Using Data Independent Acquisition (DIA) to Model High-responding Peptides for Targeted Proteomics Experiments

Multiplexed peptide analysis using data-independent acquisition and Skyline

(2015) Jarrett D Egertson et al.   Nature Protocols

Abundance-based Classifier for the Prediction of Mass Spectrometric Peptide Detectability Upon Enrichment (PPA)

(2014) Jan Muntel et al.   MOLECULAR & CELLULAR PROTEOMICS

Targeted Quantitation of Proteins by Mass Spectrometry

(2013) Daniel C. Liebler et al.   BIOCHEMISTRY

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

(2012) Paola Picotti et al.   NATURE METHODS

Targeted proteomics

(2012) Vivien Marx   NATURE METHODS

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

(2012) Michael S. Bereman et al.   PROTEOMICS

Improving SRM Assay Development: A Global Comparison between Triple Quadrupole, Ion Trap, and Higher Energy CID Peptide Fragmentation Spectra

(2011) Erik L. de Graaf et al.   JOURNAL OF PROTEOME RESEARCH

CONSeQuence: Prediction of Reference Peptides for Absolute Quantitative Proteomics Using Consensus Machine Learning Approaches

(2011) Claire E. Eyers et al.   MOLECULAR & CELLULAR PROTEOMICS

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Rapid empirical discovery of optimal peptides for targeted proteomics

(2011) Andrew B Stergachis et al.   NATURE METHODS

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

(2010) Brendan MacLean et al.   BIOINFORMATICS

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

Comparison of Database Search Strategies for High Precursor Mass Accuracy MS/MS Data

(2009) Edward J. Hsieh et al.   JOURNAL OF PROTEOME RESEARCH

Prediction of high-responding peptides for targeted protein assays by mass spectrometry

(2009) Vincent A Fusaro et al.   NATURE BIOTECHNOLOGY

MRMaid, the Web-based Tool for Designing Multiple Reaction Monitoring (MRM) Transitions

(2008) Jennifer A. Mead et al.   MOLECULAR & CELLULAR PROTEOMICS