Automated selected reaction monitoring data analysis workflow for large-scale targeted proteomic studies

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

(2012) Paola Picotti et al.   NATURE METHODS

Using iRT, a normalized retention time for more targeted measurement of peptides

(2012) Claudia Escher 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

Protein Significance Analysis in Selected Reaction Monitoring (SRM) Measurements

(2011) Ching-Yun Chang et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2011) Lukas Reiter et al.   NATURE METHODS

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

On the Development of Plasma Protein Biomarkers

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

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

(2009) Paola Picotti et al.   CELL

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

Selected reaction monitoring for quantitative proteomics: a tutorial

(2008) Vinzenz Lange et al.   Molecular Systems Biology