In-depth human plasma proteome analysis captures tissue proteins and transfer of protein variants across the placenta

Detection and localization of surgically resectable cancers with a multi-analyte blood test

(2018) Joshua D. Cohen et al.   SCIENCE

Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow

(2018) Yafeng Zhu et al.   Nature Communications

The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays

(2017) Jochen M. Schwenk et al.   JOURNAL OF PROTEOME RESEARCH

Revisiting biomarker discovery by plasma proteomics

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

Nextflow enables reproducible computational workflows

(2017) Paolo Di Tommaso et al.   NATURE BIOTECHNOLOGY

Quantitative, multiplexed workflow for deep analysis of human blood plasma and biomarker discovery by mass spectrometry

(2017) Hasmik Keshishian et al.   Nature Protocols

A subcellular map of the human proteome

(2017) Peter J. Thul et al.   SCIENCE

Isoelectric point-based fractionation by HiRIEF coupled to LC-MS allows for in-depth quantitative analysis of the phosphoproteome

(2017) Elena Panizza et al.   Scientific Reports

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

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

Proteoform profiling of peripheral blood serum proteins from pregnant women provides a molecular IUGR signature

(2016) M. Wölter et al.   Journal of Proteomics

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

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

OpenMS: a flexible open-source software platform for mass spectrometry data analysis

(2016) Hannes L Röst et al.   NATURE METHODS

Plasma Proteome Profiling to Assess Human Health and Disease

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

Proteomic Biomarker Discovery in 1000 Human Plasma Samples with Mass Spectrometry

(2015) Ornella Cominetti et al.   JOURNAL OF PROTEOME RESEARCH

Multiplexed, Quantitative Workflow for Sensitive Biomarker Discovery in Plasma Yields Novel Candidates for Early Myocardial Injury

(2015) Hasmik Keshishian 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

Quantitative variability of 342 plasma proteins in a human twin population

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

Multi-omic data analysis using Galaxy

(2015) Jorrit Boekel et al.   NATURE BIOTECHNOLOGY

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

Glucocorticoid signaling drives epigenetic and transcription factors to induce key regulators of human parturition

(2015) Anthony S. Zannas et al.   Science Signaling

Glucocorticoid signaling drives epigenetic and transcription factors to induce key regulators of human parturition

(2015) Anthony S. Zannas et al.   Science Signaling

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

Mass-spectrometry-based draft of the human proteome

(2014) Mathias Wilhelm et al.   NATURE

Proteogenomics: concepts, applications and computational strategies

(2014) Alexey I Nesvizhskii   NATURE METHODS

MS-GF+ makes progress towards a universal database search tool for proteomics

(2014) Sangtae Kim 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

The Plasma Proteome Identifies Expected and Novel Proteins Correlated with Micronutrient Status in Undernourished Nepalese Children

(2013) Robert N. Cole et al.   JOURNAL OF NUTRITION

HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics

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

Plasma Proteome Database as a resource for proteomics research: 2014 update

(2013) Vishalakshi Nanjappa et al.   NUCLEIC ACIDS RESEARCH

Identification of genetic variants influencing the human plasma proteome

(2013) A. Johansson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes

(2012) Rui Chen et al.   CELL

Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues

(2012) Alicia Lundby et al.   Nature Communications

Statistical Analysis of Variation in the Human Plasma Proteome

(2010) Todd H. Corzett et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

Fine-mapping at three loci known to affect fetal hemoglobin levels explains additional genetic variation

(2010) Geneviève Galarneau et al.   NATURE GENETICS

ToppCluster: a multiple gene list feature analyzer for comparative enrichment clustering and network-based dissection of biological systems

(2010) V. Kaimal et al.   NUCLEIC ACIDS RESEARCH

Proteome profiling reveals gender differences in the composition of human serum

(2010) Koichiro Miike et al.   PROTEOMICS

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

ProteoWizard: open source software for rapid proteomics tools development

(2008) Darren Kessner et al.   BIOINFORMATICS

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