BoxCar acquisition method enables single-shot proteomics at a depth of 10,000 proteins in 100 minutes

The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays

(2017) Jochen M. Schwenk et al.   JOURNAL OF PROTEOME RESEARCH

Performance Evaluation of the Q Exactive HF-X for Shotgun Proteomics

(2017) Christian D. Kelstrup et al.   JOURNAL OF PROTEOME RESEARCH

Loss-less Nano-fractionator for High Sensitivity, High Coverage Proteomics

(2017) Nils A. Kulak et al.   MOLECULAR & CELLULAR PROTEOMICS

Optimization of Experimental Parameters in Data-Independent Mass Spectrometry Significantly Increases Depth and Reproducibility of Results

(2017) Roland Bruderer et al.   MOLECULAR & CELLULAR PROTEOMICS

A Strategy to Combine Sample Multiplexing with Targeted Proteomics Assays for High-Throughput Protein Signature Characterization

(2017) Brian K. Erickson et al.   MOLECULAR CELL

Revisiting biomarker discovery by plasma proteomics

(2017) Philipp E Geyer et al.   Molecular Systems Biology

An Optimized Shotgun Strategy for the Rapid Generation of Comprehensive Human Proteomes

(2017) Dorte B. Bekker-Jensen et al.   Cell Systems

Phase-Constrained Spectrum Deconvolution for Fourier Transform Mass Spectrometry

(2016) Dmitry Grinfeld et al.   ANALYTICAL CHEMISTRY

DeMix-Q: Quantification-Centered Data Processing Workflow

(2016) Bo Zhang et al.   MOLECULAR & CELLULAR PROTEOMICS

Proteome complexity and the forces that drive proteome imbalance

(2016) J. Wade Harper et al.   NATURE

Mass-spectrometric exploration of proteome structure and function

(2016) Ruedi Aebersold et al.   NATURE

A multicenter study benchmarks software tools for label-free proteome quantification

(2016) Pedro Navarro et al.   NATURE BIOTECHNOLOGY

TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics

(2016) Hannes L Röst et al.   NATURE METHODS

The Perseus computational platform for comprehensive analysis of (prote)omics data

(2016) Stefka Tyanova et al.   NATURE METHODS

Plasma Proteome Profiling to Assess Human Health and Disease

(2016) Philipp E. Geyer et al.   Cell Systems

Evolution of Orbitrap Mass Spectrometry Instrumentation

(2015) Shannon Eliuk et al.   Annual Review of Analytical Chemistry

Proteome sequencing goes deep

(2015) Alicia L Richards et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data

(2015) Ying S. Ting et al.   MOLECULAR & CELLULAR PROTEOMICS

Extending the Limits of Quantitative Proteome Profiling with Data-Independent Acquisition and Application to Acetaminophen-Treated Three-Dimensional Liver Microtissues

(2015) Roland Bruderer et al.   MOLECULAR & CELLULAR PROTEOMICS

Large-Scale Targeted Proteomics Using Internal Standard Triggered-Parallel Reaction Monitoring (IS-PRM)

(2015) Sebastien Gallien et al.   MOLECULAR & CELLULAR PROTEOMICS

Reproducible quantitative proteotype data matrices for systems biology

(2015) Hannes L. Röst et al.   MOLECULAR BIOLOGY OF THE CELL

Quantitative variability of 342 plasma proteins in a human twin population

(2015) Y. Liu et al.   Molecular Systems Biology

Cell type– and brain region–resolved mouse brain proteome

(2015) Kirti Sharma et al.   NATURE NEUROSCIENCE

2016 update of the PRIDE database and its related tools

(2015) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

A “Proteomic Ruler” for Protein Copy Number and Concentration Estimation without Spike-in Standards

(2014) Jacek R. Wiśniewski 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

Multiplexed and data-independent tandem mass spectrometry for global proteome profiling

(2013) John D. Chapman et al.   MASS SPECTROMETRY REVIEWS

The Coming Age of Complete, Accurate, and Ubiquitous Proteomes

(2013) Matthias Mann et al.   MOLECULAR CELL

Multiplexed MS/MS for improved data-independent acquisition

(2013) Jarrett D Egertson et al.   NATURE METHODS

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

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

Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis

(2012) Ludovic C. Gillet et al.   MOLECULAR & CELLULAR PROTEOMICS

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

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

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

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

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser 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