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

Accurate Peptide Fragment Mass Analysis: Multiplexed Peptide Identification and Quantification

(2012) Chad R. Weisbrod et al.   JOURNAL OF PROTEOME RESEARCH

Multiplex Targeted Proteomic Assay for Biomarker Detection in Plasma: A Pancreatic Cancer Biomarker Case Study

(2012) Sheng Pan et al.   JOURNAL OF PROTEOME RESEARCH

Instant spectral assignment for advanced decision tree-driven mass spectrometry

(2012) D. J. Bailey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global kinetic analysis of proteolysis via quantitative targeted proteomics

(2012) N. J. Agard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PASSEL: The PeptideAtlas SRMexperiment library

(2012) Terry Farrah et al.   PROTEOMICS

Performance Characteristics of a New Hybrid Quadrupole Time-of-Flight Tandem Mass Spectrometer (TripleTOF 5600)

(2011) Genna L. Andrews et al.   ANALYTICAL CHEMISTRY

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

System-wide Perturbation Analysis with Nearly Complete Coverage of the Yeast Proteome by Single-shot Ultra HPLC Runs on a Bench Top Orbitrap

(2011) Nagarjuna Nagaraj et al.   MOLECULAR & CELLULAR PROTEOMICS

Mass Spectrometry-based Proteomics Using Q Exactive, a High-performance Benchtop Quadrupole Orbitrap Mass Spectrometer

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

A Framework for Intelligent Data Acquisition and Real-Time Database Searching for Shotgun Proteomics

(2011) Johannes Graumann et al.   MOLECULAR & CELLULAR PROTEOMICS

Comprehensive quantitative analysis of central carbon and amino-acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics

(2011) R. Costenoble et al.   Molecular Systems Biology

A dynamic model of proteome changes reveals new roles for transcript alteration in yeast

(2011) M. V. Lee et al.   Molecular Systems Biology

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

Mass-spectrometry-based clinical proteomics – a review and prospective

(2010) Carol E. Parker et al.   ANALYST

Shotgun proteomics: concept, key points and data mining

(2010) Sabine Matallana-Surget et al.   Expert Review of Proteomics

Implementation and evaluation of relative and absolute quantification in shotgun proteomics with label-free methods

(2010) Jonas Grossmann et al.   Journal of Proteomics

Increased Selectivity, Analytical Precision, and Throughput in Targeted Proteomics

(2010) Reiko Kiyonami et al.   MOLECULAR & CELLULAR PROTEOMICS

Proteomics: a pragmatic perspective

(2010) Parag Mallick et al.   NATURE BIOTECHNOLOGY

Free computational resources for designing selected reaction monitoring transitions

(2010) Jennifer A. Cham Mead et al.   PROTEOMICS

Peptide Quantification Using 8-Plex Isobaric Tags and Electron Transfer Dissociation Tandem Mass Spectrometry

(2009) Doug Phanstiel et al.   ANALYTICAL CHEMISTRY

Improved Electrospray Ionization Efficiency Compensates for Diminished Chromatographic Resolution and Enables Proteomics Analysis of Tyrosine Signaling in Embryonic Stem Cells

(2009) Scott B. Ficarro et al.   ANALYTICAL CHEMISTRY

MRM screening/biomarker discovery with linear ion trap MS: a library of human cancer-specific peptides

(2009) Xu Yang et al.   BMC CANCER

Full Dynamic Range Proteome Analysis of S. cerevisiae by Targeted Proteomics

(2009) Paola Picotti et al.   CELL

Directed mass spectrometry: towards hypothesis-driven proteomics

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

Expediting the Development of Targeted SRM Assays: Using Data from Shotgun Proteomics to Automate Method Development

(2009) Amol Prakash et al.   JOURNAL OF PROTEOME RESEARCH

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

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

Performance evaluation of a high-field orbitrap mass analyzer

(2009) Alexander Makarov et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

A Human Proteome Detection and Quantitation Project

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

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

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

A Dual Pressure Linear Ion Trap Orbitrap Instrument with Very High Sequencing Speed

(2009) Jesper V. Olsen 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

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

(2009) Paola Picotti et al.   NATURE METHODS

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

(2009) Mark W. Duncan et al.   PROTEOMICS

Combining selected reaction monitoring with discovery proteomics in limited biological samples

(2009) Mukesh Kumar Gupta et al.   PROTEOMICS

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

(2009) Jamie Sherman et al.   PROTEOMICS

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

Selected reaction monitoring for quantitative proteomics: a tutorial

(2008) Vinzenz Lange et al.   Molecular Systems Biology

Human Proteinpedia enables sharing of human protein data

(2008) Suresh Mathivanan et al.   NATURE BIOTECHNOLOGY

A database of mass spectrometric assays for the yeast proteome

(2008) Paola Picotti et al.   NATURE METHODS

ISPIDER Central: an integrated database web-server for proteomics

(2008) J. A. Siepen et al.   NUCLEIC ACIDS RESEARCH

Precision proteomics: The case for high resolution and high mass accuracy

(2008) M. Mann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA