Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins

Prognostic Significance in Breast Cancer of a Gene Signature Capturing Stromal PDGF Signaling

(2013) Oliver Frings et al.   AMERICAN JOURNAL OF PATHOLOGY

Targeted Quantitation of Proteins by Mass Spectrometry

(2013) Daniel C. Liebler et al.   BIOCHEMISTRY

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

(2013) Paola Picotti et al.   NATURE

Mass-Linked Immuno-Selective Assays in Targeted Proteomics

(2012) Ashraf G. Madian et al.   ANALYTICAL CHEMISTRY

GeLC-MRM Quantitation of Mutant KRAS Oncoprotein in Complex Biological Samples

(2012) Patrick J. Halvey et al.   JOURNAL OF PROTEOME RESEARCH

The Biology/Disease-driven Human Proteome Project (B/D-HPP): Enabling Protein Research for the Life Sciences Community

(2012) Ruedi Aebersold et al.   JOURNAL OF PROTEOME RESEARCH

Interlaboratory Reproducibility of Selective Reaction Monitoring Assays Using Multiple Upfront Analyte Enrichment Strategies

(2012) Amol Prakash et al.   JOURNAL OF PROTEOME RESEARCH

Secretomic Analysis Identifies Alpha-1 Antitrypsin (A1AT) as a Required Protein in Cancer Cell Migration, Invasion, and Pericellular Fibronectin Assembly for Facilitating Lung Colonization of Lung Adenocarcinoma Cells

(2012) Ying-Hua Chang et al.   MOLECULAR & CELLULAR PROTEOMICS

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions

(2012) Paola Picotti et al.   NATURE METHODS

The Proteomics Identifications (PRIDE) database and associated tools: status in 2013

(2012) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

PASSEL: The PeptideAtlas SRMexperiment library

(2012) Terry Farrah et al.   PROTEOMICS

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

(2012) R. Huttenhain et al.   Science Translational Medicine

Peptide Immunoaffinity Enrichment Coupled with Mass Spectrometry for Peptide and Protein Quantification

(2011) Jeffrey R. Whiteaker et al.   CLINICS IN LABORATORY MEDICINE

Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies

(2011) Brian D. Lehmann et al.   JOURNAL OF CLINICAL INVESTIGATION

Evaluation of Large Scale Quantitative Proteomic Assay Development Using Peptide Affinity-based Mass Spectrometry

(2011) Jeffrey R. Whiteaker et al.   MOLECULAR & CELLULAR PROTEOMICS

The Human Proteome Project: Current State and Future Direction

(2011) Pierre Legrain et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2011) Lukas Reiter et al.   NATURE METHODS

A database of reaction monitoring mass spectrometry assays for elucidating therapeutic response in cancer

(2011) Elizabeth R. Remily-Wood et al.   Proteomics Clinical Applications

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

(2010) Brendan MacLean et al.   BIOINFORMATICS

Platform for Establishing Interlaboratory Reproducibility of Selected Reaction Monitoring-Based Mass Spectrometry Peptide Assays

(2010) A. Prakash et al.   JOURNAL OF PROTEOME RESEARCH

Reconstructing the pipeline by introducing multiplexed multiple reaction monitoring mass spectrometry for cancer biomarker verification: An NCI-CPTC initiative perspective

(2010) Henry Rodriguez et al.   Proteomics Clinical Applications

Automated Detection of Inaccurate and Imprecise Transitions in Peptide Quantification by Multiple Reaction Monitoring Mass Spectrometry

(2009) S. E. Abbatiello et al.   CLINICAL CHEMISTRY

Supervised Risk Predictor of Breast Cancer Based on Intrinsic Subtypes

(2009) Joel S. Parker et al.   JOURNAL OF CLINICAL ONCOLOGY

A Human Proteome Detection and Quantitation Project

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

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

Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis

(2009) Noelle M Griffin et al.   NATURE BIOTECHNOLOGY

Molecular Profiling of Breast Cancer Cell Lines Defines Relevant Tumor Models and Provides a Resource for Cancer Gene Discovery

(2009) Jessica Kao et al.   PLoS One

Hybrid immunoaffinity–mass spectrometric methods for efficient protein biomarker verification in pharmaceutical development

(2009) Bradley L Ackermann   Bioanalysis

Relapse-Free Survival in Breast Cancer Patients Is Associated with a Gene Expression Signature Characteristic for Inflammatory Breast Cancer

(2008) S. Van Laere et al.   CLINICAL CANCER RESEARCH

Mass Spectrometry Based Targeted Protein Quantification: Methods and Applications

(2008) Sheng Pan et al.   JOURNAL OF PROTEOME RESEARCH

Selected reaction monitoring for quantitative proteomics: a tutorial

(2008) Vinzenz Lange et al.   Molecular Systems Biology

A database of mass spectrometric assays for the yeast proteome

(2008) Paola Picotti et al.   NATURE METHODS