Rapid and Deep Human Proteome Analysis by Single-dimension Shotgun Proteomics

The challenge of the proteome dynamic range and its implications for in-depth proteomics

(2013) Roman A. Zubarev   PROTEOMICS

In-house construction of a UHPLC system enabling the identification of over 4000 protein groups in a single analysis

(2012) Alba Cristobal et al.   ANALYST

Expert System for Computer-assisted Annotation of MS/MS Spectra

(2012) Nadin Neuhauser 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

Performance Characteristics of a New Hybrid Quadrupole Time-of-Flight Tandem Mass Spectrometer (TripleTOF 5600)

(2011) Genna L. Andrews 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

Characterization of human melanoma cell lines and melanocytes by proteome analysis

(2011) Emilia Caputo et al.   CELL CYCLE

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

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

Deep and Highly Sensitive Proteome Coverage by LC-MS/MS Without Prefractionation

(2011) Suman S. Thakur et al.   MOLECULAR & CELLULAR PROTEOMICS

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

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

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

Deep proteome and transcriptome mapping of a human cancer cell line

(2011) N. Nagaraj et al.   Molecular Systems Biology

The quantitative proteome of a human cell line

(2011) M. Beck et al.   Molecular Systems Biology

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Use of stable isotope labeling by amino acids in cell culture as a spike-in standard in quantitative proteomics

(2011) Tamar Geiger et al.   Nature Protocols

Comprehensive proteomics

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

Defining the transcriptome and proteome in three functionally different human cell lines

(2010) Emma Lundberg et al.   Molecular Systems Biology

Decoding signalling networks by mass spectrometry-based proteomics

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

Combination of FASP and StageTip-Based Fractionation Allows In-Depth Analysis of the Hippocampal Membrane Proteome

(2009) Jacek R. Wiśniewski 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

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

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

Universal sample preparation method for proteome analysis

(2009) Jacek R Wiśniewski et al.   NATURE METHODS

Interferences and contaminants encountered in modern mass spectrometry

(2008) Bernd O. Keller et al.   ANALYTICA CHIMICA ACTA

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