Literature DB >> 26436481

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

Yuanyue Li1, Chuan-Qi Zhong1, Xiaozheng Xu1, Shaowei Cai1, Xiurong Wu1, Yingying Zhang1, Jinan Chen1, Jianghong Shi2, Shengcai Lin1, Jiahuai Han1.   

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Year:  2015        PMID： 26436481     DOI： 10.1038/nmeth.3593

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.  Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra.

Authors:  John D Venable; Meng-Qiu Dong; James Wohlschlegel; Andrew Dillin; John R Yates
Journal:  Nat Methods       Date:  2004-09-29       Impact factor: 28.547

3.  UPLC/MS(E); a new approach for generating molecular fragment information for biomarker structure elucidation.

Authors:  Robert S Plumb; Kelly A Johnson; Paul Rainville; Brian W Smith; Ian D Wilson; Jose M Castro-Perez; Jeremy K Nicholson
Journal:  Rapid Commun Mass Spectrom       Date:  2006       Impact factor: 2.419

4.  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

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.  Precursor acquisition independent from ion count: how to dive deeper into the proteomics ocean.

Authors:  Alexandre Panchaud; Alexander Scherl; Scott A Shaffer; Priska D von Haller; Hemantha D Kulasekara; Samuel I Miller; David R Goodlett
Journal:  Anal Chem       Date:  2009-08-01       Impact factor: 6.986
  6 in total
  25 in total

1.  MSPLIT-DIA: sensitive peptide identification for data-independent acquisition.

Authors:  Jian Wang; Monika Tucholska; James D R Knight; Jean-Philippe Lambert; Stephen Tate; Brett Larsen; Anne-Claude Gingras; Nuno Bandeira
Journal:  Nat Methods       Date:  2015-12       Impact factor: 28.547

2.  Quantification of Dynamic Protein Interactions and Phosphorylation in LPS Signaling Pathway by SWATH-MS.

Authors:  Xiurong Wu; Daowei Yang; Fu Zhao; Zhang-Hua Yang; Dazheng Wang; Muzhen Qiao; Yuan Fang; Wanyun Li; Rui Wu; Peng He; Yu Cong; Chang'an Chen; Lichen Hu; Yihua Yan; Changchuan Xie; Yaying Wu; Jiahuai Han; Chuan-Qi Zhong
Journal:  Mol Cell Proteomics       Date:  2019-03-08       Impact factor: 5.911

3.  New targeted approaches for the quantification of data-independent acquisition mass spectrometry.

Authors:  Roland Bruderer; Julia Sondermann; Chih-Chiang Tsou; Alonso Barrantes-Freer; Christine Stadelmann; Alexey I Nesvizhskii; Manuela Schmidt; Lukas Reiter; David Gomez-Varela
Journal:  Proteomics       Date:  2017-05       Impact factor: 3.984

4.  Generation of High-Quality SWATH® Acquisition Data for Label-free Quantitative Proteomics Studies Using TripleTOF® Mass Spectrometers.

Authors:  Birgit Schilling; Bradford W Gibson; Christie L Hunter
Journal:  Methods Mol Biol       Date:  2017

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

Authors:  Jesse G Meyer; Sushanth Mukkamalla; Hanno Steen; Alexey I Nesvizhskii; Bradford W Gibson; Birgit Schilling
Journal:  Nat Methods       Date:  2017-06-29       Impact factor: 28.547

6.  Inner membrane complex proteomics reveals a palmitoylation regulation critical for intraerythrocytic development of malaria parasite.

Authors:  Pengge Qian; Xu Wang; Chuan-Qi Zhong; Jiaxu Wang; Mengya Cai; Wang Nguitragool; Jian Li; Huiting Cui; Jing Yuan
Journal:  Elife       Date:  2022-07-01       Impact factor: 8.713

Review 7.  Prediction of peptide mass spectral libraries with machine learning.

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

8.  Building Spectral Libraries from Narrow-Window Data-Independent Acquisition Mass Spectrometry Data.

Authors:  Lilian R Heil; William E Fondrie; Christopher D McGann; Alexander J Federation; William S Noble; Michael J MacCoss; Uri Keich
Journal:  J Proteome Res       Date:  2022-05-12       Impact factor: 5.370

Review 9.  Clinical applications of quantitative proteomics using targeted and untargeted data-independent acquisition techniques.

Authors:  Jesse G Meyer; Birgit Schilling
Journal:  Expert Rev Proteomics       Date:  2017-05       Impact factor: 3.940

10.  Gasdermin D is an executor of pyroptosis and required for interleukin-1β secretion.

Authors:  Wan-ting He; Haoqiang Wan; Lichen Hu; Pengda Chen; Xin Wang; Zhe Huang; Zhang-Hua Yang; Chuan-Qi Zhong; Jiahuai Han
Journal:  Cell Res       Date:  2015-11-27       Impact factor: 25.617
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