Label‐free single cell proteomics utilizing ultrafast LC and MS instrumentation: A valuable complementary technique to multiplexing

Robust and Easy-to-Use One-Pot Workflow for Label-Free Single-Cell Proteomics

(2023) Manuel Matzinger et al.   Analytical Chemistry

The Parallel Reaction Monitoring-Parallel Accumulation–Serial Fragmentation (prm-PASEF) Approach for Multiplexed Absolute Quantitation of Proteins in Human Plasma

(2022) Alexander Brzhozovskiy et al.   ANALYTICAL CHEMISTRY

Streamlined single-cell proteomics by an integrated microfluidic chip and data-independent acquisition mass spectrometry

(2022) Sofani Tafesse Gebreyesus et al.   Nature Communications

Label-Free Profiling of up to 200 Single-Cell Proteomes per Day Using a Dual-Column Nanoflow Liquid Chromatography Platform

(2022) Kei G. I. Webber et al.   ANALYTICAL CHEMISTRY

A human breast atlas integrating single-cell proteomics and transcriptomics

(2022) G. Kenneth Gray et al.   DEVELOPMENTAL CELL

Modern Data Acquisition Approaches in Proteomics Based on Dynamic Instrument Control

(2022) Michael J. Plank   JOURNAL OF PROTEOME RESEARCH

Real-Time Search-Assisted Acquisition on a Tribrid Mass Spectrometer Improves Coverage in Multiplexed Single-Cell Proteomics

(2022) Benjamin Furtwängler et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2022) Andreas‐David Brunner et al.   Molecular Systems Biology

Deep Visual Proteomics defines single-cell identity and heterogeneity

(2022) Andreas Mund et al.   NATURE BIOTECHNOLOGY

Three-dimensional feature matching improves coverage for single-cell proteomics based on ion mobility filtering

(2022) Jongmin Woo et al.   Cell Systems

Single-Cell Chemical Proteomics (SCCP) Interrogates the Timing and Heterogeneity of Cancer Cell Commitment to Death

(2022) Ákos Végvári et al.   ANALYTICAL CHEMISTRY

Single-Cell Quantitative Proteomic Analysis of Human Oocyte Maturation Revealed High Heterogeneity in In Vitro–Matured Oocytes

(2022) Yueshuai Guo et al.   MOLECULAR & CELLULAR PROTEOMICS

dia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts

(2022) Vadim Demichev et al.   Nature Communications

Optimized data-independent acquisition approach for proteomic analysis at single-cell level

(2022) Yuefan Wang et al.   Clinical Proteomics

On-capillary Cell Lysis Enables Top-down Proteomic Analysis of Single Mammalian Cells by CE-MS/MS

(2022) Kendall R. Johnson et al.   ANALYTICAL CHEMISTRY

DirectMS1Quant: Ultrafast Quantitative Proteomics with MS/MS-Free Mass Spectrometry

(2022) Mark V. Ivanov et al.   ANALYTICAL CHEMISTRY

High Sensitivity Limited Material Proteomics Empowered by Data-Independent Acquisition on Linear Ion Traps

(2022) Teeradon Phlairaharn et al.   JOURNAL OF PROTEOME RESEARCH

On the Feasibility of Using an Ultra-Fast DirectMS1 Method of Proteome-Wide Analysis for Searching Drug Targets in Chemical Proteomics

(2022) Elizaveta M. Solovyeva et al.   BIOCHEMISTRY-MOSCOW

Reversed-Phase Liquid Chromatography of Peptides for Bottom-Up Proteomics: A Tutorial

(2022) Juraj Lenčo et al.   Journal of Proteome Research

Spatiotemporal dissection of the cell cycle with single-cell proteogenomics

(2021) Diana Mahdessian et al.   NATURE

Boosting MS1-only Proteomics with Machine Learning Allows 2000 Protein Identifications in Single-Shot Human Proteome Analysis Using 5 min HPLC Gradient

(2021) Mark V. Ivanov et al.   JOURNAL OF PROTEOME RESEARCH

TMTpro-18plex: The Expanded and Complete Set of TMTpro Reagents for Sample Multiplexing

(2021) Jiaming Li et al.   JOURNAL OF PROTEOME RESEARCH

Single-cell atlas of early human brain development highlights heterogeneity of human neuroepithelial cells and early radial glia

(2021) Ugomma C. Eze et al.   NATURE NEUROSCIENCE

Ultrasensitive NanoLC-MS of Subnanogram Protein Samples Using Second Generation Micropillar Array LC Technology with Orbitrap Exploris 480 and FAIMS PRO

