Tutorial
 
 
CONDITION : PRACTICAL
Sometimes you want to compare peaklists from samples run under different circumstances.
This could be different time-points, difference concentrations of a key reagent, different temperatures etc..

In MassAI you can assign conditions to each of your MGF files, or to a group of these.
 
In the case below, we investigated the difference in results according to three different mass spectrometers, with four mgf files for each
instrument.

After selecting the files, we simply type in a set of conditions for each group. This way we can bundle triplicates (or in this case,
quadruplicates) run under the same conditions together. 
The result output displays the condition for the original sample, along with the result data
When you work with cross-linking, the different conditions also reflect on the result output.

Below you see the standard "heatmap" output of cross-links. You have one set of reactive residues along the top X-axis and the other set
along the vertical left axis. The individual cells are populate with the number of observations above your selected cutoff score, and you can
click any cell to view the annotated scans.

The "heatmap by conditions" tab shows another way to present the cross-linked results
When you work with a 2D cross-link heatmap and wish to compare aginst multiple conditions, we would need to go into 3D projection of the results. This would of course be really cool, but 3D monitors tend to be on the costly side of comfortable - and most journals still print in 2D.

So, instead we collapse the cross-link into one column each (e.g. residues 64 x 276) and then use colour codes to distinguish between inter and intra-protein crosslinks (blue is intra-protein A, yellow is intra-proteinB and green is an inter-protein cross-link.

In our sample below, we have selected to view intra-calreticulin crosslinks only (CALR has been selected as both proteins A and B in the frop down list). Therefore all entries are BLUE.

We observe that most of the high-scoring results have been obtained with the Qexactive instrument, with Fusion coming in as a second - in terms of identified scans. The Velos instrument however, has picked up some cross-linked precursors that the other two instruments have not.
As always, you can click on any cell to get access to the annotated scans (here we clicked the 232x238 with 17 observations).
The entries in green are matches above the score cutoff, the ones in yellow lie below the score cutoff.
We have used the trackbar to set the score-cutoff to 25.

You can then click on any of the scans listed below to actually view the annotated scan (but you knew that already).