Hi guys,
Recently we tried the TOF MRM function and in the table, we have 9 chemicals in 9 channels/rows (Figure 1). then we acquired the data but found that only 4 MSMS functions/channels appeared in the data file (Figure 2) and the order is the not order in the MRM table. Also found that two or more chemicals fallen in 1 MSMS channel (such as four chemicals in Foundation 1, see Figure 1). what is going on? why did the order change?
Then we use the data to do the quantification with Targetlynx and found out that if chemicals were in two different channels, then targeting does not work (Figure 3). but if only one channel (such as the above channel 1), then it works.
Any idea?
Many thanks.
Chang'er
I use MassLynx and TargetLynx almost everyday. My guess for your first problem (Figures 1 and 2) is that you didn't use the ms file that you have shown in figure 1 when you prepared your sample table (you didn't show your sample table). Machines don't make errors, we do. Check that you have selected the ms file with 9 compounds (figure 1) when you prepared your sample table.
For your second problem, can you explain more because I can't understand exactly what did you do and got the error, and what did you do so that you didn't get the error.
I hope this was helpful.
thanks mukhtar.
i double checked that i did select the ms file in the sample list.
we have similar problems for other people project as well.
for the second problem, i mean when set chemicals from two functions (such as function 1 and function 2) or more as we do normally in the targetlynx method, then do the processes, then i got the error. but if i only set chemicals from one function (4chemicals in funcion one for example in figure 2), then do the process to quantify, then it works.
am i clear now?
thanks a million.
The functions are consecutively filled from 1 to 2,... if your first mrm is completed in function 1, the next mrm which has not started yet will be in the lowest available function, so again in function 1. I recommend to use targetlynx how you do it, because the order should be reproducable based on your set RT windows (??)
If you use DDA and One acquisition stops because a threshold of counts was set, depending on your sample the order of functions can differ. But in your case it should Work. If you Really want to have one function per mrm and do not care too much about sensitivity, monitor them throughout your run.
thanks simon, i now understand. so it is very different to the tripleQ MS.
MANY THANKS
now problem solved thanks guys.
but have another question: we have different version of masslynx, scn949 and scn950, i suppose higher version can open data from the lower version, but seem we can not open the data aquired by scn949 with scn950, we set the path of course. any idea? what should we do?
Same problem here. I expected 5 differents MSMS function and only got 3.
Changing the RADAR interval to 7 s fixed the problem.
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