Mass spectrometric protein maps for biomarker discovery and clinical research

The Mtb Proteome Library: A Resource of Assays to Quantify the Complete Proteome of Mycobacterium tuberculosis

(2013) Olga T. Schubert et al.   Cell Host & Microbe

N-Glycoprotein SRMAtlas

(2013) Ruth Hüttenhain et al.   MOLECULAR & CELLULAR PROTEOMICS

Discovery and Mass Spectrometric Analysis of Novel Splice-junction Peptides Using RNA-Seq

(2013) Gloria M. Sheynkman et al.   MOLECULAR & CELLULAR PROTEOMICS

The Coming Age of Complete, Accurate, and Ubiquitous Proteomes

(2013) Matthias Mann et al.   MOLECULAR CELL

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

(2013) Paola Picotti et al.   NATURE

Quantitative measurements ofN-linked glycoproteins in human plasma by SWATH-MS

(2013) Yansheng Liu et al.   PROTEOMICS

In-house construction of a UHPLC system enabling the identification of over 4000 protein groups in a single analysis

(2012) Alba Cristobal et al.   ANALYST

The failure of protein cancer biomarkers to reach the clinic: why, and what can be done to address the problem?

(2012) Eleftherios P Diamandis   BMC Medicine

Trastuzumab as first-line therapy in HER2-positive metastatic breast cancer patients

(2012) Lucia Del Mastro et al.   Expert Review of Anticancer Therapy

Label-free mass spectrometry-based proteomics for biomarker discovery and validation

(2012) Thang V Pham et al.   EXPERT REVIEW OF MOLECULAR DIAGNOSTICS

The State of the Human Proteome in 2012 as Viewed through PeptideAtlas

(2012) Terry Farrah et al.   JOURNAL OF PROTEOME RESEARCH

Parallel Reaction Monitoring for High Resolution and High Mass Accuracy Quantitative, Targeted Proteomics

(2012) Amelia C. Peterson et al.   MOLECULAR & CELLULAR PROTEOMICS

Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis

(2012) Ludovic C. Gillet et al.   MOLECULAR & CELLULAR PROTEOMICS

Extensive quantitative remodeling of the proteome between normal colon tissue and adenocarcinoma

(2012) Jacek R Wiśniewski et al.   Molecular Systems Biology

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

(2012) Paola Picotti et al.   NATURE METHODS

Proteomics meets the scientific method

(2012) Paola Picotti et al.   NATURE METHODS

Risk stratification in prostate cancer screening

(2012) Monique J. Roobol et al.   Nature Reviews Urology

Range of protein detection by selected/multiple reaction monitoring mass spectrometry in an unfractionated human cell culture lysate

(2012) H. Alexander Ebhardt et al.   PROTEOMICS

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

Shotgun and targeted proteomics reveal that pre-surgery serum levels of LRG1, SAA, and C4BP may refine prognosis of resected squamous cell lung cancer

(2012) Yan-Sheng Liu et al.   Journal of Molecular Cell Biology

Proteome-wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenes

(2012) Christofer Karlsson et al.   Nature Communications

Quantitative Glycoproteomic Analysis of Optimal Cutting Temperature-Embedded Frozen Tissues Identifying Glycoproteins Associated with Aggressive Prostate Cancer

(2011) Yuan Tian et al.   ANALYTICAL CHEMISTRY

Mass spectrometry-based proteomics for systems biology

(2011) Eduard Sabidó et al.   CURRENT OPINION IN BIOTECHNOLOGY

Novel Prognostic Markers in the Serum of Patients With Castration-Resistant Prostate Cancer Derived From Quantitative Analysis of the Pten Conditional Knockout Mouse Proteome

(2011) Martin Kälin et al.   EUROPEAN UROLOGY

A high-quality secretome of A549 cells aided the discovery of C4b-binding protein as a novel serum biomarker for non-small cell lung cancer

(2011) Xiaoyang Luo et al.   Journal of Proteomics

Ultra High Resolution Linear Ion Trap Orbitrap Mass Spectrometer (Orbitrap Elite) Facilitates Top Down LC MS/MS and Versatile Peptide Fragmentation Modes

