Mass spectrometry‐based high‐throughput proteomics and its role in biomedical studies and systems biology

The proteogenomic subtypes of acute myeloid leukemia

(2022) Ashok Kumar Jayavelu et al.   CANCER CELL

Biomarker Candidates for Tumors Identified from Deep-Profiled Plasma Stem Predominantly from the Low Abundant Area

(2022) Marco Tognetti et al.   JOURNAL OF PROTEOME RESEARCH

Defining mitochondrial protein functions through deep multiomic profiling

(2022) Jarred W. Rensvold et al.   NATURE

Noninvasive proteomic biomarkers for alcohol-related liver disease

(2022) Lili Niu et al.   NATURE MEDICINE

Understudied proteins: opportunities and challenges for functional proteomics

(2022) Georg Kustatscher et al.   NATURE METHODS

The emerging role of mass spectrometry-based proteomics in drug discovery

(2022) Felix Meissner et al.   NATURE REVIEWS DRUG DISCOVERY

Proteomic profiling platforms head to head: Leveraging genetics and clinical traits to compare aptamer- and antibody-based methods

(2022) Daniel H. Katz et al.   Science Advances

Urinary proteome profiling for stratifying patients with familial Parkinson’s disease

(2021) Sebastian Virreira Winter et al.   EMBO Molecular Medicine

Automated 16-Plex Plasma Proteomics with Real-Time Search and Ion Mobility Mass Spectrometry Enables Large-Scale Profiling in Naked Mole-Rats and Mice

(2021) Aleksandr Gaun et al.   JOURNAL OF PROTEOME RESEARCH

Robust Microflow LC-MS/MS for Proteome Analysis: 38 000 Runs and Counting

(2021) Yangyang Bian et al.   ANALYTICAL CHEMISTRY

QCloud2: An Improved Cloud-based Quality-Control System for Mass-Spectrometry-based Proteomics Laboratories

(2021) Roger Olivella et al.   JOURNAL OF PROTEOME RESEARCH

A Semiautomated Paramagnetic Bead-Based Platform for Isobaric Tag Sample Preparation

(2021) Xinyue Liu et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Ultra-fast proteomics with Scanning SWATH

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

Proteogenomic characterization of pancreatic ductal adenocarcinoma

(2021) Liwei Cao et al.   CELL

A proteogenomic portrait of lung squamous cell carcinoma

(2021) Shankha Satpathy et al.   CELL

High‐resolution serum proteome trajectories in COVID‐19 reveal patient‐specific seroconversion

(2021) Philipp E Geyer et al.   EMBO Molecular Medicine

Dissociation of Biomolecules by an Intense Low-Energy Electron Beam in a High Sensitivity Time-of-Flight Mass Spectrometer

(2021) Takashi Baba et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Diagnostics and correction of batch effects in large‐scale proteomic studies: a tutorial

(2021) Jelena Čuklina et al.   Molecular Systems Biology

From variant to function in human disease genetics

(2021) Tuuli Lappalainen et al.   SCIENCE

Time-resolved in vivo ubiquitinome profiling by DIA-MS reveals USP7 targets on a proteome-wide scale

(2021) Martin Steger et al.   Nature Communications

A time-resolved proteomic and prognostic map of COVID-19

(2021) Vadim Demichev et al.   Cell Systems

A serum proteome signature to predict mortality in severe COVID-19 patients

(2021) Franziska Völlmy et al.   Life Science Alliance

Standardized Workflow for Precise Mid- and High-Throughput Proteomics of Blood Biofluids

(2021) Angela Mc Ardle et al.   CLINICAL CHEMISTRY

Automated proteomic sample preparation: The key component for high throughput and quantitative mass spectrometry analysis

(2021) Qin Fu et al.   MASS SPECTROMETRY REVIEWS

Mapping the proteo-genomic convergence of human diseases

(2021) Maik Pietzner et al.   SCIENCE

Synergistic insights into human health from aptamer- and antibody-based proteomic profiling

(2021) Maik Pietzner et al.   Nature Communications

Proline: an efficient and user-friendly software suite for large-scale proteomics

(2020) David Bouyssié et al.   BIOINFORMATICS

Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma

(2020) David J. Clark et al.   CELL

Quantitative Proteomics of the Cancer Cell Line Encyclopedia

(2020) David P. Nusinow et al.   CELL

Accelerated Protein Biomarker Discovery from FFPE Tissue Samples Using Single-Shot, Short Gradient Microflow SWATH MS

(2020) Rui Sun et al.   JOURNAL OF PROTEOME RESEARCH

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

Automated sample preparation with SP 3 for low‐input clinical proteomics

(2020) Torsten Müller et al.   Molecular Systems Biology

Personal aging markers and ageotypes revealed by deep longitudinal profiling

(2020) Sara Ahadi et al.   NATURE MEDICINE

Robust, reproducible and quantitative analysis of thousands of proteomes by micro-flow LC–MS/MS

