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The quantification efficiency (the percentage of identified peptides assigned a confident 14N/15N ratio) was dramatically different between the samples.
The low quantification efficiency of the proteins from the brain analysis suggests that a 15N liver peptide for the corresponding 14N brain peptide was absent or below the limit of detection of the mass spectrometer.
The quantification efficiency for unmodified peptides was 56.3% and 84.0% for the brain and liver, respectively, suggesting it is indeed the choice of internal standard and not restricted to the phosphopeptide analysis (Figure 3A).
Alignment and quantification efficiency are important aspects to take into consideration when using an automated analysis pipeline.
In the past several years, solution-based or gel-free technologies on the membrane proteome have gained popularity due to their excellent proteome sensitivity and rapid quantification efficiency (Hooker et al., 2008; Poetsch & Wolters, 2008; Weiner & Li, 2008).
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Gene delivery in combination with molecular imaging and targeting enables diagnostic assessment, treatment monitoring and quantification of efficiency, and confirmation of cure, thus fulfilling the great promise of efficient and personalized medicine.
Relative quantification (with efficiency correction) of gene transcription was carried out with the software included in the LightCycler480 package.
In our evaluation of extraction and matrix effects on GMO quantification, PCR efficiency was identified as the primary parameter that determines the suitability of the DNA for quantitative analysis.
For quantification and efficiency calculations, diluted standards were used and the CT (cycle threshold) values were plotted against the log of given templates to obtain standard graphs as described in Bustin et al. (2009).
For accurate quantification, the efficiency of the PCR (i.e. the actual fold increase in amplicon accumulation for each round of amplification) was determined by constructing a standard curve, and the samples assayed contained an amount of target that was within the region of the standard curve for which the efficiency could be accurately determined.
Together with the amount of DNA needed for reliable quantification, PCR efficiency is the crucial parameter determining the reliability of quantitative results, therefore it was chosen as the primary criterion by which to evaluate the quality and performance on different matrixes and extraction techniques.
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