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PXD000955

PXD000955 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleHighly accurate protein complex retrieval by affinity enrichment MS rather than affinity purification MS
DescriptionProtein-protein interactions are fundamental to the understanding of biological processes. Affinity purification coupled to mass spectrometry (AP-MS) is one of the most promising methods for their investigation. Previously, complexes were purified as much as possible, frequently followed by identification of individual gel bands. However, today mass spectrometers are highly sensitive, and powerful quantitative proteomics strategies are available to distinguish true interactors from background binders. Here we describe a high performance affinity enrichment-mass spectrometry (AE-MS) method for investigating protein-protein interactions, in which no attempt at purifying complexes to homogeneity is made. Instead, we developed analysis methods that take advantage of specific enrichment of interactors in the context of a large amount of unspecific background binders. We perform single-step affinity enrichment of endogenously expressed GFP-tagged proteins and their interactors in budding yeast, followed by single-run, intensity-based label-free quantitative LC-MS/MS analysis. Each pull-down contains around 2000 background binders, which are reinterpreted from troubling contaminants to crucial elements in a novel data analysis strategy. Firstly, the background serves for accurate normalization. Secondly, interacting proteins are not identified by comparison to a single untagged control strain, but instead to the other tagged strains. Thirdly, potential interactors are further validated by their intensity profiles across all samples. We demonstrate the power of our AE-MS method using several well-known and challenging yeast complexes of various abundances. AE-MS is not only highly efficient and robust, but also cost effective, broadly applicable and feasible to perform in any laboratory.
HostingRepositoryPRIDE
AnnounceDate2015-03-26
AnnouncementXMLSubmission_2015-03-26_04:46:38.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterMario Oroshi
SpeciesList scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationListNo PTMs are included in the dataset
InstrumentLTQ Orbitrap
Dataset History
RevisionDatetimeStatusChangeLog Entry
02014-05-06 07:45:54ID requested
12015-03-26 04:46:39announced
Publication List
Keilhauer EC, Hein MY, Mann M, Accurate protein complex retrieval by affinity enrichment mass spectrometry (AE-MS) rather than affinity purification mass spectrometry (AP-MS). Mol Cell Proteomics, 14(1):120-35(2015) [pubmed]
Keyword List
curator keyword: Technical
submitter keyword: Yeast, interaction proteomics, AP-MS, AE-MS, label-free quantification
Contact List
Matthias Mann
contact affiliationDepartment of Proteomics and Signal Transduction Max Planck Institute of Biochemistry Germany
contact emailmmann@biochem.mpg.de
lab head
Mario Oroshi
contact affiliationProteomics
contact emailoroshi@biochem.mpg.de
dataset submitter
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Dataset FTP location
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