(2021) Karel Stejskal et al.   ANALYTICAL CHEMISTRY

Use of Linear Ion Traps in Data-Independent Acquisition Methods Benefits Low-Input Proteomics

(2021) Eva Borràs et al.   ANALYTICAL CHEMISTRY

CD34+ progenitors are predictive of mortality and are associated with physical activity in cardiovascular disease patients

(2021) David Muggeridge et al.   ATHEROSCLEROSIS

IceR improves proteome coverage and data completeness in global and single-cell proteomics

(2021) Mathias Kalxdorf et al.   Nature Communications

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

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

Quantitative Accuracy and Precision in Multiplexed Single-Cell Proteomics

(2021) Claudia Ctortecka et al.   ANALYTICAL CHEMISTRY

Deciphering functional tumor states at single‐cell resolution

(2021) Rolando Vegliante et al.   EMBO JOURNAL

Features of Peptide Fragmentation Spectra in Single-Cell Proteomics

(2021) Hannah Boekweg et al.   JOURNAL OF PROTEOME RESEARCH

Multiplexed single-cell proteomics using SCoPE2

(2021) Aleksandra A. Petelski et al.   Nature Protocols

Automation of single‐cell proteomic sample preparation

(2021) Michal Alexovič et al.   PROTEOMICS

A simple, rapid, and practical method for single-cell proteomics based on mass-adaptive coating of synthetic peptides

(2021) Siqi Li et al.   Science Bulletin

DirectMS1: MS/MS-Free Identification of 1000 Proteins of Cellular Proteomes in 5 Minutes

(2020) Mark V. Ivanov et al.   ANALYTICAL CHEMISTRY

A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients

(2020) Dorte B. Bekker-Jensen et al.   MOLECULAR & CELLULAR PROTEOMICS

Liquid chromatography above 20,000 PSI

(2020) Matthew J. Sorensen et al.   TRAC-TRENDS IN ANALYTICAL CHEMISTRY

Picoflow Liquid Chromatography–Mass Spectrometry for Ultrasensitive Bottom-Up Proteomics Using 2-μm-i.d. Open Tubular Columns

(2020) Piliang Xiang et al.   ANALYTICAL CHEMISTRY

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

Standardization and harmonization of distributed multi-center proteotype analysis supporting precision medicine studies

(2020) Yue Xuan et al.   Nature Communications

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

MaxQuant.Live enables global targeting of more than 25,000 peptides

(2019) Christoph Wichmann et al.   MOLECULAR & CELLULAR PROTEOMICS

Boosting to Amplify Signal with Isobaric Labeling (BASIL) Strategy for Comprehensive Quantitative Phosphoproteomic Characterization of Small Populations of Cells

(2019) Lian Yi et al.   ANALYTICAL CHEMISTRY

Exploiting the dynamic relationship between peptide separation quality and peptide co-isolation in a mPSM approach offers a new strategy to optimize bottom-up proteomics throughput and depth

(2019) Manuel I. Villalobos Solis et al.   ANALYTICAL CHEMISTRY

Step-Wise Assessment and Optimization of Sample Handling Recovery Yield for Nanoproteomic Analysis of 1000 Mammalian Cells

(2019) Ruilin Wu et al.   ANALYTICAL CHEMISTRY

TMTpro: Design, Synthesis, and Initial Evaluation of a Proline-Based Isobaric 16-Plex Tandem Mass Tag Reagent Set

(2019) Andrew Thompson et al.   ANALYTICAL CHEMISTRY

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

(2019) Vadim Demichev et al.   NATURE METHODS

Single-cell proteomics reveals changes in expression during hair-cell development

(2019) Ying Zhu et al.   eLife

Combining Precursor and Fragment Information for Improved Detection of Differential Abundance in Data Independent Acquisition

(2019) Ting Huang et al.   MOLECULAR & CELLULAR PROTEOMICS

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

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

Comprehensive Single-Shot Proteomics with FAIMS on a Hybrid Orbitrap Mass Spectrometer

(2018) Alexander S. Hebert et al.   ANALYTICAL CHEMISTRY

Proteomic Analysis of Single Mammalian Cells Enabled by Microfluidic Nanodroplet Sample Preparation and Ultrasensitive NanoLC-MS

(2018) Ying Zhu et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Trapped ion mobility spectrometry: A short review

