Literature DB >> 26550773

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

Jian Wang1,2, Monika Tucholska3, James D R Knight3, Jean-Philippe Lambert3, Stephen Tate4, Brett Larsen3, Anne-Claude Gingras3,5, Nuno Bandeira1,2,6.   

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Year:  2015        PMID： 26550773      PMCID： PMC4857761          DOI： 10.1038/nmeth.3655

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


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  7 in total

1.  The generating function of CID, ETD, and CID/ETD pairs of tandem mass spectra: applications to database search.

Authors:  Sangtae Kim; Nikolai Mischerikow; Nuno Bandeira; J Daniel Navarro; Louis Wich; Shabaz Mohammed; Albert J R Heck; Pavel A Pevzner
Journal:  Mol Cell Proteomics       Date:  2010-09-09       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.  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

4.  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

5.  A repository of assays to quantify 10,000 human proteins by SWATH-MS.

Authors:  George Rosenberger; Ching Chiek Koh; Tiannan Guo; Hannes L Röst; Petri Kouvonen; Ben C Collins; Moritz Heusel; Yansheng Liu; Etienne Caron; Anton Vichalkovski; Marco Faini; Olga T Schubert; Pouya Faridi; H Alexander Ebhardt; Mariette Matondo; Henry Lam; Samuel L Bader; David S Campbell; Eric W Deutsch; Robert L Moritz; Stephen Tate; Ruedi Aebersold
Journal:  Sci Data       Date:  2014-09-16       Impact factor: 6.444

6.  Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition.

Authors:  Jean-Philippe Lambert; Gordana Ivosev; Amber L Couzens; Brett Larsen; Mikko Taipale; Zhen-Yuan Lin; Quan Zhong; Susan Lindquist; Marc Vidal; Ruedi Aebersold; Tony Pawson; Ron Bonner; Stephen Tate; Anne-Claude Gingras
Journal:  Nat Methods       Date:  2013-10-27       Impact factor: 28.547

7.  SAINTexpress: improvements and additional features in Significance Analysis of INTeractome software.

Authors:  Guoci Teo; Guomin Liu; Jianping Zhang; Alexey I Nesvizhskii; Anne-Claude Gingras; Hyungwon Choi
Journal:  J Proteomics       Date:  2013-10-26       Impact factor: 4.044
  7 in total
  39 in total

1.  Quantitative proteomics: challenges and opportunities in basic and applied research.

Authors:  Olga T Schubert; Hannes L Röst; Ben C Collins; George Rosenberger; Ruedi Aebersold
Journal:  Nat Protoc       Date:  2017-06-01       Impact factor: 13.491

2.  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

3.  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

4.  Spectral Library Search Improves Assignment of TMT Labeled MS/MS Spectra.

Authors:  Jianqiao Shen; Vishwajeeth R Pagala; Alex M Breuer; Junmin Peng; Xusheng Wang
Journal:  J Proteome Res       Date:  2018-08-16       Impact factor: 4.466

5.  SWATH Mass Spectrometry Performance Using Extended Peptide MS/MS Assay Libraries.

Authors:  Jemma X Wu; Xiaomin Song; Dana Pascovici; Thiri Zaw; Natasha Care; Christoph Krisp; Mark P Molloy
Journal:  Mol Cell Proteomics       Date:  2016-05-09       Impact factor: 5.911

6.  Systematic Discovery of Short Linear Motifs Decodes Calcineurin Phosphatase Signaling.

Authors:  Callie P Wigington; Jagoree Roy; Nikhil P Damle; Vikash K Yadav; Cecilia Blikstad; Eduard Resch; Cassandra J Wong; Douglas R Mackay; Jennifer T Wang; Izabella Krystkowiak; Devin A Bradburn; Eirini Tsekitsidou; Su Hyun Hong; Malika Amyn Kaderali; Shou-Ling Xu; Tim Stearns; Anne-Claude Gingras; Katharine S Ullman; Ylva Ivarsson; Norman E Davey; Martha S Cyert
Journal:  Mol Cell       Date:  2020-07-08       Impact factor: 17.970

7.  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 8.  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

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.  Data Independent Acquisition analysis in ProHits 4.0.

Authors:  Guomin Liu; James D R Knight; Jian Ping Zhang; Chih-Chiang Tsou; Jian Wang; Jean-Philippe Lambert; Brett Larsen; Mike Tyers; Brian Raught; Nuno Bandeira; Alexey I Nesvizhskii; Hyungwon Choi; Anne-Claude Gingras
Journal:  J Proteomics       Date:  2016-04-29       Impact factor: 4.044
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