Analysis of fractionated samples in TransOmics™ Informatics is a 2-step process:
Let's look at these in a little more detail with a simple example.
For illustrative purposes, let's consider an experiment in which gel fractionation has been used. In the experiment, protein expression in 3 subjects treated with a novel drug is being compared against expression in 3 control subjects. In an attempt to increase peptide coverage, each sample is electrophoretically fractionated in a 1D gel, producing 4 gel slices for each sample:
(In the simplified diagram above, the red lines indicate where the gel is sliced to produce the fractions. In reality, you may choose to slice between bands, but for this example, all fractions are of an equal size.)
Consequently, we'll end up with 4 runs for each sample, giving us a total of 24 sample runs going through our LC‑MS machine.
Once we have collected the run data, we'll need to create 4 separate experiments in TransOmics™ Informatics, using the runs as shown here:
1st experiment:
2nd experiment:
3rd experiment:
4th experiment:
We'll refer to these experiments as our single-fraction experiments. To create each of the single-fraction experiments, you can do either of the following in the TransOmics™ Informatics start-up screen:
Those buttons are exactly equivalent; a new experiment is created and can be analysed in the standard TransOmics™ Informatics workflow (as described in the online tutorial). Which button you use is a matter of preference. Note, however, that the Perform analysis tab has the benefit of also listing all of your recently-used single-fraction experiments, helping you to keep track of your progress in analysing them.
When all single-fraction experiments have been fully analysed — including identification of proteins and the resolution of any peptide conflicts — we can recombine all our of protein information in one multi-fraction experiment.
Again, from the TransOmics™ Informatics start-up screen, select the Combine analysed fractions tab. Now, click the Recombine analysed fractions button at the left of the screen. This creates a new multi-fraction experiment and activates the Import Data screen at the start of the fractionation workflow:
From here, it's a simple matter of:
The Review Proteins then gives you the tools to explore the statistics and protein behaviour for the whole experiment.