(2020) Yangyang Bian et al.   Nature Communications

Rapid and site-specific deep phosphoproteome profiling by data-independent acquisition without the need for spectral libraries

(2020) Dorte B. Bekker-Jensen et al.   Nature Communications

Signal Drift in Liquid Chromatography Tandem Mass Spectrometry and Its Internal Standard Calibration Strategy for Quantitative Analysis

(2020) Fulin Jiang et al.   ANALYTICAL CHEMISTRY

Proteomic and Metabolomic Characterization of COVID-19 Patient Sera

(2020) Bo Shen et al.   CELL

Separation Efficiency Kinetics of Capillary Flow Micro-Pillar Array Columns for Liquid Chromatography

(2020) Gert Desmet et al.   JOURNAL OF CHROMATOGRAPHY A

A streamlined mass spectrometry–based proteomics workflow for large‐scale FFPE tissue analysis

(2020) Fabian Coscia et al.   JOURNAL OF PATHOLOGY

PolySTest: Robust statistical testing of proteomics data with missing values improves detection of biologically relevant features

(2020) Veit Schwämmle et al.   MOLECULAR & CELLULAR PROTEOMICS

TMTpro reagents: a set of isobaric labeling mass tags enables simultaneous proteome-wide measurements across 16 samples

(2020) Jiaming Li et al.   NATURE METHODS

Ultrasonic-Based Filter Aided Sample Preparation as the General Method to Sample Preparation in Proteomics

(2020) Luís B. Carvalho et al.   ANALYTICAL CHEMISTRY

Genome-wide pQTL analysis of protein expression regulatory networks in the human liver

(2020) Bing He et al.   BMC BIOLOGY

Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma

(2020) Michael A. Gillette et al.   CELL

Proteome profiling in cerebrospinal fluid reveals novel biomarkers of Alzheimer's disease

(2020) Jakob M Bader et al.   Molecular Systems Biology

The proteome landscape of the kingdoms of life

(2020) Johannes B. Müller et al.   NATURE

A mass spectrometry-based proteome map of drug action in lung cancer cell lines

(2020) Benjamin Ruprecht et al.   Nature Chemical Biology

Reproducibility of animal research in light of biological variation

(2020) Bernhard Voelkl et al.   NATURE REVIEWS NEUROSCIENCE

Strategies to enable large-scale proteomics for reproducible research

(2020) Rebecca C. Poulos et al.   Nature Communications

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

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

Phenome-wide Mendelian randomization mapping the influence of the plasma proteome on complex diseases

(2020) Jie Zheng et al.   NATURE GENETICS

Large-Scale Multi-omic Analysis of COVID-19 Severity

(2020) Katherine A. Overmyer et al.   Cell Systems

Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer

(2020) Francesca Petralia et al.   CELL

The functional proteome landscape of Escherichia coli

(2020) André Mateus et al.   NATURE

Quantitative shotgun proteome analysis by direct infusion

(2020) Jesse G. Meyer et al.   NATURE METHODS

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

(2020) Florian Meier et al.   NATURE METHODS

DIA-based systems biology approach unveils E3 ubiquitin ligase-dependent responses to a metabolic shift

(2020) Ozge Karayel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

COVID-19 research risks ignoring important host genes due to pre-established research patterns

(2020) Thomas Stoeger et al.   eLife

Proteomics identifies new therapeutic targets of early-stage hepatocellular carcinoma

(2019) Ying Jiang et al.   NATURE

Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities

(2019) Suhas Vasaikar et al.   CELL

Analysis of 1508 plasma samples by capillary flow data-independent acquisition profiles proteomics of weight loss and maintenance

(2019) Roland Bruderer et al.   MOLECULAR & CELLULAR PROTEOMICS

Novelty in science should not come at the cost of reproducibility

(2019) Andrew N. Holding   FEBS Journal

Plasma Proteome Profiling to detect and avoid sample‐related biases in biomarker studies

(2019) Philipp E Geyer et al.   EMBO Molecular Medicine

Automated “Cells-To-Peptides” Sample Preparation Workflow for High-Throughput, Quantitative Proteomic Assays of Microbes

(2019) Yan Chen et al.   JOURNAL OF PROTEOME RESEARCH

High‐throughput proteomic analysis of FFPE tissue samples facilitates tumor stratification

(2019) Yi Zhu et al.   Molecular Oncology

An omics perspective on drug target discovery platforms

(2019) Jussi Paananen et al.   BRIEFINGS IN BIOINFORMATICS

Integrated Proteogenomic Characterization of HBV-Related Hepatocellular Carcinoma

(2019) Qiang Gao et al.   CELL

Mass Spectrometry-Based Plasma Proteomics: Considerations from Sample Collection to Achieving Translational Data

