Reproducible and Consistent Quantification of theSaccharomyces cerevisiaeProteome by SWATH-mass spectrometry

MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments

(2014) Meena Choi et al.   BIOINFORMATICS

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

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

(2013) Paola Picotti et al.   NATURE

Selectivity of LC-MS/MS analysis: Implication for proteomics experiments

(2012) Sebastien Gallien et al.   Journal of Proteomics

Mass Spectrometry: Reconnaissance at the Frontiers of Biology

(2012) Alma L. Burlingame et al.   MOLECULAR & CELLULAR PROTEOMICS

Targeted Proteomic Quantification on Quadrupole-Orbitrap Mass Spectrometer

(2012) Sebastien Gallien et al.   MOLECULAR & CELLULAR PROTEOMICS

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

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

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

(2012) Paola Picotti et al.   NATURE METHODS

Highly multiplexed targeted proteomics using precise control of peptide retention time

(2012) Sebastien Gallien et al.   PROTEOMICS

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

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

(2012) Christofer Karlsson et al.   Nature Communications

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

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 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

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

(2011) Lukas Reiter et al.   NATURE METHODS

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

(2010) Brendan MacLean et al.   BIOINFORMATICS

Options and considerations when selecting a quantitative proteomics strategy

(2010) Bruno Domon et al.   NATURE BIOTECHNOLOGY

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

Unique Ion Signature Mass Spectrometry, a Deterministic Method to Assign Peptide Identity

(2009) Jamie Sherman 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

Selected reaction monitoring for quantitative proteomics: a tutorial

(2008) Vinzenz Lange et al.   Molecular Systems Biology

Building consensus spectral libraries for peptide identification in proteomics

(2008) Henry Lam et al.   NATURE METHODS

A database of mass spectrometric assays for the yeast proteome

(2008) Paola Picotti et al.   NATURE METHODS