ArticleMolecular & cellular proteomics : MCP2012
Extending the dynamic range of label-free mass spectrometric quantification of affinity purifications.
Article in Molecular & cellular proteomics : MCP, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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32 citing papers in PubMed.
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- Synaptotagmin-11 facilitates assembly of a presynaptic signaling complex in post-Golgi cargo vesicles.EMBO reports · 2024Article
- GSG1L-containing AMPA receptor complexes are defined by their spatiotemporal expression, native interactome and allosteric sites.Nature communications · 2023Article
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- A slit-diaphragm-associated protein network for dynamic control of renal filtration.Nature communications · 2022Article
- The molecular appearance of native TRPM7 channel complexes identified by high-resolution proteomics.eLife · 2021Article
- Identification of the GlialCAM interactome: the G protein-coupled receptors GPRC5B and GPR37L1 modulate megalencephalic leukoencephalopathy proteins.Human molecular genetics · 2021Article
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- Flavonol-mediated stabilization of PIN efflux complexes regulates polar auxin transport.The EMBO journal · 2021Article
- Deorphanizing FAM19A proteins as pan-neurexin ligands with an unusual biosynthetic binding mechanism.The Journal of cell biology · 2020Article
- The Phosphatase PP2A Interacts With ArnA and ArnB to Regulate the Oligomeric State and the Stability of the ArnA/B Complex.Frontiers in microbiology · 2020Article
- AMPA receptors and their minions: auxiliary proteins in AMPA receptor trafficking.Cellular and molecular life sciences : CMLS · 2019Review
- Complex formation of APP with GABANature communications · 2019Article
- Heteromeric channels formed by TRPC1, TRPC4 and TRPC5 define hippocampal synaptic transmission and working memory.The EMBO journal · 2017Article
- The two-pore channel TPC1 is required for efficient protein processing through early and recycling endosomes.Scientific reports · 2017Article
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8 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Affinity purification (AP) of protein complexes combined with LC-MS/MS analysis is the current method of choice for identification of protein-protein interactions. Their interpretation with respect to significance, specificity, and selectivity requires quantification methods coping with enrichment factors of more than 1000-fold, variable amounts of total protein, and low abundant, unlabeled samples. We used standardized samples (0.1-1000 fmol) measured on high resolution hybrid linear ion trap instruments (LTQ-FT/Orbitrap) to characterize and improve linearity and dynamic range of label-free approaches. Quantification based on spectral counts was limited by saturation and ion suppression effects with samples exceeding 100 ng of protein, depending on the instrument setup. In contrast, signal intensities of peptides (peak volumes) selected by a novel correlation-based method (TopCorr-PV) were linear over at least 4 orders of magnitude and allowed for accurate relative quantification of standard proteins spiked into a complex protein background. Application of this procedure to APs of the voltage-gated potassium channel Kv1.1 as a model membrane protein complex unambiguously identified the whole set of known interaction partners together with novel candidates. In addition to discriminating these proteins from background, we could determine efficiency, cross-reactivities, and selection biases of the used purification antibodies. The enhanced dynamic range of the developed quantification procedure appears well suited for sensitive identification of specific protein-protein interactions, detection of antibody-related artifacts, and optimization of AP conditions.
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