(2019) Vera Ignjatovic et al.   JOURNAL OF PROTEOME RESEARCH

Co-regulation map of the human proteome enables identification of protein functions

(2019) Georg Kustatscher et al.   NATURE BIOTECHNOLOGY

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

(2019) Vadim Demichev et al.   NATURE METHODS

R2‐P2 rapid‐robotic phosphoproteomics enables multidimensional cell signaling studies

(2019) Mario Leutert et al.   Molecular Systems Biology

ProTargetMiner as a proteome signature library of anticancer molecules for functional discovery

(2019) Amir Ata Saei et al.   Nature Communications

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

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

Reproducibility crisis in science or unrealistic expectations?

(2018) Thiago FA França et al.   EMBO REPORTS

A Cost-Effective High-Throughput Plasma and Serum Proteomics Workflow Enables Mapping of the Molecular Impact of Total Pancreatectomy with Islet Autotransplantation

(2018) Tue Bjerg Bennike et al.   JOURNAL OF PROTEOME RESEARCH

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

(2018) Florian Meier et al.   NATURE METHODS

Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography–mass spectrometry

(2018) Philipp Mertins et al.   Nature Protocols

Unexplored therapeutic opportunities in the human genome

(2018) Tudor I. Oprea et al.   NATURE REVIEWS DRUG DISCOVERY

Cost-effective generation of precise label-free quantitative proteomes in high-throughput by microLC and data-independent acquisition

(2018) Jakob Vowinckel et al.   Scientific Reports

Ultra-High Pressure (>30,000 psi) Packing of Capillary Columns Enhancing Depth of Shotgun Proteomic Analyses

(2018) Evgenia Shishkova et al.   ANALYTICAL CHEMISTRY

S-Trap, an Ultrafast Sample-Preparation Approach for Shotgun Proteomics

(2018) Milkessa HaileMariam 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

Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial

(2018) Christina Ludwig et al.   Molecular Systems Biology

Genomic atlas of the human plasma proteome

(2018) Benjamin B. Sun et al.   NATURE

High-throughput and high-sensitivity phosphoproteomics with the EasyPhos platform

(2018) Sean J. Humphrey et al.   Nature Protocols

Machine Learning Predicts the Yeast Metabolome from the Quantitative Proteome of Kinase Knockouts

(2018) Aleksej Zelezniak et al.   Cell Systems

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

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

Immunohistochemistry on old archival paraffin blocks: is there an expiry date?

(2017) Federica Grillo et al.   JOURNAL OF CLINICAL PATHOLOGY

Scanning Quadrupole Data-Independent Acquisition, Part B: Application to the Analysis of the Calcineurin-Interacting Proteins during Treatment of Aspergillus fumigatus with Azole and Echinocandin Antifungal Drugs

(2017) Praveen R. Juvvadi et al.   JOURNAL OF PROTEOME RESEARCH

Scanning Quadrupole Data-Independent Acquisition, Part A: Qualitative and Quantitative Characterization

(2017) M. Arthur Moseley et al.   JOURNAL OF PROTEOME RESEARCH

Highly Reproducible Automated Proteomics Sample Preparation Workflow for Quantitative Mass Spectrometry

(2017) Qin Fu et al.   JOURNAL OF PROTEOME RESEARCH

Quick 96FASP for high throughput quantitative proteome analysis

(2017) Yanbao Yu et al.   Journal of Proteomics

MSstatsQC: Longitudinal System Suitability Monitoring and Quality Control for Targeted Proteomic Experiments

(2017) Eralp Dogu 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

Revisiting biomarker discovery by plasma proteomics

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

Detection of dysregulated protein-association networks by high-throughput proteomics predicts cancer vulnerabilities

(2017) John D Lapek et al.   NATURE BIOTECHNOLOGY

Quantitative proteomics: challenges and opportunities in basic and applied research

(2017) Olga T Schubert et al.   Nature Protocols

Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry

(2017) Ben C. Collins et al.   Nature Communications

Functional Metabolomics Describes the Yeast Biosynthetic Regulome

(2016) Michael Mülleder et al.   CELL

Predicting Ovarian Cancer Patients’ Clinical Response to Platinum-Based Chemotherapy by Their Tumor Proteomic Signatures

(2016) Kun-Hsing Yu et al.   JOURNAL OF PROTEOME RESEARCH

An Automated Pipeline to Monitor System Performance in Liquid Chromatography–Tandem Mass Spectrometry Proteomic Experiments

(2016) Michael S. Bereman et al.   JOURNAL OF PROTEOME RESEARCH

Robust, Sensitive, and Automated Phosphopeptide Enrichment Optimized for Low Sample Amounts Applied to Primary Hippocampal Neurons

