The Impact II, a Very High-Resolution Quadrupole Time-of-Flight Instrument (QTOF) for Deep Shotgun Proteomics

Rapid and Deep Proteomes by Faster Sequencing on a Benchtop Quadrupole Ultra-High-Field Orbitrap Mass Spectrometer

(2014) Christian D. Kelstrup et al.   JOURNAL OF PROTEOME RESEARCH

Ion Mobility Tandem Mass Spectrometry Enhances Performance of Bottom-up Proteomics

(2014) Dominic Helm et al.   MOLECULAR & CELLULAR PROTEOMICS

The Q Exactive HF, a Benchtop Mass Spectrometer with a Pre-filter, High-performance Quadrupole and an Ultra-high-field Orbitrap Analyzer

(2014) Richard Alexander Scheltema et al.   MOLECULAR & CELLULAR PROTEOMICS

Deep Proteomic Evaluation of Primary and Cell Line Motoneuron Disease Models Delineates Major Differences in Neuronal Characteristics

(2014) Daniel Hornburg et al.   MOLECULAR & CELLULAR PROTEOMICS

Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ

(2014) Jürgen Cox et al.   MOLECULAR & CELLULAR PROTEOMICS

Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells

(2014) Nils A Kulak et al.   NATURE METHODS

Orbitrap Mass Spectrometry

(2013) Roman A. Zubarev et al.   ANALYTICAL CHEMISTRY

Correct primary structure assessment and extensive glyco-profiling of cetuximab by a combination of intact, middle-up, middle-down and bottom-up ESI and MALDI mass spectrometry techniques

(2013) Daniel Ayoub et al.   mAbs

The One Hour Yeast Proteome

(2013) Alexander S. Hebert et al.   MOLECULAR & CELLULAR PROTEOMICS

Drift time-specific collision energies enable deep-coverage data-independent acquisition proteomics

(2013) Ute Distler et al.   NATURE METHODS

1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data

(2012) Juergen Cox et al.   BMC BIOINFORMATICS

Next-generation proteomics: towards an integrative view of proteome dynamics

(2012) A. F. Maarten Altelaar et al.   NATURE REVIEWS GENETICS

Structural Analysis of Intact Monoclonal Antibodies by Electron Transfer Dissociation Mass Spectrometry

(2011) Yury O. Tsybin et al.   ANALYTICAL CHEMISTRY

Ultra-High-Pressure RPLC Hyphenated to an LTQ-Orbitrap Velos Reveals a Linear Relation between Peak Capacity and Number of Identified Peptides

(2011) Thomas Köcher et al.   ANALYTICAL CHEMISTRY

Quantitative, High-Resolution Proteomics for Data-Driven Systems Biology

(2011) Jürgen Cox et al.   Annual Review of Biochemistry

Proteomic reactors and their applications in biology

(2011) Hu Zhou et al.   FEBS Journal

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

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

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

(2011) Yuexi Wang et al.   PROTEOMICS

Practical Implementation of 2D HPLC Scheme with Accurate Peptide Retention Prediction in Both Dimensions for High-Throughput Bottom-Up Proteomics

(2008) Ravi C. Dwivedi et al.   ANALYTICAL CHEMISTRY

How Much Peptide Sequence Information Is Contained in Ion Trap Tandem Mass Spectra?

(2008) J COX et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Comparative Proteomic Phenotyping of Cell Lines and Primary Cells to Assess Preservation of Cell Type-specific Functions

(2008) Cuiping Pan 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

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

Precision proteomics: The case for high resolution and high mass accuracy

(2008) M. Mann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA