The development of selected reaction monitoring methods for targeted proteomics via empirical refinement

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

(2012) Claudia Escher et al.   PROTEOMICS

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

More than 100,000 Detectable Peptide Species Elute in Single Shotgun Proteomics Runs but the Majority is Inaccessible to Data-Dependent LC−MS/MS

(2011) Annette Michalski et al.   JOURNAL OF PROTEOME RESEARCH

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

(2011) Lukas Reiter et al.   NATURE METHODS

Effect of Collision Energy Optimization on the Measurement of Peptides by Selected Reaction Monitoring (SRM) Mass Spectrometry

(2010) Brendan MacLean et al.   ANALYTICAL CHEMISTRY

Measurement of Human Surfactant Protein-B Turnover in Vivo from Tracheal Aspirates Using Targeted Proteomics

(2010) Daniela M. Tomazela et al.   ANALYTICAL CHEMISTRY

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

(2010) Brendan MacLean et al.   BIOINFORMATICS

Collision Energy Optimization of b- and y-Ions for Multiple Reaction Monitoring Mass Spectrometry

(2010) Carly A. Holstein (Sherwood) et al.   JOURNAL OF PROTEOME RESEARCH

Free computational resources for designing selected reaction monitoring transitions

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

Post Analysis Data Acquisition for the Iterative MS/MS Sampling of Proteomics Mixtures

(2009) Michael R. Hoopmann et al.   JOURNAL OF PROTEOME RESEARCH

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

Absolute Quantification of C-Reactive Protein in Human Plasma Derived from Patients with Epithelial Ovarian Cancer Utilizing Protein Cleavage Isotope Dilution Mass Spectrometry

(2009) D. Keith Williams 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

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

(2009) Mark W. Duncan et al.   PROTEOMICS

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

(2009) Jamie Sherman et al.   PROTEOMICS

A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics

(2008) Bobbie-Jo M. Webb-Robertson et al.   BIOINFORMATICS

ProteoWizard: open source software for rapid proteomics tools development

(2008) Darren Kessner et al.   BIOINFORMATICS

Human Proteinpedia as a Resource for Clinical Proteomics

(2008) Suresh Mathivanan et al.   MOLECULAR & CELLULAR PROTEOMICS

Selected reaction monitoring for quantitative proteomics: a tutorial

(2008) Vinzenz Lange et al.   Molecular Systems Biology

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

Human Proteinpedia: a unified discovery resource for proteomics research

(2008) Kumaran Kandasamy et al.   NUCLEIC ACIDS RESEARCH