Plug-and-play analysis of the human phosphoproteome by targeted high-resolution mass spectrometry

Signal Transduction Reaction Monitoring Deciphers Site-Specific PI3K-mTOR/MAPK Pathway Dynamics in Oncogene-Induced Senescence

(2015) Erik L. de Graaf et al.   JOURNAL OF PROTEOME RESEARCH

Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data

(2015) Ying S. Ting et al.   MOLECULAR & CELLULAR PROTEOMICS

DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics

(2015) Chih-Chiang Tsou et al.   NATURE METHODS

Targeted phosphoproteomics of insulin signaling using data-independent acquisition mass spectrometry

(2015) Benjamin L. Parker et al.   Science Signaling

An Augmented Multiple-Protease-Based Human Phosphopeptide Atlas

(2015) Piero Giansanti et al.   Cell Reports

Targeted phosphoproteomics of insulin signaling using data-independent acquisition mass spectrometry

(2015) Benjamin L. Parker et al.   Science Signaling

Impact of Digestion Conditions on Phosphoproteomics

(2014) Clarissa Dickhut et al.   JOURNAL OF PROTEOME RESEARCH

Single-step Enrichment by Ti4+-IMAC and Label-free Quantitation Enables In-depth Monitoring of Phosphorylation Dynamics with High Reproducibility and Temporal Resolution

(2014) Erik L. de Graaf et al.   MOLECULAR & CELLULAR PROTEOMICS

OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data

(2014) Hannes L Röst et al.   NATURE BIOTECHNOLOGY

A sentinel protein assay for simultaneously quantifying cellular processes

(2014) Martin Soste et al.   NATURE METHODS

PhosphoSitePlus, 2014: mutations, PTMs and recalibrations

(2014) Peter V. Hornbeck et al.   NUCLEIC ACIDS RESEARCH

Ultradeep Human Phosphoproteome Reveals a Distinct Regulatory Nature of Tyr and Ser/Thr-Based Signaling

(2014) Kirti Sharma et al.   Cell Reports

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

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

Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis

(2012) Ludovic C. Gillet et al.   MOLECULAR & CELLULAR PROTEOMICS

Comet: An open-source MS/MS sequence database search tool

(2012) Jimmy K. Eng et al.   PROTEOMICS

Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues

(2012) Alicia Lundby et al.   Nature Communications

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

(2010) Brendan MacLean et al.   BIOINFORMATICS

A Tissue-Specific Atlas of Mouse Protein Phosphorylation and Expression

(2010) Edward L. Huttlin et al.   CELL