Specify retention time in command line transition list?

Specify retention time in command line transition list? dsullivan  2019-08-26

Hi all,

I have an experiment where I know the expected retention time for some MS1 data. Is there a way to add this information to my precursor transition list that I'm importing? Currently I'm importing something like the attached file.

There may be a totally different and better way to do this too, so please let me know if the way I have set this up does not make sense.


Brendan MacLean responded:  2019-08-29

So, you are pretending your peptides are small molecules? That may mean you can add "Explicit Retention Time" as a field name.

Otherwise, I can't think of an easy way to do this.


dsullivan responded:  2019-08-30

I guess so. Yes, it turns out I can add "Explicit Retention Time" and "Explicit Retention Time Window" to the transition list.

I would love to import the peptides as peptides, but then I have to create an entire spectral library right? Is there a better way to import a peptide list from a csv or similar? I know I can import a custom spectral library in xml, but I can't seem to find a simple way to create a custom spectral library. Any suggestions?