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Genetic
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Knockout or knockdown cells/tissues
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Antibody of interest
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Antibody-based method of choice
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Orthogonal
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Several samples
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Antibody of interest
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Correlation between antibody-based and antibody-independent assays
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Independent antibodies
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Lysate or tissue with target protein
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Several independent antibodies with different epitopes
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Specificity analysis through comparative and quantitative analysis
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Tagged proteins
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Lysate or tissue containing tagged and native protein
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Anti-tag antibody compared with antibody of interest
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Correlating the signal from the tagged and non-tagged proteins
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Immunocapture followed by MS
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Lysate containing protein of interest
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Antibody of interest
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Target immunocapture and mass spectrometry of target and potential binding partners
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