How to set Dual AJS ESI and TOF Parameters for non-target measurements?

Dear Dawn,

Thank you very much for your fast response and detailed explanation.

For me there are some unclear points remaining.

1) In Ref Mass tab: Does the detection window parameter influence much.

2) If I understand correctly a nozzle voltage helps creating droplets. So a value of 0 should be very bad. I will set it 1000 but is there a easy logic how to choose this value?

Kind regards

In terms of reference mass- you need to know first if you will be running in positive or negative ion mode and what your intended mass range is going to be.  I would assume small molecules meaning you will collect from around 100 to 1000 m/z.  In this case, a good choice would be to use purine and HP-0921 in your reference mix (bottle A).  You will need to make sure your bottle A is filled with this reference solution that can be purchased as a kit with ampoules.  In positive ion mode purine will make the 121.0508 ion and HP-0921 will make the 922.0098 ion.  If you intend to work in negative ion mode, you can also use these two compounds for reference and purine will form a M-H species however you will need to form a formate or acetate ion of HP-0921 in negative ion mode (many mobile phases will have either formic acid or acetate in it to help you form this ion with no need to add anything additional into the reference bottle).  Also, the help menu in masshunter acquisition has good information on reference solutions (search for reference mix in the help).

For your source parameters, you may want to set these fairly generic as you are not necessarily targeted in your analysis.  Many people have developed a set of parameters that they like to start with so there will not necessarily be one correct answer to this and you may choose to refine these settings over time.  I like to start with a drying gas temperature of 325C, drying gas flow of 10L/min (do not lower this one too much as you can dirty your entrance capillary), nebulizer should be ok around 25-35 psig for your flow rate, sheath temperature of 275C, sheath flow of 12L/min, nozzle 1000V, capillary voltage of 3500-4500 (lower this around 500V if you run in negative ion mode) and fragmentor around 150V (this one needs to be increased as the mass of your unknowns in your sample increase- if you are analyzing less than 200Da I would lower this from my suggested starting point).  For your application, I would not change the skimmer or OCT RF from the default setting.  Try loading the default.m method to double check these defaults as I think the values you have them set to now are for older style ion optics (6210 and 6220 TOFs).

For your acquisition parameters, you could chose to narrow your mass range to 100 to 1000 m/z which is more typical for small molecule analysis (remember not to cut off your reference mass around 922 though by going below it).  For the acquisition rate, consider what your typical chromatographic peak width would be.  I'm not sure the chromatography you will be using but most people will have peak widths around 6-12 seconds wide.  If you consider on the narrower side being 6 seconds, the acquisition rate of 2.5 spectra/sec will give you 15 points across your peak which is ideal. 

You're very welcome. 

To answer your remaining questions . . .

1.  The detection window of 100ppm and 1000 counts means the instrument has to see each reference ion within 100 ppm of it's theoretical exact mass and at least 1000 counts.  If you can't detect the reference ions within 100 ppm- it could be that the TOF was not calibrated recently enough (this should be performed every day you intend to run samples on the TOF) or in some cases it could be that it is picking up a small background interference which can occasionally happen for purine.  If you don't have at least 1000 counts of reference ion, you should first check that reference solution is coming out of the reference nebulizer (about 1 drop every 8-10 seconds) and if it is following ok then you can consider increasing the concentration of those reference ions in bottle A.  You should not be in the habit of increasing the 100ppm or decreasing the 1000 counts in order to detect reference as you could be referencing off the wrong ion. 

2.  Before the jet stream, the nebulizer could be easily seen when you opened the source however now it is enclosed in that "nozzle."  Nozzle voltage can be thought of as an extraction voltage and is compound dependent.  A value of zero is ok to use and you will see many references where the nozzle is set anywhere from 0 up to 2000.  I typically will choose 1000V when I don't know specifically where to set it because there could be many compounds of interest (not all in the same class of compounds either) in my sample just as is your situation.  If you get into a situation where you have a class of compounds or one specific compound that you need to optimize the source towards to get the best sensitivity, this is where you would optimize this nozzle voltage (typically will be done from 0 to 2000V in increments of 500V).  

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