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Predicting direct protein interactions from affinity purification mass spectrometry data

Ethan DH Kim, Ashish Sabharwal, Adrian R Vetta, Mathieu Blanchette
2010 Algorithms for Molecular Biology  
Affinity purification followed by mass spectrometry identification (AP-MS) is an increasingly popular approach to observe protein-protein interactions (PPI) in vivo.  ...  Then the algorithm is used to predict direct interactions from a set of AP-MS PPI data from yeast, and its performance is measured against a high-quality interaction dataset.  ...  The leading technologies for identifying PPIs are Yeast 2-Hybrid (Y2H) [1, 2] and Affinity Purification followed by Mass Spectrometry (AP-MS) [3] [4] [5] [6] .  ... 
doi:10.1186/1748-7188-5-34 pmid:21034440 pmcid:PMC2991326 fatcat:2gqwx4uobfgerhnwglkfqvergi

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

Nevan J. Krogan, Gerard Cagney, Haiyuan Yu, Gouqing Zhong, Xinghua Guo, Alexandr Ignatchenko, Joyce Li, Shuye Pu, Nira Datta, Aaron P. Tikuisis, Thanuja Punna, José M. Peregrín-Alvarez (+41 others)
2006 Nature  
Among 4,087 different proteins identified with high confidence by mass spectrometry from 2,357 successful purifications, our core data set (median precision of 0.69) comprises 7,123 protein-protein interactions  ...  Other efforts were made to catalogue physical interactions among yeast proteins, primarily using the yeast two-hybrid method 11,12 and direct purification via affinity tags 13,14 ; many of these interactions  ...  studies of yeast complexes using affinity purification and mass spectrometry (Fig. 3a) .  ... 
doi:10.1038/nature04670 pmid:16554755 fatcat:rucsmvajvzfifc274574hfdhca

Navigating the Deubiquitinating Proteome with a CompPASS

Peter K. Jackson
2009 Cell  
These interacting proteins are cleaved into small fragments by trypsin, and duplicate samples from the purification are analyzed by liquid chromatography followed by tandem mass spectrometry (LC-MS/MS)  ...  With this standard single-epitope tag affinity purification scheme, substantial nonspecific interacting proteins are also isolated.  ...  to find high-confidence interaction proteins of DUBs from mass spectrometry data is systematic and unbiased.  ... 
doi:10.1016/j.cell.2009.07.008 pmid:19632171 fatcat:bf6rd27cz5do7ntw6qvh2zld6e

Mapping the human protein interactome

Daniel Figeys
2008 Cell Research  
In recent years, the mapping of protein-protein interactions in different species has been reported, but few reports have focused on the large-scale mapping of protein-protein interactions in human.  ...  Here, we review the developments in protein interaction mapping and we discuss issues and strategies for the mapping of the human protein interactome.  ...  purification/mass spectrometry data (direct and indirect interactions).  ... 
doi:10.1038/cr.2008.72 pmid:18574500 fatcat:ge5uf5okcba35n64ra4j7642p4

Mass spectrometry–based functional proteomics: from molecular machines to protein networks

Thomas Köcher, Giulio Superti-Furga
2007 Nature Methods  
Bioinformatics tools can use existing protein-protein interaction data sets from the literature, binding prediction and structural considerations to compose a possible interaction diagram for each complex  ...  (iv) the capturing of endogenous complexes from native cells and tissues, (v) the integration of mass spectrometry-based data sets with the data sets from binary interaction screens, localization studies  ... 
doi:10.1038/nmeth1093 pmid:17901870 fatcat:ysutotn5orgi3hsaz55lg4c67m

Spotlite: Web Application and Augmented Algorithms for Predicting Co-Complexed Proteins from Affinity Purification – Mass Spectrometry Data

