ProteomicsDB: toward a FAIR open-source resource for life-science research

Universal Spectrum Explorer: A Standalone (Web-)Application for Cross-Resource Spectrum Comparison

(2021) Tobias Schmidt et al.   JOURNAL OF PROTEOME RESEARCH

Spectral prediction features as a solution for the search space size problem in proteogenomics

(2021) Steven Verbruggen et al.   MOLECULAR & CELLULAR PROTEOMICS

PredictProtein - Predicting Protein Structure and Function for 29 Years

(2021) Michael Bernhofer et al.   NUCLEIC ACIDS RESEARCH

Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics

(2021) Mathias Wilhelm et al.   Nature Communications

Mass-spectrometry-based draft of the Arabidopsis proteome

(2020) Julia Mergner et al.   NATURE

SMART: recent updates, new developments and status in 2020

(2020) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences

(2020) Stephen K Burley et al.   NUCLEIC ACIDS RESEARCH

UniProt: the universal protein knowledgebase in 2021

(2020) et al.   NUCLEIC ACIDS RESEARCH

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

(2019) Dongxue Wang et al.   Molecular Systems Biology

Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning

(2019) Siegfried Gessulat et al.   NATURE METHODS

Gene Information eXtension (GIX): effortless retrieval of gene product information on any website

(2019) James D. R. Knight et al.   NATURE METHODS

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

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

Building ProteomeTools based on a complete synthetic human proteome

(2017) Daniel P Zolg et al.   NATURE METHODS

Expression Atlas: gene and protein expression across multiple studies and organisms

(2017) Irene Papatheodorou et al.   NUCLEIC ACIDS RESEARCH

ProteomicsDB

(2017) Tobias Schmidt et al.   NUCLEIC ACIDS RESEARCH

A Golden Age for Working with Public Proteomics Data

(2017) Lennart Martens et al.   TRENDS IN BIOCHEMICAL SCIENCES

Protein profile changes in the frontotemporal lobes in human severe traumatic brain injury

(2016) Benhong Xu et al.   BRAIN RESEARCH

Temporal lobe in human aging: A quantitative protein profiling study of samples from Chinese Human Brain Bank

(2016) Benhong Xu et al.   EXPERIMENTAL GERONTOLOGY

Proteome rearrangements after auditory learning: high-resolution profiling of synapse-enriched protein fractions from mouse brain

(2016) Thilo Kähne et al.   JOURNAL OF NEUROCHEMISTRY

In-Depth Cerebrospinal Fluid Quantitative Proteome and Deglycoproteome Analysis: Presenting a Comprehensive Picture of Pathways and Processes Affected by Multiple Sclerosis

(2016) Ann Cathrine Kroksveen et al.   JOURNAL OF PROTEOME RESEARCH

Proteome Profiling and Ultrastructural Characterization of the Human RCMH Cell Line: Myoblastic Properties and Suitability for Myopathological Studies

(2016) Laxmikanth Kollipara et al.   JOURNAL OF PROTEOME RESEARCH

Looking for Missing Proteins in the Proteome of Human Spermatozoa: An Update

(2016) Yves Vandenbrouck et al.   JOURNAL OF PROTEOME RESEARCH

Plug-and-play analysis of the human phosphoproteome by targeted high-resolution mass spectrometry

(2016) Robert T Lawrence et al.   NATURE METHODS

OmniPath: guidelines and gateway for literature-curated signaling pathway resources

(2016) Dénes Türei et al.   NATURE METHODS

Quantitative protein profiling of hippocampus during human aging

(2016) Benhong Xu et al.   NEUROBIOLOGY OF AGING

Histological effects of givinostat in boys with Duchenne muscular dystrophy

(2016) Paolo Bettica et al.   NEUROMUSCULAR DISORDERS

Proteomic maps of breast cancer subtypes

(2016) Stefka Tyanova et al.   Nature Communications

Synovial fluid proteome in rheumatoid arthritis

(2016) Mitali Bhattacharjee et al.   Clinical Proteomics

The FAIR Guiding Principles for scientific data management and stewardship

(2016) Mark D. Wilkinson et al.   Scientific Data

Comprehensive transcriptomic and proteomic characterization of human mesenchymal stem cells reveals source specific cellular markers

(2016) Anja M. Billing et al.   Scientific Reports

Better prediction of functional effects for sequence variants

(2015) Maximilian Hecht et al.   BMC GENOMICS

Tissue-Based Proteogenomics Reveals that Human Testis Endows Plentiful Missing Proteins

