Thesaurus: quantifying phosphopeptide positional isomers

Nature Methods
Brian C SearleJudit Villén

Abstract

Proteins can be phosphorylated at neighboring sites resulting in different functional states, and studying the regulation of these sites has been challenging. Here we present Thesaurus, a search engine that detects and quantifies phosphopeptide positional isomers from parallel reaction monitoring and data-independent acquisition mass spectrometry experiments. We apply Thesaurus to analyze phosphorylation events in the PI3K/AKT signaling pathway and show neighboring sites with distinct regulation.

References

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Citations

Dec 31, 2019·Molecular Systems Biology·Mario LeutertJudit Villén
Mar 28, 2020·Nature Communications·Brian C SearleMathias Wilhelm
Apr 22, 2020·Molecular & Cellular Proteomics : MCP·Lindsay K PinoBrian C Searle
Nov 26, 2020·Developmental Cell·Chongde WuYansheng Liu
Dec 30, 2020·Molecular & Cellular Proteomics : MCP·Zilu Ye, Sergey Y Vakhrushev
Jan 20, 2021·Journal of Proteome Research·Paige HaasRuth Hüttenhain
Jan 17, 2021·Molecular & Cellular Proteomics : MCP·Lindsay K PinoBrian C Searle
May 7, 2021·Nature Communications·Reta Birhanu KitataYu-Ju Chen
Mar 25, 2021·Rapid Communications in Mass Spectrometry : RCM·Viktoria DorferKarl Mechtler
May 29, 2020·Journal of the American Society for Mass Spectrometry·Niveda SundararamanVidya Venkatraman
Sep 29, 2020·Journal of Proteome Research·Yi YangLiang Qiao
Jan 25, 2020·Journal of Proteome Research·Marie Locard-PauletLars J Jensen
Sep 2, 2021·Expert Review of Proteomics·Jacqueline S Gerritsen, Forest M White
Sep 2, 2021·Analytical Chemistry·Caleb W Cranney, Jesse G Meyer
Nov 25, 2021·Journal of Proteome Research·Evan E HubbardRyan R Julian

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Methods Mentioned

BETA
acetylation

Software Mentioned

Comet
Daily
PeptideProphet
EncyclopeDIA
PTMProphet
Thesaurus
Skyline
PyProphet
TraML
ReAdW

Related Concepts

Related Feeds

AKT Pathway

This feed focuses on the AKT serine/threonine kinase, which is an important signaling pathway involved in processes such as glucose metabolism and cell survival.

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