Protein Significance Analysis in Selected Reaction Monitoring (SRM) Measurements

ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry

(2011) Mi-Youn K Brusniak et al.   BMC BIOINFORMATICS

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

Variance Component Analysis of a Multi-Site Study for the Reproducibility of Multiple Reaction Monitoring Measurements of Peptides in Human Plasma

(2011) Jessie Q. Xia et al.   PLoS One

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

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

(2010) Brendan MacLean et al.   BIOINFORMATICS

Increased Selectivity, Analytical Precision, and Throughput in Targeted Proteomics

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

Options and considerations when selecting a quantitative proteomics strategy

(2010) Bruno Domon et al.   NATURE BIOTECHNOLOGY

Generating and navigating proteome maps using mass spectrometry

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

Free computational resources for designing selected reaction monitoring transitions

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

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

(2009) Paola Picotti et al.   CELL

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

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

Systems biology: experimental design

(2009) Clemens Kreutz et al.   FEBS Journal

Protein Quantification in Label-Free LC-MS Experiments

(2009) Timothy Clough et al.   JOURNAL OF PROTEOME RESEARCH

Statistical Design of Quantitative Mass Spectrometry-Based Proteomic Experiments

(2009) Ann L. Oberg et al.   JOURNAL OF PROTEOME RESEARCH

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

Selected reaction monitoring for quantitative proteomics: a tutorial

(2008) Vinzenz Lange et al.   Molecular Systems Biology