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Although targeted proteomics methods can be applied to the quantification of many biological samples, accurate and precise proteomic profiling with many biological replicates remain challenging.
An interesting approach is represented by the expression of QconCATs of tryptic standard peptides (Beynon et al., 2005), which has proven useful and highly cost efficient when many biological replicates are to be studied.
In a setting with many biological replicates per level (e.g. comparison of two large groups) the differences in correlation between the ratio-based and intensity-based analysis are likely to be smaller.
In this case the scale of the deep proteome experiment and huge volume of instrument and analysis time involved simply precludes it being done with many biological replicates, given current technology.
Since we were interested only in the presence/absence of the transgenic proteins, we did not use formal replicates, but extracted proteins from each of at least four different positive lines obtained from transformation with each of the three transgenes, and compared to as many biological replicates of the null segregant.
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However, if the experiments involve a common reference sample, which is not of biological interest and the goal is to identify gene expression differences between two groups (both of which are co-hybridized again the common reference), using twice as many independent biological replicates is preferable to dye swapped technical replicates.
These experiments, however, require many technical and biological replicates to account for run-to-run variability.
Thus, in combination with profiling of as many as six individual biological replicates from each phenotypic group, our array results validated by qPCR experiments undoubtedly identified genuine miRNA expression differences in the pancreatic islets of the two sets of animals.
However, in additional biological replicates many of these could not be confirmed.
Moreover variation across technical replicates is likely to be lower than that typically observed across true biological replicates, and many biological effects of interest may be smaller than two-fold [12].
The meaning of the error bars is not indicated as well as whether they represent technical or biological replicates and how many.
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