Reproducible Quantification of Cancer-Associated Proteins in Body Fluids Using Targeted Proteomics

Protein Expression Changes in Ovarian Cancer during the Transition from Benign to Malignant

(2012) Sofia Waldemarson et al.   JOURNAL OF PROTEOME RESEARCH

Using iRT, a normalized retention time for more targeted measurement of peptides

(2012) Claudia Escher et al.   PROTEOMICS

PASSEL: The PeptideAtlas SRMexperiment library

(2012) Terry Farrah et al.   PROTEOMICS

Protein Significance Analysis in Selected Reaction Monitoring (SRM) Measurements

(2011) Ching-Yun Chang et al.   MOLECULAR & CELLULAR PROTEOMICS

A High-Confidence Human Plasma Proteome Reference Set with Estimated Concentrations in PeptideAtlas

(2011) Terry Farrah et al.   MOLECULAR & CELLULAR PROTEOMICS

The quantitative proteome of a human cell line

(2011) M. Beck et al.   Molecular Systems Biology

Too many roads not taken

(2011) Aled M. Edwards et al.   NATURE

Integrated genomic analyses of ovarian carcinoma

(2011) D. Bell et al.   NATURE

A pipeline that integrates the discovery and verification of plasma protein biomarkers reveals candidate markers for cardiovascular disease

(2011) Terri A Addona et al.   NATURE BIOTECHNOLOGY

A targeted proteomics–based pipeline for verification of biomarkers in plasma

(2011) Jeffrey R Whiteaker et al.   NATURE BIOTECHNOLOGY

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

(2011) Lukas Reiter et al.   NATURE METHODS

Cancer genetics-guided discovery of serum biomarker signatures for diagnosis and prognosis of prostate cancer

(2011) I. Cima et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reactome pathway analysis to enrich biological discovery in proteomics data sets

(2011) Robin Haw et al.   PROTEOMICS

Systematic quantification of peptides/proteins in urine using selected reaction monitoring

(2011) Nathalie Selevsek et al.   PROTEOMICS

DAXX/ATRX, MEN1, and mTOR Pathway Genes Are Frequently Altered in Pancreatic Neuroendocrine Tumors

(2011) Y. Jiao et al.   SCIENCE

CAERUS: Predicting CAncER oUtcomeS Using Relationship between Protein Structural Information, Protein Networks, Gene Expression Data, and Mutation Data

(2011) Kelvin Xi Zhang et al.   PLoS Computational Biology

High-abundance proteins depletion for serum proteomic analysis: concomitant removal of non-targeted proteins

(2010) Elisa Bellei et al.   AMINO ACIDS

The Road from Discovery to Clinical Diagnostics: Lessons Learned from the First FDA-Cleared In Vitro Diagnostic Multivariate Index Assay of Proteomic Biomarkers

(2010) Z. Zhang et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

A Recipe for Proteomics Diagnostic Test Development: The OVA1 Test, from Biomarker Discovery to FDA Clearance

(2010) E. T. Fung   CLINICAL CHEMISTRY

Depletion of Abundant Plasma Proteins and Limitations of Plasma Proteomics

(2010) Chengjian Tu et al.   JOURNAL OF PROTEOME RESEARCH

On the Development of Plasma Protein Biomarkers

(2010) Silvia Surinova et al.   JOURNAL OF PROTEOME RESEARCH

Options and considerations when selecting a quantitative proteomics strategy

(2010) Bruno Domon et al.   NATURE BIOTECHNOLOGY

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

Automated Network Analysis Identifies Core Pathways in Glioblastoma

(2010) Ethan Cerami et al.   PLoS One

Integrative Proteomic Analysis of Serum and Peritoneal Fluids Helps Identify Proteins that Are Up-Regulated in Serum of Women with Ovarian Cancer

(2010) Lynn M. Amon et al.   PLoS One

Quantitative proteomic analysis by iTRAQ® for the identification of candidate biomarkers in ovarian cancer serum

(2010) Kristin LM Boylan et al.   Proteome Science

Frequent Mutations of Chromatin Remodeling Gene ARID1A in Ovarian Clear Cell Carcinoma

