Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation

Deep learning the collisional cross sections of the peptide universe from a million experimental values

(2021) Florian Meier et al.   Nature Communications

Ultra-fast proteomics with Scanning SWATH

(2021) Christoph B. Messner et al.   NATURE BIOTECHNOLOGY

Quantitative single-cell proteomics as a tool to characterize cellular hierarchies

(2021) Erwin M. Schoof et al.   Nature Communications

An improved Boosting to Amplify Signal with Isobaric Labeling (iBASIL) strategy for precise quantitative single-cell proteomics

(2020) Chia-Feng Tsai et al.   MOLECULAR & CELLULAR PROTEOMICS

The single-cell pathology landscape of breast cancer

(2020) Hartland W. Jackson et al.   NATURE

Droplet scRNA-seq is not zero-inflated

(2020) Valentine Svensson   NATURE BIOTECHNOLOGY

Extending the Separation Space with Trapped Ion Mobility Spectrometry Improves the Accuracy of Isobaric Tag-Based Quantitation in Proteomic LC/MS/MS

(2020) Kosuke Ogata et al.   ANALYTICAL CHEMISTRY

MaxQuant Software for Ion Mobility Enhanced Shotgun Proteomics

(2020) Nikita Prianichnikov et al.   MOLECULAR & CELLULAR PROTEOMICS

Automated Coupling of Nanodroplet Sample Preparation with Liquid Chromatography–Mass Spectrometry for High-Throughput Single-Cell Proteomics

(2020) Sarah M. Williams et al.   ANALYTICAL CHEMISTRY

mRNAs, proteins and the emerging principles of gene expression control

(2020) Christopher Buccitelli et al.   NATURE REVIEWS GENETICS

Ultra-High-Throughput Clinical Proteomics Reveals Classifiers of COVID-19 Infection

(2020) Christoph B. Messner et al.   Cell Systems

Improved Sensitivity of Ultralow Flow LC–MS-Based Proteomic Profiling of Limited Samples Using Monolithic Capillary Columns and FAIMS Technology

(2020) Michal Greguš et al.   ANALYTICAL CHEMISTRY

Fully Automated Sample Processing and Analysis Workflow for Low-Input Proteome Profiling

(2020) Yiran Liang et al.   ANALYTICAL CHEMISTRY

diaPASEF: parallel accumulation–serial fragmentation combined with data-independent acquisition

(2020) Florian Meier et al.   NATURE METHODS

Defining the carrier proteome limit for single-cell proteomics

(2020) Tommy K. Cheung et al.   NATURE METHODS

Spatial proteomics: a powerful discovery tool for cell biology

(2019) Emma Lundberg et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Multi-omic measurements of heterogeneity in HeLa cells across laboratories

(2019) Yansheng Liu et al.   NATURE BIOTECHNOLOGY

Multi-batch TMT reveals false positives, batch effects and missing values

(2019) Alejandro Brenes et al.   MOLECULAR & CELLULAR PROTEOMICS

MS-Empire utilizes peptide-level noise distributions for ultra sensitive detection of differentially abundant proteins

(2019) Constantin Ammar et al.   MOLECULAR & CELLULAR PROTEOMICS

DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput

(2019) Vadim Demichev et al.   NATURE METHODS

HeLa-CCL2 cell heterogeneity studied by single-cell DNA and RNA sequencing

(2019) Wan-er Hu et al.   PLoS One

Nanoliter-Scale Oil-Air-Droplet Chip-Based Single Cell Proteomic Analysis

(2018) Zi-Yi Li et al.   ANALYTICAL CHEMISTRY

EASI-tag enables accurate multiplexed and interference-free MS2-based proteome quantification

(2018) Sebastian Virreira Winter et al.   NATURE METHODS

Structural absorption by barbule microstructures of super black bird of paradise feathers

(2018) Dakota E. McCoy et al.   Nature Communications

A general and flexible method for signal extraction from single-cell RNA-seq data

(2018) Davide Risso et al.   Nature Communications

A novel LC system embeds analytes in pre-formed gradients for rapid, ultra-robust proteomics

(2018) Nicolai Bache et al.   MOLECULAR & CELLULAR PROTEOMICS

Online Parallel Accumulation–Serial Fragmentation (PASEF) with a Novel Trapped Ion Mobility Mass Spectrometer

(2018) Florian Meier et al.   MOLECULAR & CELLULAR PROTEOMICS

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

(2018) et al.   NATURE

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

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

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics

(2017) Andy T Kong et al.   NATURE METHODS

Super-resolution microscopy with DNA-PAINT

(2017) Joerg Schnitzbauer et al.   Nature Protocols

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

Proteomic analysis of cell cycle progression in asynchronous cultures, including mitotic subphases, using PRIMMUS

(2017) Tony Ly et al.   eLife

Mass-spectrometric exploration of proteome structure and function

(2016) Ruedi Aebersold et al.   NATURE

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

(2016) Stefka Tyanova et al.   NATURE METHODS

A Human Interactome in Three Quantitative Dimensions Organized by Stoichiometries and Abundances

(2015) Marco Y. Hein et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Parallel Accumulation–Serial Fragmentation (PASEF): Multiplying Sequencing Speed and Sensitivity by Synchronized Scans in a Trapped Ion Mobility Device

(2015) Florian Meier et al.   JOURNAL OF PROTEOME RESEARCH

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

Multidimensional proteomics for cell biology

(2015) Mark Larance et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

Uncovering Hidden Layers of Cell Cycle Regulation through Integrative Multi-omic Analysis

(2015) Ranen Aviner et al.   PLoS Genetics

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

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

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types

(2014) D. A. Jaitin et al.   SCIENCE

Quantitative single-cell RNA-seq with unique molecular identifiers

(2013) Saiful Islam et al.   NATURE METHODS

Accurate Multiplexed Proteomics at the MS2 Level Using the Complement Reporter Ion Cluster

(2012) Martin Wühr et al.   ANALYTICAL CHEMISTRY

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

Dynamic single-cell imaging of direct reprogramming reveals an early specifying event

(2010) Zachary D Smith et al.   NATURE BIOTECHNOLOGY

The SUMO pathway: emerging mechanisms that shape specificity, conjugation and recognition

(2010) Jaclyn R. Gareau et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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