Dennis Goldfarb, Bridgid E. Hast, Wei Wang, Michael B. Major
2014 Journal of Proteome Research  
Protein-protein interactions defined by affinity purification and mass spectrometry (APMS) approaches suffer from high false discovery rates.  ...  Additionally, we developed novel mathematical models to include a variety of indirect data, such as mRNA co-expression, gene ontologies and homologous protein interactions as features within the classification  ...  Sowa, Alexey Nesvizhskii, Hyungwon Choi, Jun Qin and Anna Malovannaya for kindly providing APMS data in a format suitable for use in Spotlite.  ... 
doi:10.1021/pr5008416 pmid:25300367 pmcid:PMC4360886 fatcat:spkcu7jahvecpcd77ykyle7hsi

Driving integrative structural modeling with serial capture affinity purification

Xingyu Liu, Ying Zhang, Zhihui Wen, Yan Hao, Charles A. S. Banks, Jeffrey J. Lange, Brian D. Slaughter, Jay R. Unruh, Laurence Florens, Susan M. Abmayr, Jerry L. Workman, Michael P. Washburn
2020 Proceedings of the National Academy of Sciences of the United States of America  
Our approach combines serial affinity purification, live cell imaging, and cross-linking mass spectrometry to build integrative structural models of protein complexes.  ...  Here we describe serial capture affinity purification (SCAP), in which two separate proteins are tagged with either the HaloTag or the SNAP-tag, permitting a multistep affinity enrichment of specific protein  ...  Here we describe serial capture affinity purification (SCAP), which can be used for the study of protein interactions in live cells and, when combined with cross-linking mass spectrometry, contribute distance  ... 
doi:10.1073/pnas.2007931117 pmid:33257578 fatcat:5hlqxgela5bkviwp3hydis2ozi

Mass Spectrometry-Based Proteomics to Study Protein Complexes in Legume-Rhizobium Symbiosis

Uma K Aryal
2014 MOJ Proteomics & Bioinformatics  
This large-scale protein complex data may be used as an inexpensive tool to direct future biological experiments.  ...  This review suggests a new mass spectrometry-based proteomics approach to identify protein complexes involved in legume-Rhizobium symbiosis.  ...  The yeast two hybrid system (Y2H) [8, 9] , and tandem affinity purification (TAP) and mass spectrometry (MS) [10] are the most common and widely used methods for large-scale study of protein-protein  ... 
doi:10.15406/mojpb.2014.01.00030 fatcat:mt465sycwjfprph4evggnp53tm

compleXView: a server for the interpretation of protein abundance and connectivity information to identify protein complexes

Victor Solis-Mezarino, Franz Herzog
2017 Nucleic Acids Research  
In particular, protein abundances obtained by quantitative mass spectrometry and direct protein contacts detected by crosslinking and mass spectrometry (XL-MS) provide complementary datasets for revealing  ...  Affinity-purification and mass spectrometric analysis (AP-MS) are performed on a routine basis to detect proteins assembled in complexes.  ...  Affinity purification coupled to mass spectrometry (AP-MS) is a widely used technique to detect protein interactions in biological samples.  ... 
doi:10.1093/nar/gkx411 pmid:28498958 pmcid:PMC5570167 fatcat:nimp3ubjxncyxfjgwjc2dschky

Driving Integrative Structural Modeling with Serial Capture Affinity Purification [article]

Xingyu Liu, Ying Zhang, Zhiui Wen, Yan Hao, Charles Banks, Jeffrey J Lange, Brian Slaughter, Jay Unruh, Laurence Florens, Susan Abmayr, Jerry Workman, Michael Washburn
2020 bioRxiv   pre-print
Here, we describe Serial Capture Affinity Purification (SCAP) where two separate proteins are tagged with either the HaloTag or the SNAP-tag, permitting a multi-step affinity enrichment of specific protein  ...  , live cell imaging, and cross linking mass spectrometry approach for the building of integrative structural models of protein complexes.  ...  In ProteoCellomics, protein interactions are characterized ex vivo using affinity purification and protein mass spectrometry, and in vivo using live cell imaging.  ... 
doi:10.1101/2020.04.08.032151 fatcat:wc5kxu7obvhe3nr7j37itq5mz4

