Thesaurus: quantifying phosphopeptide positional isomers

Specter: linear deconvolution for targeted analysis of data-independent acquisition mass spectrometry proteomics

(2018) Ryan Peckner et al.   NATURE METHODS

Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry

(2018) Brian C. Searle et al.   Nature Communications

Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS

(2017) George Rosenberger et al.   NATURE BIOTECHNOLOGY

PIQED: automated identification and quantification of protein modifications from DIA-MS data

(2017) Jesse G Meyer et al.   NATURE METHODS

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

(2016) Robert T Lawrence et al.   NATURE METHODS

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

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

Hunting for Unexpected Post-Translational Modifications by Spectral Library Searching with Tier-Wise Scoring

(2014) Chun Wai Manson Ma et al.   JOURNAL OF PROTEOME RESEARCH

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

(2014) Hannes L Röst et al.   NATURE BIOTECHNOLOGY

LuciPHOr: Algorithm for Phosphorylation Site Localization with False Localization Rate Estimation Using Modified Target-Decoy Approach

(2013) Damian Fermin 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

NEMO/NLK Phosphorylates PERIOD to Initiate a Time-Delay Phosphorylation Circuit that Sets Circadian Clock Speed

(2011) Joanna C. Chiu et al.   CELL

Universal and Confident Phosphorylation Site Localization Using phosphoRS

(2011) Thomas Taus et al.   JOURNAL OF PROTEOME RESEARCH

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

(2010) Brendan MacLean et al.   BIOINFORMATICS

Cooperativity within proximal phosphorylation sites is revealed from large-scale proteomics data

(2010) Regev Schweiger et al.   Biology Direct

Confident Phosphorylation Site Localization Using the Mascot Delta Score

(2010) Mikhail M. Savitski et al.   MOLECULAR & CELLULAR PROTEOMICS

In-depth Qualitative and Quantitative Profiling of Tyrosine Phosphorylation Using a Combination of Phosphopeptide Immunoaffinity Purification and Stable Isotope Dimethyl Labeling

(2009) Paul J. Boersema et al.   MOLECULAR & CELLULAR PROTEOMICS