(2010) Siân Jones et al.   SCIENCE

The Genetic Landscape of the Childhood Cancer Medulloblastoma

(2010) D. W. Parsons et al.   SCIENCE

An Integrative -omics Approach to Identify Functional Sub-Networks in Human Colorectal Cancer

(2010) Rod K. Nibbe et al.   PLoS Computational Biology

A human functional protein interaction network and its application to cancer data analysis

(2010) Guanming Wu et al.   GENOME BIOLOGY

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

(2009) N. L. Anderson   CLINICAL CHEMISTRY

Developing Multiplexed Assays for Troponin I and Interleukin-33 in Plasma by Peptide Immunoaffinity Enrichment and Targeted Mass Spectrometry

(2009) E. Kuhn et al.   CLINICAL CHEMISTRY

Perspectives of targeted mass spectrometry for protein biomarker verification

(2009) Ruth Hüttenhain et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Preoperative serum tetranectin, CA125 and menopausal status used as single markers in screening and in a risk assessment index (RAI) in discriminating between benign and malignant ovarian tumors

(2009) F.D. Begum et al.   GYNECOLOGIC ONCOLOGY

Comprehensive Analysis of Conditioned Media from Ovarian Cancer Cell Lines Identifies Novel Candidate Markers of Epithelial Ovarian Cancer

(2009) C. Geeth Gunawardana et al.   JOURNAL OF PROTEOME RESEARCH

A Human Proteome Detection and Quantitation Project

(2009) N. Leigh Anderson et al.   MOLECULAR & CELLULAR PROTEOMICS

Unique Ion Signature Mass Spectrometry, a Deterministic Method to Assign Peptide Identity

(2009) Jamie Sherman et al.   MOLECULAR & CELLULAR PROTEOMICS

Prediction of high-responding peptides for targeted protein assays by mass spectrometry

(2009) Vincent A Fusaro et al.   NATURE BIOTECHNOLOGY

Multi-site assessment of the precision and reproducibility of multiple reaction monitoring–based measurements of proteins in plasma

(2009) Terri A Addona et al.   NATURE BIOTECHNOLOGY

High-throughput generation of selected reaction-monitoring assays for proteins and proteomes

(2009) Paola Picotti et al.   NATURE METHODS

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

(2009) Da Wei Huang et al.   Nature Protocols

Quantifying proteins by mass spectrometry: The selectivity of SRM is only part of the problem

(2009) Mark W. Duncan et al.   PROTEOMICS

How specific is my SRM?: The issue of precursor and product ion redundancy

(2009) Jamie Sherman et al.   PROTEOMICS

Protein networks in disease

(2008) T. Ideker et al.   GENOME RESEARCH

Mining the Ovarian Cancer Ascites Proteome for Potential Ovarian Cancer Biomarkers

(2008) Cynthia Kuk et al.   MOLECULAR & CELLULAR PROTEOMICS

Targeted proteomic strategy for clinical biomarker discovery

(2008) Ralph Schiess et al.   Molecular Oncology

Selected reaction monitoring for quantitative proteomics: a tutorial

(2008) Vinzenz Lange et al.   Molecular Systems Biology

Concentration and preservation of very low abundance biomarkers in urine, such as human growth hormone (hGH), by Cibacron Blue F3G-A loaded hydrogel particles

(2008) Claudia Fredolini et al.   Nano Research

A database of mass spectrometric assays for the yeast proteome

(2008) Paola Picotti et al.   NATURE METHODS

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

Proteomic Analysis of Ovarian Cancer Cells Reveals Dynamic Processes of Protein Secretion and Shedding of Extra-Cellular Domains

(2008) Vitor M. Faça et al.   PLoS One

The interface between biomarker discovery and clinical validation: The tar pit of the protein biomarker pipeline

(2008) Amanda G. Paulovich et al.   Proteomics Clinical Applications

Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses

(2008) S. Jones et al.   SCIENCE

An Integrated Genomic Analysis of Human Glioblastoma Multiforme

(2008) D. W. Parsons et al.   SCIENCE

Smart Hydrogel Particles:  Biomarker Harvesting:  One-Step Affinity Purification, Size Exclusion, and Protection against Degradation

(2007) Alessandra Luchini et al.   NANO LETTERS