Journal ArticleDOI
Native mass spectrometry: a bridge between interactomics and structural biology.
TLDR
The current state of native mass spectrometry technology is reviewed and several important biological applications are discussed, including high-throughput interactomics studies and current experimental challenges.Abstract:
Native mass spectrometry is an emerging technology that allows the topological investigation of intact protein complexes with high sensitivity and a theoretically unrestricted mass range. This unique tool provides complementary information to established technologies in structural biology, and also provides a link to high-throughput interactomics studies, which do not generate information on exact protein complex-composition, structure or dynamics. Here I review the current state of native mass spectrometry technology and discuss several important biological applications. I also describe current experimental challenges in native mass spectrometry, encouraging readers to contribute to solutions.read more
Citations
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Journal ArticleDOI
Protein Analysis by Shotgun/Bottom-up Proteomics
TL;DR: The progress of proteomics has been driven by the development of new technologies for peptide/protein separation, mass spectrometry analysis, isotope labeling for quantification, and bioinformatics data analysis.
Journal ArticleDOI
The power of ion mobility-mass spectrometry for structural characterization and the study of conformational dynamics
Francesco Lanucara,Stephen W. Holman,Stephen W. Holman,Christopher J. Gray,Claire E. Eyers,Claire E. Eyers +5 more
TL;DR: Ion mobility-mass spectrometry can be used to gain insights into the conformational dynamics of a system, offering a unique means of characterizing flexibility and folding mechanisms.
Journal ArticleDOI
Towards single-molecule nanomechanical mass spectrometry
Akshay Naik,Mehmet Selim Hanay,Wayne K. Hiebert,Wayne K. Hiebert,X. L. Feng,Michael L. Roukes +5 more
TL;DR: In this article, a nanoelectromechanical-based mass spectrometer was used for the detection of individual molecular species in real-time with a few to single molecules.
Journal ArticleDOI
Next-generation proteomics: towards an integrative view of proteome dynamics
TL;DR: MS-based proteomics is starting to mature and to deliver through a combination of developments in instrumentation, sample preparation and computational analysis, and to highlight recent applications.
Journal ArticleDOI
Bayesian deconvolution of mass and ion mobility spectra: from binary interactions to polydisperse ensembles.
Michael T. Marty,Andrew Baldwin,Erik G. Marklund,Georg K. A. Hochberg,Justin L. P. Benesch,Carol V. Robinson +5 more
TL;DR: UniDec (Universal Deconvolution), software that provides a rapid, robust, and flexible deconvolution of mass spectra and ion mobility-mass spectra with minimal user intervention is developed, using systems of increasing complexity.
References
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The Structure of the Potassium Channel: Molecular Basis of K+ Conduction and Selectivity
Declan A. Doyle,João H.Morais Cabral,Richard A. Pfuetzner,Anling Kuo,Jacqueline M. Gulbis,Steven L. Cohen,Brian T. Chait,Roderick MacKinnon +7 more
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Journal ArticleDOI
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
Nevan J. Krogan,Gerard Cagney,Gerard Cagney,Haiyuan Yu,Gouqing Zhong,Xinghua Guo,Alexandr Ignatchenko,Joyce Li,Shuye Pu,Nira Datta,Aaron Tikuisis,Thanuja Punna,José M. Peregrín-Alvarez,Michael Shales,Xin Zhang,Michael Davey,Mark D. Robinson,Alberto Paccanaro,James E. Bray,Anthony Sheung,Bryan Beattie,Dawn Richards,Veronica Canadien,Atanas Iliev Lalev,Frank Mena,Peter D Wong,Andrei Starostine,Myra M. Canete,James Vlasblom,Samuel Wu,Chris Orsi,Sean R. Collins,Shamanta Chandran,Robin Haw,Jennifer J. Rilstone,Kiran Gandi,Natalie J. Thompson,Gabe Musso,Peter St Onge,Shaun Ghanny,Mandy H. Y. Lam,Gareth Butland,Amin M. Altaf-Ul,Shigehiko Kanaya,Ali Shilatifard,Erin K. O'Shea,Jonathan S. Weissman,C. James Ingles,Timothy P. Hughes,John Parkinson,Mark Gerstein,Shoshana J. Wodak,Andrew Emili,Jack Greenblatt +53 more
TL;DR: T tandem affinity purification was used to process 4,562 different tagged proteins of the yeast Saccharomyces cerevisiae to identify protein–protein interactions, which will help future studies on individual proteins as well as functional genomics and systems biology.
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A generic protein purification method for protein complex characterization and proteome exploration.
Guillaume Rigaut,Anna Shevchenko,Berthold Rutz,Matthias Wilm,Matthias Mann,Bertrand Séraphin +5 more
TL;DR: A generic procedure to purify proteins expressed at their natural level under native conditions using a novel tandem affinity purification (TAP) tag and Combined with mass spectrometry, the TAP strategy allows for the identification of proteins interacting with a given target protein.
Journal ArticleDOI
Proteome survey reveals modularity of the yeast cell machinery
Anne-Claude Gavin,Patrick Aloy,Paola Grandi,Roland Krause,Markus Boesche,Martina Marzioch,Christina Rau,Lars Juhl Jensen,Sonja Bastuck,Birgit Dümpelfeld,Angela Edelmann,Marie-Anne Heurtier,Verena Hoffman,Christian Hoefert,Karin Klein,Manuela Hudak,Anne-Marie Michon,Malgorzata Schelder,Markus Schirle,Marita Remor,Tatjana Rudi,Sean D. Hooper,Andreas Bauer,Tewis Bouwmeester,Georg Casari,Gerard Drewes,Gitte Neubauer,Jens Rick,Bernhard Kuster,Peer Bork,Robert B. Russell,Giulio Superti-Furga +31 more
TL;DR: This study reports the first genome-wide screen for complexes in an organism, budding yeast, using affinity purification and mass spectrometry and provides the largest collection of physically determined eukaryotic cellular machines so far and a platform for biological data integration and modelling.
Journal ArticleDOI
A human protein-protein interaction network : a resource for annotating the proteome
Ulrich Stelzl,Uwe Worm,Maciej Lalowski,Christian Haenig,Felix H. Brembeck,Heike Goehler,Martin Stroedicke,Martina Zenkner,Anke Schoenherr,Susanne Koeppen,Jan Timm,Sascha Mintzlaff,Claudia Abraham,Nicole Bock,Silvia Kietzmann,Astrid Goedde,Engin Toksöz,Anja Droege,Sylvia Krobitsch,Bernhard Korn,Walter Birchmeier,Hans Lehrach,Erich E. Wanker +22 more
TL;DR: A large, highly connected network of interacting pairs of human proteins was identified, characterizing ANP32A and CRMP1 as modulators of Wnt signaling and two novel Axin-1 interactions were validated experimentally.