Literature DB >> 28661500

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

Jesse G Meyer1, Sushanth Mukkamalla1, Hanno Steen2, Alexey I Nesvizhskii3,4, Bradford W Gibson1, Birgit Schilling1.   

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Year:  2017        PMID： 28661500      PMCID： PMC5663633          DOI： 10.1038/nmeth.4334

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


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  6 in total

1.  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

2.  Group-DIA: analyzing multiple data-independent acquisition mass spectrometry data files.

Authors:  Yuanyue Li; Chuan-Qi Zhong; Xiaozheng Xu; Shaowei Cai; Xiurong Wu; Yingying Zhang; Jinan Chen; Jianghong Shi; Shengcai Lin; Jiahuai Han
Journal:  Nat Methods       Date:  2015-12       Impact factor: 28.547

3.  Multiplexed peptide analysis using data-independent acquisition and Skyline.

Authors:  Jarrett D Egertson; Brendan MacLean; Richard Johnson; Yue Xuan; Michael J MacCoss
Journal:  Nat Protoc       Date:  2015-05-21       Impact factor: 13.491

4.  Advancing Urinary Protein Biomarker Discovery by Data-Independent Acquisition on a Quadrupole-Orbitrap Mass Spectrometer.

Authors:  Jan Muntel; Yue Xuan; Sebastian T Berger; Lukas Reiter; Richard Bachur; Alex Kentsis; Hanno Steen
Journal:  J Proteome Res       Date:  2015-10-22       Impact factor: 4.466

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

Authors:  Chih-Chiang Tsou; Dmitry Avtonomov; Brett Larsen; Monika Tucholska; Hyungwon Choi; Anne-Claude Gingras; Alexey I Nesvizhskii
Journal:  Nat Methods       Date:  2015-01-19       Impact factor: 28.547

6.  mapDIA: Preprocessing and statistical analysis of quantitative proteomics data from data independent acquisition mass spectrometry.

Authors:  Guoshou Teo; Sinae Kim; Chih-Chiang Tsou; Ben Collins; Anne-Claude Gingras; Alexey I Nesvizhskii; Hyungwon Choi
Journal:  J Proteomics       Date:  2015-09-15       Impact factor: 4.044
  6 in total
  15 in total

1.  Dietary Sugars Alter Hepatic Fatty Acid Oxidation via Transcriptional and Post-translational Modifications of Mitochondrial Proteins.

Authors:  Samir Softic; Jesse G Meyer; Guo-Xiao Wang; Manoj K Gupta; Thiago M Batista; Hans P M M Lauritzen; Shiho Fujisaka; Dolors Serra; Laura Herrero; Jennifer Willoughby; Kevin Fitzgerald; Olga Ilkayeva; Christopher B Newgard; Bradford W Gibson; Birgit Schilling; David E Cohen; C Ronald Kahn
Journal:  Cell Metab       Date:  2019-10-01       Impact factor: 27.287

2.  Acquiring and Analyzing Data Independent Acquisition Proteomics Experiments without Spectrum Libraries.

Authors:  Lindsay K Pino; Seth C Just; Michael J MacCoss; Brian C Searle
Journal:  Mol Cell Proteomics       Date:  2020-04-20       Impact factor: 5.911

Review 3.  Precision Profiling of the Cardiovascular Post-Translationally Modified Proteome: Where There Is a Will, There Is a Way.

Authors:  Justyna Fert-Bober; Christopher I Murray; Sarah J Parker; Jennifer E Van Eyk
Journal:  Circ Res       Date:  2018-04-27       Impact factor: 17.367

4.  High-Resolution Mass Spectrometry to Identify and Quantify Acetylation Protein Targets.

Authors:  Birgit Schilling; Jesse G Meyer; Lei Wei; Melanie Ott; Eric Verdin
Journal:  Methods Mol Biol       Date:  2019

5.  Regulation of UCP1 and Mitochondrial Metabolism in Brown Adipose Tissue by Reversible Succinylation.

Authors:  GuoXiao Wang; Jesse G Meyer; Weikang Cai; Samir Softic; Mengyao Ella Li; Eric Verdin; Christopher Newgard; Birgit Schilling; C Ronald Kahn
Journal:  Mol Cell       Date:  2019-04-15       Impact factor: 17.970

Review 6.  Prediction of peptide mass spectral libraries with machine learning.

Authors:  Jürgen Cox
Journal:  Nat Biotechnol       Date:  2022-08-25       Impact factor: 68.164

7.  Global and Site-Specific Effect of Phosphorylation on Protein Turnover.

Authors:  Chongde Wu; Qian Ba; Dayun Lu; Wenxue Li; Barbora Salovska; Pingfu Hou; Torsten Mueller; George Rosenberger; Erli Gao; Yi Di; Hu Zhou; Eugenio F Fornasiero; Yansheng Liu
Journal:  Dev Cell       Date:  2020-11-24       Impact factor: 12.270

8.  Quantification of Site-specific Protein Lysine Acetylation and Succinylation Stoichiometry Using Data-independent Acquisition Mass Spectrometry.

Authors:  Lei Wei; Jesse G Meyer; Birgit Schilling
Journal:  J Vis Exp       Date:  2018-04-04       Impact factor: 1.355

9.  Identification of Novel Protein Lysine Acetyltransferases in Escherichia coli.

Authors:  David G Christensen; Jesse G Meyer; Jackson T Baumgartner; Alexandria K D'Souza; William C Nelson; Samuel H Payne; Misty L Kuhn; Birgit Schilling; Alan J Wolfe
Journal:  mBio       Date:  2018-10-23       Impact factor: 7.867

10.  Simultaneous Quantification of the Acetylome and Succinylome by 'One-Pot' Affinity Enrichment.

Authors:  Nathan Basisty; Jesse G Meyer; Lei Wei; Bradford W Gibson; Birgit Schilling
Journal:  Proteomics       Date:  2018-08-19       Impact factor: 3.984
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