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Literature DB >> 28569762

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

Olga T Schubert¹, Hannes L Röst², Ben C Collins³, George Rosenberger³, Ruedi Aebersold^3,4.

Abstract

In this Perspective, we discuss developments in mass-spectrometry-based proteomic technology over the past decade from the viewpoint of our laboratory. We also reflect on existing challenges and limitations, and explore the current and future roles of quantitative proteomics in molecular systems biology, clinical research and personalized medicine.

Mesh：

Year: 2017 PMID： 28569762 DOI： 10.1038/nprot.2017.040

Source DB: PubMed Journal: Nat Protoc ISSN： 1750-2799 Impact factor: 13.491

76 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

Review 2. Protein biomarker discovery and validation: the long and uncertain path to clinical utility.

Authors: Nader Rifai; Michael A Gillette; Steven A Carr
Journal: Nat Biotechnol Date: 2006-08 Impact factor: 54.908

3. Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma.

Authors: Terri A Addona; Susan E Abbatiello; Birgit Schilling; Steven J Skates; D R Mani; David M Bunk; Clifford H Spiegelman; Lisa J Zimmerman; Amy-Joan L Ham; Hasmik Keshishian; Steven C Hall; Simon Allen; Ronald K Blackman; Christoph H Borchers; Charles Buck; Helene L Cardasis; Michael P Cusack; Nathan G Dodder; Bradford W Gibson; Jason M Held; Tara Hiltke; Angela Jackson; Eric B Johansen; Christopher R Kinsinger; Jing Li; Mehdi Mesri; Thomas A Neubert; Richard K Niles; Trenton C Pulsipher; David Ransohoff; Henry Rodriguez; Paul A Rudnick; Derek Smith; David L Tabb; Tony J Tegeler; Asokan M Variyath; Lorenzo J Vega-Montoto; Asa Wahlander; Sofia Waldemarson; Mu Wang; Jeffrey R Whiteaker; Lei Zhao; N Leigh Anderson; Susan J Fisher; Daniel C Liebler; Amanda G Paulovich; Fred E Regnier; Paul Tempst; Steven A Carr
Journal: Nat Biotechnol Date: 2009-06-28 Impact factor: 54.908

4. Too many roads not taken.

Authors: Aled M Edwards; Ruth Isserlin; Gary D Bader; Stephen V Frye; Timothy M Willson; Frank H Yu
Journal: Nature Date: 2011-02-10 Impact factor: 49.962

5. 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

6. Systems proteomics of liver mitochondria function.

Authors: Evan G Williams; Yibo Wu; Pooja Jha; Sébastien Dubuis; Peter Blattmann; Carmen A Argmann; Sander M Houten; Tiffany Amariuta; Witold Wolski; Nicola Zamboni; Ruedi Aebersold; Johan Auwerx
Journal: Science Date: 2016-06-10 Impact factor: 47.728

7. Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer.

Authors: Hui Zhang; Tao Liu; Zhen Zhang; Samuel H Payne; Bai Zhang; Jason E McDermott; Jian-Ying Zhou; Vladislav A Petyuk; Li Chen; Debjit Ray; Shisheng Sun; Feng Yang; Lijun Chen; Jing Wang; Punit Shah; Seong Won Cha; Paul Aiyetan; Sunghee Woo; Yuan Tian; Marina A Gritsenko; Therese R Clauss; Caitlin Choi; Matthew E Monroe; Stefani Thomas; Song Nie; Chaochao Wu; Ronald J Moore; Kun-Hsing Yu; David L Tabb; David Fenyö; Vineet Bafna; Yue Wang; Henry Rodriguez; Emily S Boja; Tara Hiltke; Robert C Rivers; Lori Sokoll; Heng Zhu; Ie-Ming Shih; Leslie Cope; Akhilesh Pandey; Bing Zhang; Michael P Snyder; Douglas A Levine; Richard D Smith; Daniel W Chan; Karin D Rodland
Journal: Cell Date: 2016-06-29 Impact factor: 41.582

8. A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells.

Authors: Kyle J Roux; Dae In Kim; Manfred Raida; Brian Burke
Journal: J Cell Biol Date: 2012-03-12 Impact factor: 10.539

9. Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen-treated three-dimensional liver microtissues.

Authors: Roland Bruderer; Oliver M Bernhardt; Tejas Gandhi; Saša M Miladinović; Lin-Yang Cheng; Simon Messner; Tobias Ehrenberger; Vito Zanotelli; Yulia Butscheid; Claudia Escher; Olga Vitek; Oliver Rinner; Lukas Reiter
Journal: Mol Cell Proteomics Date: 2015-02-27 Impact factor: 5.911

10. aLFQ: an R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data.

Authors: George Rosenberger; Christina Ludwig; Hannes L Röst; Ruedi Aebersold; Lars Malmström
Journal: Bioinformatics Date: 2014-04-20 Impact factor: 6.937

68 in total

1. Proteomics Profiling of Host Cell Response via Protein Expression and Phosphorylation upon Dengue Virus Infection.

Authors: Meng Miao; Fei Yu; Danya Wang; Yongjia Tong; Liuting Yang; Jiuyue Xu; Yang Qiu; Xi Zhou; Xiaolu Zhao
Journal: Virol Sin Date: 2019-05-27 Impact factor: 4.327

2. Absolute Quantitation of Oxidizable Peptides by Coulometric Mass Spectrometry.

Authors: Pengyi Zhao; Richard N Zare; Hao Chen
Journal: J Am Soc Mass Spectrom Date: 2019-08-19 Impact factor: 3.109

3. Toward a Consensus on Applying Quantitative Liquid Chromatography-Tandem Mass Spectrometry Proteomics in Translational Pharmacology Research: A White Paper.

Authors: Bhagwat Prasad; Brahim Achour; Per Artursson; Cornelis E C A Hop; Yurong Lai; Philip C Smith; Jill Barber; Jacek R Wisniewski; Daniel Spellman; Yasuo Uchida; Michael A Zientek; Jashvant D Unadkat; Amin Rostami-Hodjegan
Journal: Clin Pharmacol Ther Date: 2019-07-26 Impact factor: 6.875

4. DIAlignR Provides Precise Retention Time Alignment Across Distant Runs in DIA and Targeted Proteomics.

Authors: Shubham Gupta; Sara Ahadi; Wenyu Zhou; Hannes Röst
Journal: Mol Cell Proteomics Date: 2019-01-31 Impact factor: 5.911

5. Gingival Exudatome Dynamics Implicate Inhibition of the Alternative Complement Pathway in the Protective Action of the C3 Inhibitor Cp40 in Nonhuman Primate Periodontitis.

Authors: Nagihan Bostanci; Kai Bao; Xiaofei Li; Tomoki Maekawa; Jonas Grossmann; Christian Panse; Ruel A Briones; Ranillo R G Resuello; Joel V Tuplano; Cristina A G Garcia; Edimara S Reis; John D Lambris; George Hajishengallis
Journal: J Proteome Res Date: 2018-08-29 Impact factor: 4.466

Review 6. Genomic, proteomic, and systems biology approaches in biomarker discovery for multiple sclerosis.

Authors: Carol Chase Huizar; Itay Raphael; Thomas G Forsthuber
Journal: Cell Immunol Date: 2020-09-20 Impact factor: 4.868

Review 7. Illuminating the kinome: Visualizing real-time kinase activity in biological systems using genetically encoded fluorescent protein-based biosensors.

Authors: Danielle L Schmitt; Sohum Mehta; Jin Zhang
Journal: Curr Opin Chem Biol Date: 2020-01-03 Impact factor: 8.822