How can I setup a MRM analysis mode in a 6530 Qtof equipped with a AJS Dual ESI ion source?
I have only access to targeted MS/MS in Mass Hunter.
Thanks in advance
A QTOF will not do MRM in the same way that a triple quad (QQQ) would in that the TOF cannot isolate particular product ions. It always acquires data over the mass range specified in the instrument state and acquisition method. It will always give you product ion spectra of precursor ions isolated in the Quadrupole.
In my experience a QTOF makes a good quantitative instrument in MS mode. If you need specificity of fragment ion confirmation and potentially reduced noise you can use targeted MSMS mode to do quantitation on the product ions. However, if you just specify one precursor ion in the table the instrument will continuously switch between MS and MS/MS. This will result in jagged rough peaks that are difficult to integrate reproducibly.
A trick you can do is to repeat the same line multiple times in the targeted list (Maybe 20-30 or 40 times). This way the instrument will remain in MSMS mode until it has worked through all of the lines in the list. This should allow you to acquire smooth chromatograms for any of the product ions.
Set your MSMS acquisition rate to ensure you get enough points across the Chromatographic peak to ensure the peak is reliably drawn. Aim for a minimum of 12 data points (spectra) across the peak. Closer to 20 is possibly better. You can go too far and collect to fast and make your data more noisy. Faster acquisition will also reduce spectral abundance. So try to strike a balance here.
Optimise fragmentor voltage in MS mode to maximise the abundance of precursor ions of interest. Optimise collision energy to maximiase abundance of productions of interest. This will involve multiple runs first in MS mode with different fragmentor voltages then in Targeted MSMS with different collision energies. (Hint you can override these settings in the worklist table so you don't have to rewrite multiple methods to change one parameter, you may need to select hidden columns in the worklist table to do this). Other parameters can be optimised too, but these are the most important, compound specific parameters you can optimise
I would also suggest running in the 2GHz instrument state this will give best dynamic range without saturating the detector. If you are looking at small molecules with m/z below 1700 run in 1700 mode rather than 3200. The instrument will collect more transients per spectrum. This too will help with spectral abundance.
Don't set your data collection range too narrow. It will have minimal increase in sensitivity (unlike scanning instruments such as single or triple quadrupoles). It mostly influences the size of the data file. Ensure that your data acquisition range is not so narrow that you don't acquire your reference ions!
I hope this helps you get started.
Retrieving data ...