(2018) Mark E. Ridgeway et al.   INTERNATIONAL JOURNAL OF MASS SPECTROMETRY

Single-cell characterization of haematopoietic progenitors and their trajectories in homeostasis and perturbed haematopoiesis

(2018) Amir Giladi et al.   NATURE CELL BIOLOGY

IonStar enables high-precision, low-missing-data proteomics quantification in large biological cohorts

(2018) Xiaomeng Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Limits for Resolving Isobaric Tandem Mass Tag Reporter Ions Using Phase-Constrained Spectrum Deconvolution

(2018) Christian D. Kelstrup et al.   JOURNAL OF PROTEOME RESEARCH

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

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

Integrated Proteome Analysis Device for Fast Single-Cell Protein Profiling

(2018) Xi Shao et al.   ANALYTICAL CHEMISTRY

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

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

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

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

(2017) Andy T Kong et al.   NATURE METHODS

Single-Cell Mass Spectrometry for Discovery Proteomics: Quantifying Translational Cell Heterogeneity in the 16-Cell Frog (Xenopus ) Embryo

(2016) Camille Lombard-Banek et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Identification of Maturation-Specific Proteins by Single-Cell Proteomics of Human Oocytes

(2016) Irma Virant-Klun et al.   MOLECULAR & CELLULAR PROTEOMICS

Proteomics reveals the effects of sustained weight loss on the human plasma proteome

(2016) Philipp E Geyer et al.   Molecular Systems Biology

Now, More Than Ever, Proteomics Needs Better Chromatography

(2016) Evgenia Shishkova et al.   Cell Systems

Plasma Proteome Profiling to Assess Human Health and Disease

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

Complete De Novo Assembly of Monoclonal Antibody Sequences

(2016) Ngoc Hieu Tran et al.   Scientific Reports

High-Sensitivity N-Glycoproteomic Analysis of Mouse Brain Tissue by Protein Extraction with a Mild Detergent of N-Dodecyl β-D-Maltoside

(2015) Jing Liu et al.   ANALYTICAL CHEMISTRY

Combined Single-Cell Functional and Gene Expression Analysis Resolves Heterogeneity within Stem Cell Populations

(2015) Nicola K. Wilson et al.   Cell Stem Cell

New Mass-Spectrometry-Compatible Degradable Surfactant for Tissue Proteomics

(2015) Ying-Hua Chang et al.   JOURNAL OF PROTEOME RESEARCH

In vitro maturation as an alternative to standard in vitro fertilization for patients diagnosed with polycystic ovaries: a comparative analysis of fresh, frozen and cumulative cycle outcomes

(2014) M. L. Walls et al.   HUMAN REPRODUCTION

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

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

Perspectives on the Evolution of the Column Efficiency in Liquid Chromatography

(2013) Fabrice Gritti et al.   ANALYTICAL CHEMISTRY

Dual LC–MS Platform for High-Throughput Proteome Analysis

(2013) Dennis J. Orton et al.   JOURNAL OF PROTEOME RESEARCH

Measuring and Managing Ratio Compression for Accurate iTRAQ/TMT Quantification

(2013) Mikhail M. Savitski et al.   JOURNAL OF PROTEOME RESEARCH

Characterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis

(2013) Victoria Moignard et al.   NATURE CELL BIOLOGY

High-Resolution Enabled TMT 8-plexing

(2012) Thilo Werner et al.   ANALYTICAL CHEMISTRY

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

Realization of 1 × 106 Theoretical Plates in Liquid Chromatography Using Very Long Pillar Array Columns

(2011) Wim De Malsche et al.   ANALYTICAL CHEMISTRY

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

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

mProphet: automated data processing and statistical validation for large-scale SRM experiments

(2011) Lukas Reiter et al.   NATURE METHODS

A comparison of the accuracy of iTRAQ quantification by nLC-ESI MSMS and nLC-MALDI MSMS methods

(2010) Sally L. Shirran et al.   Journal of Proteomics

Addressing Accuracy and Precision Issues in iTRAQ Quantitation

(2010) Natasha A. Karp et al.   MOLECULAR & CELLULAR PROTEOMICS

iTRAQ Underestimation in Simple and Complex Mixtures: “The Good, the Bad and the Ugly”

(2009) Saw Yen Ow et al.   JOURNAL OF PROTEOME RESEARCH

Accelerated tryptic digestion of proteins in plasma for absolute quantitation using a protein internal standard by liquid chromatography/tandem mass spectrometry

(2009) Fumin Li et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

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