Literature DB >> 24727770

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

Hannes L Röst1, George Rosenberger1, Pedro Navarro2, Ludovic Gillet2, Saša M Miladinović3, Olga T Schubert4, Witold Wolski5, Ben C Collins2, Johan Malmström6, Lars Malmström2, Ruedi Aebersold7.   

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Year:  2014        PMID： 24727770     DOI： 10.1038/nbt.2841

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN： 1087-0156            Impact factor:   54.908


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  36 in total

1.  Options and considerations when selecting a quantitative proteomics strategy.

Authors:  Bruno Domon; Ruedi Aebersold
Journal:  Nat Biotechnol       Date:  2010-07-09       Impact factor: 54.908

2.  Database searching and accounting of multiplexed precursor and product ion spectra from the data independent analysis of simple and complex peptide mixtures.

Authors:  Guo-Zhong Li; Johannes P C Vissers; Jeffrey C Silva; Dan Golick; Marc V Gorenstein; Scott J Geromanos
Journal:  Proteomics       Date:  2009-03       Impact factor: 3.984

3.  XDIA: improving on the label-free data-independent analysis.

Authors:  Paulo C Carvalho; Xuemei Han; Tao Xu; Daniel Cociorva; Maria da Gloria Carvalho; Valmir C Barbosa; John R Yates
Journal:  Bioinformatics       Date:  2010-01-26       Impact factor: 6.937

4.  More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS.

Authors:  Annette Michalski; Juergen Cox; Matthias Mann
Journal:  J Proteome Res       Date:  2011-02-28       Impact factor: 4.466

5.  Software for quantitative proteomic analysis using stable isotope labeling and data independent acquisition.

Authors:  Xin Huang; Miao Liu; Michael J Nold; Changhai Tian; Kai Fu; Jialin Zheng; Scott J Geromanos; Shi-Jian Ding
Journal:  Anal Chem       Date:  2011-08-23       Impact factor: 6.986

6.  Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics.

Authors:  Paola Picotti; Bernd Bodenmiller; Lukas N Mueller; Bruno Domon; Ruedi Aebersold
Journal:  Cell       Date:  2009-08-06       Impact factor: 41.582

7.  Distinct signatures of diversifying selection revealed by genome analysis of respiratory tract and invasive bacterial populations.

Authors:  Patrick R Shea; Stephen B Beres; Anthony R Flores; Amy L Ewbank; Javier H Gonzalez-Lugo; Alexandro J Martagon-Rosado; Juan C Martinez-Gutierrez; Hina A Rehman; Monica Serrano-Gonzalez; Nahuel Fittipaldi; Stephen D Ayers; Paul Webb; Barbara M Willey; Donald E Low; James M Musser
Journal:  Proc Natl Acad Sci U S A       Date:  2011-03-07       Impact factor: 11.205

8.  The detection, correlation, and comparison of peptide precursor and product ions from data independent LC-MS with data dependant LC-MS/MS.

Authors:  Scott J Geromanos; Johannes P C Vissers; Jeffrey C Silva; Craig A Dorschel; Guo-Zhong Li; Marc V Gorenstein; Robert H Bateman; James I Langridge
Journal:  Proteomics       Date:  2009-03       Impact factor: 3.984

9.  Using iRT, a normalized retention time for more targeted measurement of peptides.

Authors:  Claudia Escher; Lukas Reiter; Brendan MacLean; Reto Ossola; Franz Herzog; John Chilton; Michael J MacCoss; Oliver Rinner
Journal:  Proteomics       Date:  2012-04       Impact factor: 3.984

10.  Deconvolution of mixture spectra from ion-trap data-independent-acquisition tandem mass spectrometry.

Authors:  Marshall Bern; Gregory Finney; Michael R Hoopmann; Gennifer Merrihew; Michael J Toth; Michael J MacCoss
Journal:  Anal Chem       Date:  2010-02-01       Impact factor: 6.986
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  226 in total

1.  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

2.  Software Analysis of Uncorrelated MS1 Peaks for Discovery of Post-Translational Modifications.

Authors:  Bruce D Pascal; Graham M West; Catherina Scharager-Tapia; Ricardo Flefil; Tina Moroni; Pablo Martinez-Acedo; Patrick R Griffin; Anthony C Carvalloza
Journal:  J Am Soc Mass Spectrom       Date:  2015-08-12       Impact factor: 3.109

3.  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

4.  Mapping Biological Networks from Quantitative Data-Independent Acquisition Mass Spectrometry: Data to Knowledge Pipelines.

Authors:  Erin L Crowgey; Andrea Matlock; Vidya Venkatraman; Justyna Fert-Bober; Jennifer E Van Eyk
Journal:  Methods Mol Biol       Date:  2017

5.  Standardized Profiling of The Membrane-Enriched Proteome of Mouse Dorsal Root Ganglia (DRG) Provides Novel Insights Into Chronic Pain.

Authors:  Tom Rouwette; Julia Sondermann; Luca Avenali; David Gomez-Varela; Manuela Schmidt
Journal:  Mol Cell Proteomics       Date:  2016-04-21       Impact factor: 5.911

Review 6.  A Review on Quantitative Multiplexed Proteomics.

Authors:  Nishant Pappireddi; Lance Martin; Martin Wühr
Journal:  Chembiochem       Date:  2019-04-18       Impact factor: 3.164

7.  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

Review 8.  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

Review 9.  Identification of small molecules using accurate mass MS/MS search.

Authors:  Tobias Kind; Hiroshi Tsugawa; Tomas Cajka; Yan Ma; Zijuan Lai; Sajjan S Mehta; Gert Wohlgemuth; Dinesh Kumar Barupal; Megan R Showalter; Masanori Arita; Oliver Fiehn
Journal:  Mass Spectrom Rev       Date:  2017-04-24       Impact factor: 10.946

10.  Targeted proteomic assays for the verification of global proteomics insights.

Authors:  Stefani N Thomas; Hui Zhang
Journal:  Expert Rev Proteomics       Date:  2016-09-01       Impact factor: 3.940
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