(2016) Harm Post et al.   JOURNAL OF PROTEOME RESEARCH

Reduced-representation Phosphosignatures Measured by Quantitative Targeted MS Capture Cellular States and Enable Large-scale Comparison of Drug-induced Phenotypes

(2016) Jennifer G. Abelin 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

Mass-spectrometric exploration of proteome structure and function

(2016) Ruedi Aebersold et al.   NATURE

1,500 scientists lift the lid on reproducibility

(2016) Monya Baker   NATURE

Proteogenomics connects somatic mutations to signalling in breast cancer

(2016) Philipp Mertins et al.   NATURE

Mitochondrial protein functions elucidated by multi-omic mass spectrometry profiling

(2016) Jonathan A Stefely et al.   NATURE BIOTECHNOLOGY

Systems proteomics of liver mitochondria function

(2016) E. G. Williams et al.   SCIENCE

Plasma Proteome Profiling to Assess Human Health and Disease

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

The CPTAC Data Portal: A Resource for Cancer Proteomics Research

(2015) Nathan J. Edwards 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

Quantitative variability of 342 plasma proteins in a human twin population

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

Multidimensional proteomics for cell biology

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

Development of an Automated, High-throughput Sample Preparation Protocol for Proteomics Analysis

(2015) Albert-Baskar Arul et al.   BULLETIN OF THE KOREAN CHEMICAL SOCIETY

Reproducible Automated Phosphopeptide Enrichment Using Magnetic TiO2 and Ti-IMAC

(2014) Christopher J. Tape et al.   ANALYTICAL CHEMISTRY

Large-Scale Genetic Perturbations Reveal Regulatory Networks and an Abundance of Gene-Specific Repressors

(2014) Patrick Kemmeren et al.   CELL

Core–shell particles: Preparation, fundamentals and applications in high performance liquid chromatography

(2014) Richard Hayes et al.   JOURNAL OF CHROMATOGRAPHY A

OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data

(2014) Hannes L Röst et al.   NATURE BIOTECHNOLOGY

Analysis of variance and blocking

(2014) Martin Krzywinski et al.   NATURE METHODS

Homogenous 96-Plex PEA Immunoassay Exhibiting High Sensitivity, Specificity, and Excellent Scalability

(2014) Erika Assarsson et al.   PLoS One

Why have so few proteomic biomarkers “survived” validation? (Sample size and independent validation considerations)

(2014) Belinda Hernández et al.   PROTEOMICS

Biomarker Discovery for Heterogeneous Diseases

(2013) G. Wallstrom et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis

(2013) Paola Picotti et al.   NATURE

Variation and genetic control of protein abundance in humans

(2013) Linfeng Wu et al.   NATURE

Power and sample size

(2013) Martin Krzywinski et al.   NATURE METHODS

A high-throughput sample preparation method for cellular proteomics using 96-well filter plates

(2013) Linda Switzar et al.   PROTEOMICS

Mass Spectrometry–Based Proteomics and Network Biology

(2012) Ariel Bensimon et al.   Annual Review of Biochemistry

Mass spectrometry-based proteomics for systems biology

(2011) Eduard Sabidó et al.   CURRENT OPINION IN BIOTECHNOLOGY

Aptamer-Based Multiplexed Proteomic Technology for Biomarker Discovery

(2011) Larry Gold et al.   PLoS One

High-throughput profiling of amino acids in strains of the Saccharomyces cerevisiae deletion collection

(2010) S. J. Cooper et al.   GENOME RESEARCH

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

The Clinical Plasma Proteome: A Survey of Clinical Assays for Proteins in Plasma and Serum

(2009) N. L. Anderson   CLINICAL CHEMISTRY

Statistical Design of Quantitative Mass Spectrometry-Based Proteomic Experiments

(2009) Ann L. Oberg et al.   JOURNAL OF PROTEOME RESEARCH

A novel ion trap that enables high duty cycle and wide m/z range on an orthogonal injection TOF mass spectrometer

(2009) Alexander V. Loboda et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Applying mass spectrometry-based proteomics to genetics, genomics and network biology

(2009) Matthias Gstaiger et al.   NATURE REVIEWS GENETICS

Relative Quantification of Proteins in Human Cerebrospinal Fluids by MS/MS Using 6-Plex Isobaric Tags

(2008) Loïc Dayon et al.   ANALYTICAL CHEMISTRY

Multiple Reaction Monitoring of mTRAQ-Labeled Peptides Enables Absolute Quantification of Endogenous Levels of a Potential Cancer Marker in Cancerous and Normal Endometrial Tissues

(2008) Leroi V. DeSouza et al.   JOURNAL OF PROTEOME RESEARCH

The Chemical Genomic Portrait of Yeast: Uncovering a Phenotype for All Genes

(2008) M. E. Hillenmeyer et al.   SCIENCE