A region‐resolved proteomic map of the human brain enabled by high‐throughput proteomics

Target deconvolution of HDAC pharmacopoeia reveals MBLAC2 as common off-target

(2022) Severin Lechner et al.   Nature Chemical Biology

DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update)

(2022) Brad T Sherman et al.   NUCLEIC ACIDS RESEARCH

Regionally defined proteomic profiles of human cerebral tissue and organoids reveal conserved molecular modules of neurodevelopment

(2022) Sofia Melliou et al.   Cell Reports

Spatial proteomics in three-dimensional intact specimens

(2022) Harsharan Singh Bhatia et al.   CELL

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

(2021) Yangyang Bian et al.   ANALYTICAL CHEMISTRY

A guidebook for DISCO tissue clearing

(2021) Muge Molbay et al.   Molecular Systems Biology

Ultra-fast proteomics with Scanning SWATH

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

Identification of 7 000–9 000 Proteins from Cell Lines and Tissues by Single-Shot Microflow LC–MS/MS

(2021) Yangyang Bian et al.   ANALYTICAL CHEMISTRY

Deciphering the Interregional and Interhemisphere Proteome of the Human Brain in the Context of the Human Proteome Project

(2021) Deeptarup Biswas et al.   JOURNAL OF PROTEOME RESEARCH

Evaluation of Disposable Trap Column nanoLC–FAIMS–MS/MS for the Proteomic Analysis of FFPE Tissue

(2021) Stephan Eckert et al.   JOURNAL OF PROTEOME RESEARCH

A Global Multiregional Proteomic Map of the Human Cerebral Cortex

(2021) Zhengguang Guo et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

HYPERsol: High-Quality Data from Archival FFPE Tissue for Clinical Proteomics

(2020) Dylan M. Marchione et al.   JOURNAL OF PROTEOME RESEARCH

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

(2020) Torsten Müller et al.   Molecular Systems Biology

An atlas of the protein-coding genes in the human, pig, and mouse brain

(2020) Evelina Sjöstedt et al.   SCIENCE

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

(2020) Yangyang Bian et al.   Nature Communications

Proteomic Analysis of Brain Region and Sex-Specific Synaptic Protein Expression in the Adult Mouse Brain

(2020) Ute Distler et al.   Cells

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

(2020) Fabian Coscia et al.   JOURNAL OF PATHOLOGY

Crystal-C: A Computational Tool for Refinement of Open Search Results

(2020) Hui-Yin Chang et al.   JOURNAL OF PROTEOME RESEARCH

Fast quantitative analysis of timsTOF PASEF data with MSFragger and IonQuant

(2020) Fengchao Yu et al.   MOLECULAR & CELLULAR PROTEOMICS

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

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

Identification of modified peptides using localization-aware open search

(2020) Fengchao Yu et al.   Nature Communications

MassIVE.quant: a community resource of quantitative mass spectrometry–based proteomics datasets

(2020) Meena Choi et al.   NATURE METHODS

PTM-Shepherd: analysis and summarization of post-translational and chemical modifications from open search results

(2020) Daniel J. Geiszler et al.   MOLECULAR & CELLULAR PROTEOMICS

A deep proteome and transcriptome abundance atlas of 29 healthy human tissues

(2019) Dongxue Wang et al.   Molecular Systems Biology

The Human Brain Project—Synergy between neuroscience, computing, informatics, and brain-inspired technologies

(2019) Katrin Amunts et al.   PLOS BIOLOGY

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

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

Single-pot, solid-phase-enhanced sample preparation for proteomics experiments

(2018) Christopher S. Hughes et al.   Nature Protocols

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

(2017) Andy T Kong et al.   NATURE METHODS

A multiregional proteomic survey of the postnatal human brain

(2017) Becky C. Carlyle et al.   NATURE NEUROSCIENCE

PROCAL: A Set of 40 Peptide Standards for Retention Time Indexing, Column Performance Monitoring, and Collision Energy Calibration

(2017) Daniel Paul Zolg et al.   PROTEOMICS

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

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

Plasma Proteome Profiling to Assess Human Health and Disease

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

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

The PsychENCODE project

(2015) Schahram Akbarian et al.   NATURE NEUROSCIENCE

Cell type– and brain region–resolved mouse brain proteome

(2015) Kirti Sharma et al.   NATURE NEUROSCIENCE

DMSO enhances electrospray response, boosting sensitivity of proteomic experiments

(2013) Hannes Hahne et al.   NATURE METHODS

Equal numbers of neuronal and nonneuronal cells make the human brain an isometrically scaled-up primate brain

(2009) Frederico A.C. Azevedo et al.   JOURNAL OF COMPARATIVE NEUROLOGY

Atmospheric pressure ion sources

(2009) Thomas R. Covey et al.   MASS SPECTROMETRY REVIEWS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

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