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Thus, the profile of differential protein expression in the lesion center was studied using the proteomic analysis.
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All transcriptome experiments were done using three independent time series for each strain (biological replicates), and two of these replicate sets of samples were used for the proteomic analysis.
The precipitated OS membrane pellet was washed twice with 100 µL of 100 mM ABC and used for the proteomic analysis described below.
This requirement eliminated majority of the samples from being used in the proteomic analysis.
Such restrictions would affect the study scope and accuracy of the coevolution approach used in the proteomic analysis of eukaryotes.
The quadrupole ion trap mass spectrometer (LTQ) used in the proteomic analysis was manufactured by Thermo (Palo Alto, CA, USA).
A total of eight adenocarcinoma and tumor-matched normal control lung tissues were used for the proteomic analysis.
For a description of the statistical approach used in the proteomic analysis see the mass spectrometry and data analysis section above.
A cohort of 24 subjects was used for the proteomic analysis, a cohort of 52 subjects for the validation phase and 56 hypertensive patients for the microalbuminuria test.
Samples used for the proteomic analysis came from B. abortus either grown extracellularly in media or isolated from infected RAW264.7 macrophages.
Subsequent washing away of all nonbinding entities (e.g., proteins, membranes, and small molecules) followed by release of all binding proteins (by, e.g., heat shock, pH shock, chaotropic agents, organic modifiers, ligand-based displacement, or tryptic digestion when a bottom-up approach is used) allows the proteomic analysis of the interactome.
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