J. Hsieh et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Discovery ofO-GlcNAc-modified Proteins in Published Large-scale Proteome Data

(2012) Hannes Hahne et al.   MOLECULAR & CELLULAR PROTEOMICS

Comparative Proteomic Analysis of Eleven Common Cell Lines Reveals Ubiquitous but Varying Expression of Most Proteins

(2012) Tamar Geiger et al.   MOLECULAR & CELLULAR PROTEOMICS

Analysis of protein mixtures from whole-cell extracts by single-run nanoLC-MS/MS using ultralong gradients

(2012) Thomas Köcher et al.   Nature Protocols

Ultra-high intra-spectrum mass accuracy enables unambiguous identification of fragment reporter ions in isobaric multiplexed quantitative proteomics

(2012) Fiona Pachl et al.   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

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

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

Ultra High Resolution Linear Ion Trap Orbitrap Mass Spectrometer (Orbitrap Elite) Facilitates Top Down LC MS/MS and Versatile Peptide Fragmentation Modes

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

Proteomic and phosphoproteomic comparison of human ES and iPS cells

(2011) Douglas H Phanstiel et al.   NATURE METHODS

Automated Broadband Phase Correction of Fourier Transform Ion Cyclotron Resonance Mass Spectra

(2010) Feng Xian et al.   ANALYTICAL CHEMISTRY

Proteomics: a pragmatic perspective

(2010) Parag Mallick et al.   NATURE BIOTECHNOLOGY

Highly efficient peptide separations in proteomicsPart 2: Bi- and multidimensional liquid-based separation techniques

(2009) Koen Sandra et al.   JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES

Repeatability and Reproducibility in Proteomic Identifications by Liquid Chromatography−Tandem Mass Spectrometry

(2009) David L. Tabb et al.   JOURNAL OF PROTEOME RESEARCH

Performance evaluation of a high-field orbitrap mass analyzer

(2009) Alexander Makarov et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Universal sample preparation method for proteome analysis

(2009) Jacek R Wiśniewski et al.   NATURE METHODS

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

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

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