(2015) Yao Zhang et al.   JOURNAL OF PROTEOME RESEARCH

Human Spermatozoa as a Model for Detecting Missing Proteins in the Context of the Chromosome-Centric Human Proteome Project

(2015) Fanny Jumeau et al.   JOURNAL OF PROTEOME RESEARCH

Quantitative Tissue Proteomics Analysis Reveals Versican as Potential Biomarker for Early-Stage Hepatocellular Carcinoma

(2015) Wael Naboulsi et al.   JOURNAL OF PROTEOME RESEARCH

Analysis of Disease-Associated Protein Expression Using Quantitative Proteomics—Fibulin-5 Is Expressed in Association with Hepatic Fibrosis

(2015) Thilo Bracht et al.   JOURNAL OF PROTEOME RESEARCH

Comparative Proteomics of Human and Macaque Milk Reveals Species-Specific Nutrition during Postnatal Development

(2015) Kristen L. Beck et al.   JOURNAL OF PROTEOME RESEARCH

Feasibility of label-free phosphoproteomics and application to base-line signaling of colorectal cancer cell lines

(2015) Sander R. Piersma et al.   Journal of Proteomics

Deep, Quantitative Coverage of the Lysine Acetylome Using Novel Anti-acetyl-lysine Antibodies and an Optimized Proteomic Workflow

(2015) Tanya Svinkina et al.   MOLECULAR & CELLULAR PROTEOMICS

A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets

(2015) Mikhail M. Savitski et al.   MOLECULAR & CELLULAR PROTEOMICS

Cell type– and brain region–resolved mouse brain proteome

(2015) Kirti Sharma et al.   NATURE NEUROSCIENCE

Proteomics of Human Aqueous Humor

(2015) Krishna R. Murthy et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

A proteomic glimpse into human ureter proteome

(2015) Sameh Magdeldin et al.   PROTEOMICS

Defining the phospho-adhesome through the phosphoproteomic analysis of integrin signalling

(2015) Joseph Robertson et al.   Nature Communications

Global phosphotyrosine survey in triple-negative breast cancer reveals activation of multiple tyrosine kinase signaling pathways

(2015) Xinyan Wu et al.   Oncotarget

An Augmented Multiple-Protease-Based Human Phosphopeptide Atlas

(2015) Piero Giansanti et al.   Cell Reports

Proteomic analysis of colon and rectal carcinoma using standard and customized databases

(2015) Robbert J.C. Slebos et al.   Scientific Data

Proteome-Wide Discovery of Unknown ATP-Binding Proteins and Kinase Inhibitor Target Proteins Using an ATP Probe

(2014) Jun Adachi et al.   JOURNAL OF PROTEOME RESEARCH

Heterogeneity of Pancreatic Cancer Metastases in a Single Patient Revealed by Quantitative Proteomics

(2014) Min-Sik Kim et al.   MOLECULAR & CELLULAR PROTEOMICS

Mass-spectrometry-based draft of the human proteome

(2014) Mathias Wilhelm et al.   NATURE

Simultaneous dissection and comparison of IL-2 and IL-15 signaling pathways by global quantitative phosphoproteomics

(2014) Nerea Osinalde et al.   PROTEOMICS

Refined phosphopeptide enrichment by phosphate additive and the analysis of human brain phosphoproteome

(2014) Haiyan Tan et al.   PROTEOMICS

Deep proteomic profiling of human carotid atherosclerotic plaques using multidimensional LC-MS/MS

(2014) Piliang Hao et al.   Proteomics Clinical Applications

Integrated Omic analysis of lung cancer reveals metabolism proteome signatures with prognostic impact

(2014) Lei Li et al.   Nature Communications

Ultradeep Human Phosphoproteome Reveals a Distinct Regulatory Nature of Tyr and Ser/Thr-Based Signaling

(2014) Kirti Sharma et al.   Cell Reports

HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics

(2013) Rui M M Branca et al.   NATURE METHODS

Analysis of High Accuracy, Quantitative Proteomics Data in the MaxQB Database

(2012) Christoph Schaab et al.   MOLECULAR & CELLULAR PROTEOMICS

A Tissue-Specific Atlas of Mouse Protein Phosphorylation and Expression

(2010) Edward L. Huttlin et al.   CELL