Mass spectrometry for translational proteomics: progress and clinical implications

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

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

A Computational Tool to Detect and Avoid Redundancy in Selected Reaction Monitoring

(2012) Hannes Röst et al.   MOLECULAR & CELLULAR PROTEOMICS

Platform-independent and Label-free Quantitation of Proteomic Data Using MS1 Extracted Ion Chromatograms in Skyline

(2012) Birgit Schilling 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

PASSEL: The PeptideAtlas SRMexperiment library

(2012) Terry Farrah et al.   PROTEOMICS

Pulsed Multiple Reaction Monitoring Approach to Enhancing Sensitivity of a Tandem Quadrupole Mass Spectrometer

(2011) Mikhail E. Belov et al.   ANALYTICAL CHEMISTRY

Personalized Medicine: Progress and Promise

(2011) Isaac S. Chan et al.   Annual Review of Genomics and Human Genetics

Mass Spectrometry in Biomarker Applications: From Untargeted Discovery to Targeted Verification, and Implications for Platform Convergence and Clinical Application

(2011) R. D. Smith   CLINICAL CHEMISTRY

Liquid Chromatography-Mass Spectrometry-based Quantitative Proteomics

(2011) Fang Xie et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Comparison of Bruker Biotyper Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometer to BD Phoenix Automated Microbiology System for Identification of Gram-Negative Bacilli

(2011) R. T. Saffert et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Selected reaction monitoring applied to proteomics

(2011) Sebastien Gallien et al.   JOURNAL OF MASS SPECTROMETRY

Target-Decoy Approach and False Discovery Rate: When Things May Go Wrong

(2011) Nitin Gupta et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

IgY14 and SuperMix immunoaffinity separations coupled with liquid chromatography–mass spectrometry for human plasma proteomics biomarker discovery

(2011) Tujin Shi et al.   METHODS

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

Personalized cancer medicine: era of promise and progress

(2011) Lisa Hutchinson   Nature Reviews Clinical Oncology

Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum

(2011) S. C. Bendall et al.   SCIENCE

Performance of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Identification of Bacterial Strains Routinely Isolated in a Clinical Microbiology Laboratory

(2010) A. Bizzini et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Newborn screening for disorders of fatty-acid oxidation: experience and recommendations from an expert meeting

(2010) Martin Lindner et al.   JOURNAL OF INHERITED METABOLIC DISEASE

On the Development of Plasma Protein Biomarkers

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

A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics

(2010) Alexey I. Nesvizhskii   Journal of Proteomics

Super-SILAC mix for quantitative proteomics of human tumor tissue

(2010) Tamar Geiger et al.   NATURE METHODS

Simultaneous analysis of relative protein expression levels across multiple samples using iTRAQ isobaric tags with 2D nano LC–MS/MS

(2010) Richard D Unwin et al.   Nature Protocols

Precursor Acquisition Independent From Ion Count: How to Dive Deeper into the Proteomics Ocean

(2009) Alexandre Panchaud et al.   ANALYTICAL CHEMISTRY

Protein Extraction of Formalin-fixed, Paraffin-embedded Tissue Enables Robust Proteomic Profiles by Mass Spectrometry

(2009) Marshall S. Scicchitano et al.   JOURNAL OF HISTOCHEMISTRY & CYTOCHEMISTRY

Mouse-Specific Tandem IgY7-SuperMix Immunoaffinity Separations for Improved LC-MS/MS Coverage of the Plasma Proteome

(2009) Jian-Ying Zhou et al.   JOURNAL OF PROTEOME RESEARCH

An LC-IMS-MS Platform Providing Increased Dynamic Range for High-Throughput Proteomic Studies

(2009) Erin Shammel Baker et al.   JOURNAL OF PROTEOME RESEARCH

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

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

Comparison of Two-Dimensional Fractionation Techniques for Shotgun Proteomics

(2008) James A. Dowell et al.   ANALYTICAL CHEMISTRY

Spectral Probabilities and Generating Functions of Tandem Mass Spectra: A Strike against Decoy Databases

(2008) Sangtae Kim et al.   JOURNAL OF PROTEOME RESEARCH

Large-Scale Multiplexed Quantitative Discovery Proteomics Enabled by the Use of an18O-Labeled “Universal” Reference Sample

(2008) Wei-Jun Qian et al.   JOURNAL OF PROTEOME RESEARCH

Enhanced Detection of Low Abundance Human Plasma Proteins Using a Tandem IgY12-SuperMix Immunoaffinity Separation Strategy

(2008) Wei-Jun Qian et al.   MOLECULAR & CELLULAR PROTEOMICS

Decision tree–driven tandem mass spectrometry for shotgun proteomics

(2008) Danielle L Swaney et al.   NATURE METHODS

A database of mass spectrometric assays for the yeast proteome

(2008) Paola Picotti et al.   NATURE METHODS

Iodoacetamide-induced artifact mimics ubiquitination in mass spectrometry

(2008) Michael L Nielsen et al.   NATURE METHODS

Simultaneous fragmentation of multiple ions using IMS drift time dependent collision energies

(2007) Erin Shammel Baker et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY