Additional scans during targeting mode?

[Ulrike Leurs]

Dear developers! 

We have recently tried the targeting function in MQ.Live and found that MQ identifies many more peptides than the ones we target in our experiment. 

Is this because MQ.Live does normal TopN scans in the idle time between targeting peptides?

Also -  are the targeting peptide lists from the paper (Figure 6B, 100, 1K, 2K, 5K, 10K, 20K and 30K peptides) available?

Thanks and best regards! 

Ulrike

[Edward Emmott]

Hi Ulrike,

This is what we seemed to find when we were trying MQ.Live on a QE classic, as you say the default behavior seens equivalent to having xcaliburs scan when idle option turned on, though there doesn't appear to be a means of turning this off (this would be a really helpful feature to add!).

Normally, you can just copy the relevant columns of the maxquant evidence.txt file. In some cases (e.g. TMT) the mass may be off and need correcting.

A link to an example targeting list of mine for TMT labelled peptides can be found here:

https://www.dropbox.com/s/lf7m40eg8oa3a1f/exampleTargListMQL.csv?dl=0

I've been generating TMT targeting lists with this matlab script:

https://github.com/edemmott/TMTtargMatlab

The software will crash if any of the empty cells contain spaces. However the order of the columns in the document you copy from doesn't matter.

Best

Ed

[Ulrike Leurs]

Hi Ed,

thanks for the prompt answer! I will check out the Matlab script :)

We did find the info about the additional TopN scans in the MQ.Live protocol under point 7.3.3:

"The TopN strategy is applied on top of the targeting scans. Note, that peptides can also be excluded from being selected a precursor by using the “ExcludeFromTopN” feature."

Now we are just in doubt whether we should exclude targeted peptides from TopN or not?

BR

Ulrike