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Literature DB >> 27301801

Differential quantification of isobaric phosphopeptides using data-independent acquisition mass spectrometry.

Simone Sidoli¹, Rina Fujiwara¹, Katarzyna Kulej², Benjamin A Garcia¹.

Abstract

Phosphorylation is a post-translational modification (PTM) fundamental for processes such as signal transduction and enzyme activity. We propose to apply data-independent acquisition (DIA) using mass spectrometry (MS) to determine unexplored phosphorylation events on isobarically modified peptides. Such peptides are commonly not quantitatively discriminated in phosphoproteomics due to their identical mass.

Entities: CellLine Chemical Disease Gene

Mesh：

Substances：
Phosphopeptides

Year: 2016 PMID： 27301801 PMCID： PMC5091076 DOI： 10.1039/c6mb00385k

Source DB: PubMed Journal: Mol Biosyst ISSN： 1742-2051

15 in total

Review 1. The regulation of protein function by multisite phosphorylation--a 25 year update.

Authors: P Cohen
Journal: Trends Biochem Sci Date: 2000-12 Impact factor: 13.807

2. Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis.

Authors: Ludovic C Gillet; Pedro Navarro; Stephen Tate; Hannes Röst; Nathalie Selevsek; Lukas Reiter; Ron Bonner; Ruedi Aebersold
Journal: Mol Cell Proteomics Date: 2012-01-18 Impact factor: 5.911

Review 3. Epigenetic modifications and human disease.

Authors: Anna Portela; Manel Esteller
Journal: Nat Biotechnol Date: 2010-10 Impact factor: 54.908

4. High-resolution mass spectrometry for integrated qualitative and quantitative analysis of pharmaceuticals in biological matrices.

Authors: Gérard Hopfgartner; David Tonoli; Emmanuel Varesio
Journal: Anal Bioanal Chem Date: 2011-12-28 Impact factor: 4.142

Review 5. Protein analysis by shotgun/bottom-up proteomics.

Authors: Yaoyang Zhang; Bryan R Fonslow; Bing Shan; Moon-Chang Baek; John R Yates
Journal: Chem Rev Date: 2013-02-26 Impact factor: 60.622

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

Authors: Hannes L Röst; George Rosenberger; Pedro Navarro; Ludovic Gillet; Saša M Miladinović; Olga T Schubert; Witold Wolski; Ben C Collins; Johan Malmström; Lars Malmström; Ruedi Aebersold
Journal: Nat Biotechnol Date: 2014-03 Impact factor: 54.908

Review 7. Covalent histone modifications--miswritten, misinterpreted and mis-erased in human cancers.

Authors: Ping Chi; C David Allis; Gang Greg Wang
Journal: Nat Rev Cancer Date: 2010-07 Impact factor: 60.716

8. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks.

Authors: Jesper V Olsen; Blagoy Blagoev; Florian Gnad; Boris Macek; Chanchal Kumar; Peter Mortensen; Matthias Mann
Journal: Cell Date: 2006-11-03 Impact factor: 41.582

9. Antipsychotic treatment alters protein expression associated with presynaptic function and nervous system development in rat frontal cortex.

Authors: Dan Ma; Man K Chan; Helen E Lockstone; Sandra R Pietsch; Declan N C Jones; Jackie Cilia; Mark D Hill; Melanie J Robbins; Isabel M Benzel; Yagnesh Umrania; Paul C Guest; Yishai Levin; Peter R Maycox; Sabine Bahn
Journal: J Proteome Res Date: 2009-07 Impact factor: 4.466

Differential quantification of isobaric phosphopeptides using data-independent acquisition mass spectrometry.

Review 1. The regulation of protein function by multisite phosphorylation--a 25 year update.

2. Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis.

Review 3. Epigenetic modifications and human disease.

4. High-resolution mass spectrometry for integrated qualitative and quantitative analysis of pharmaceuticals in biological matrices.

Review 5. Protein analysis by shotgun/bottom-up proteomics.

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

Review 7. Covalent histone modifications--miswritten, misinterpreted and mis-erased in human cancers.

8. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks.

9. Antipsychotic treatment alters protein expression associated with presynaptic function and nervous system development in rat frontal cortex.

Review 10. Identification and interrogation of combinatorial histone modifications.

1. EpiProfile 2.0: A Computational Platform for Processing Epi-Proteomics Mass Spectrometry Data.

2. Phosphoproteomics-Based Profiling of Kinase Activities in Cancer Cells.

3. Quantitative Phosphoproteomic Analysis Reveals Key Mechanisms of Cellular Proliferation in Liver Cancer Cells.

Review 4. Proteomic Analysis of Histone Variants and Their PTMs: Strategies and Pitfalls.