Assigning Function to Yeast Proteins by Integration of Technologies

Tony R Hazbun, Lars Malmström, Scott Anderson, Beth J Graczyk, Bethany Fox, Michael Riffle, Bryan A Sundin, J.Derringer Aranda, W.Hayes McDonald, Chun-Hwei Chiu, Brian E Snydsman, Phillip Bradley (+5 others)
2003 Molecular Cell  
to right are purification and mass spectrometry, two-hybrid analysis, localization, and protein structure prediction.  ...  The large-scale protein purification and mass spectrometry analyses identified 79 (Gavin et al., 2002) and 10 (Ho et al., 2002) of the interactions.  ...  ., 2002), and References domains matching a protein family were annotated.  ... 
doi:10.1016/s1097-2765(03)00476-3 pmid:14690591 fatcat:ywo6vng2xfd7xo6hvcnr7htuqm

Untangling the protein web

Nathan Blow
2009 Nature  
Still, some researchers suggest that although affinity purification followed by mass spectrometry gives important information on how proteins interact in complexes, the approach does not reveal everything  ...  purifications -says this is where the use of mass spectrometry helps out.  ... 
doi:10.1038/460415a pmid:19606150 fatcat:4rosbfvjf5gmlil7hi5pnicf3y

Drosophila Protein interaction Map (DPiM)

K.G. Guruharsha, Robert A. Obar, Julian Mintseris, K. Aishwarya, R.T. Krishnan, K. VijayRaghavan, Spyros Artavanis-Tsakonas
2012 Fly  
We generated a large-scale resource of affinity-tagged expression-ready clones and used co-affinity purification combined with tandem mass-spectrometry to identify protein partners of nearly 5,000 Drosophila  ...  At any given point in time, thousands of proteins are interacting with other proteins inside a cell. Protein interactions can be relatively long lasting to form stable  ...  Acknowledgments This work was supported by a grant from the National Institutes of Health (NIH 5RO1HG003616) to S.A.T.  ... 
doi:10.4161/fly.22108 pmid:23222005 pmcid:PMC3519659 fatcat:olihtdety5gtnlxfkuzszu5a5a

Mammalian Electron Transferring Flavoprotein·Flavoprotein Dehydrogenase Complexes Observed by Microelectrospray Ionization-Mass Spectrometry and Surface Plasmon Resonance

Heidi M. Hoard-Fruchey, Eric Goetzman, Linda Benson, Stephen Naylor, Jerry Vockley
2004 Journal of Biological Chemistry  
Microelectrospray ionization-mass spectrometry was used to directly observe electron transferring flavopro-tein⅐flavoprotein dehydrogenase interactions.  ...  to the flavo-protein⅐electron transferring flavoprotein complex was observed, providing the first direct observation of these mammalian complexes.  ...  Microelectrospray ionization-mass spectrometry has been used to characterize noncovalent protein-protein, protein-DNA, protein-small ligand, protein-lipid, and protein-cofactor interactions (18 -24) .  ... 
doi:10.1074/jbc.m313914200 pmid:14744856 fatcat:ozpkyulrqvefxeeqzmoarzgcfe

In VivoAnalysis of Proteomes and Interactomes Using Parallel Affinity Capture (iPAC) Coupled to Mass Spectrometry

Johanna S. Rees, Nick Lowe, Irina M. Armean, John Roote, Glynnis Johnson, Emma Drummond, Helen Spriggs, Edward Ryder, Steven Russell, Daniel St Johnston, Kathryn S. Lilley
2011 Molecular & Cellular Proteomics  
1 The abbreviations used are: Y2H, yeast two-hybrid; iPAC, interactomes by parallel affinity capture; m/z, mass/charge ratio; YFP, yellow fluorescent protein; MS, Mass Spectrometry.  ...  Acknowledgments-We would like to thank Serena Tolin for assistance in the high-throughput purifications, Julie Howard and Svenja Hester for performing some LC-MS/MS. We thank J. Drummond, E.  ...  Affinity purification coupled to mass spectrometry provides a reliable method for identifying proteins and their binding partners.  ... 
doi:10.1074/mcp.m110.002386 pmid:21447707 pmcid:PMC3108830 fatcat:ewtpj7cglbflhbtelxgkicno5a
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