(2011) Annette Michalski et al.   MOLECULAR & CELLULAR PROTEOMICS

Interlaboratory Evaluation of Automated, Multiplexed Peptide Immunoaffinity Enrichment Coupled to Multiple Reaction Monitoring Mass Spectrometry for Quantifying Proteins in Plasma

(2011) Eric Kuhn 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

Deep proteome and transcriptome mapping of a human cancer cell line

(2011) N. Nagaraj et al.   Molecular Systems Biology

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

Streamlining biomarker discovery

(2011) Martin Latterich et al.   NATURE BIOTECHNOLOGY

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

Mutant proteins as cancer-specific biomarkers

(2011) Q. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

(2011) Nathalie Selevsek et al.   PROTEOMICS

Precision Mapping of an In Vivo N-Glycoproteome Reveals Rigid Topological and Sequence Constraints

(2010) Dorota F. Zielinska et al.   CELL

Lung Cancer Serum Biomarker Discovery Using Glycoprotein Capture and Liquid Chromatography Mass Spectrometry

(2010) Xuemei Zeng et al.   JOURNAL OF PROTEOME RESEARCH

Proteome, Phosphoproteome, and N-Glycoproteome Are Quantitatively Preserved in Formalin-Fixed Paraffin-Embedded Tissue and Analyzable by High-Resolution Mass Spectrometry

(2010) Paweł Ostasiewicz et al.   JOURNAL OF PROTEOME RESEARCH

On the Development of Plasma Protein Biomarkers

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

Secretome proteomics for discovery of cancer biomarkers

(2010) Manousos Makridakis et al.   Journal of Proteomics

Defining the transcriptome and proteome in three functionally different human cell lines

(2010) Emma Lundberg et al.   Molecular Systems Biology

Options and considerations when selecting a quantitative proteomics strategy

(2010) Bruno Domon et al.   NATURE BIOTECHNOLOGY

Super-SILAC mix for quantitative proteomics of human tumor tissue

(2010) Tamar Geiger et al.   NATURE METHODS

Mass spectrometry in high-throughput proteomics: ready for the big time

(2010) Tommy Nilsson et al.   NATURE METHODS

Ovarian cancer: the duplicity of CA125 measurement

(2010) Amer K. Karam et al.   Nature Reviews Clinical Oncology

Generating and navigating proteome maps using mass spectrometry

(2010) Christian H. Ahrens et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The Path to Personalized Medicine

(2010) Margaret A. Hamburg et al.   NEW ENGLAND JOURNAL OF MEDICINE

Reference map for liquid chromatography–mass spectrometry-based quantitative proteomics

(2009) Yeoun Jin Kim et al.   ANALYTICAL BIOCHEMISTRY

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

Directed mass spectrometry: towards hypothesis-driven proteomics

(2009) Alexander Schmidt et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Perspectives of targeted mass spectrometry for protein biomarker verification

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

Repeatability and Reproducibility in Proteomic Identifications by Liquid Chromatography−Tandem Mass Spectrometry

(2009) David L. Tabb et al.   JOURNAL OF PROTEOME RESEARCH

Multiple Reaction Monitoring-based, Multiplexed, Absolute Quantitation of 45 Proteins in Human Plasma

(2009) Michael A. Kuzyk et al.   MOLECULAR & CELLULAR PROTEOMICS

An Automated and Multiplexed Method for High Throughput Peptide Immunoaffinity Enrichment and Multiple Reaction Monitoring Mass Spectrometry-based Quantification of Protein Biomarkers

(2009) Jeffrey R. Whiteaker 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

Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins

(2009) Bernd Wollscheid et al.   NATURE BIOTECHNOLOGY

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

(2009) Paola Picotti et al.   NATURE METHODS

PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows

(2008) Eric W Deutsch et al.   EMBO REPORTS

An Integrated, Directed Mass Spectrometric Approach for In-depth Characterization of Complex Peptide Mixtures

(2008) Alexander Schmidt et al.   MOLECULAR & CELLULAR PROTEOMICS

Accurate Inclusion Mass Screening

(2008) Jacob D. Jaffe 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

The cancer biomarker problem

(2008) Charles L. Sawyers   NATURE

Human Proteinpedia enables sharing of human protein data

(2008) Suresh Mathivanan et al.   NATURE BIOTECHNOLOGY

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

Building consensus spectral libraries for peptide identification in proteomics

(2008) Henry Lam et al.   NATURE METHODS