Clean the Ion source of LCMS

[thohry]

Hi all,
I sometimes have to clean the ESI source of 6410 and I just leave the instrument in standby. In case, I have to clean the capillary, do I have to turn off the system or just leave it in standby ?

Thanks.

[Pepter]

Hi.
There should be a thread about cappillary cleaning.
Shortly two ways:
1) Like in Agilent guide you need to switch off detector then pull the cappilary from it (would be hard to do this with "vaccum on")
2) You can do it while detector is on. Just allow cappilary to pull inside one small droplet of isopropanol and methanol.

Sorry for my english.

[Camisotro]

We have a 6460 here. In standby it still keeps the ion source heated up to a gas temp of 300 and a sheath gas temp of 125. Usually when I'm ready to do some maintenance I open up the ion source first and give it a few minutes to cool down while I attend to other tasks so it's not scalding when I get to it.

You can also unplug the ion source heaters without shutting the entire instrument off.

[Mr.Brown]

To clean the cappillary I shut down the MS

You could do the second suggestion of pepter but I would not recommend it
as you just transfer all the gunk into the ms

I usually clean with isoprop
Using a thin wire with a small loop and some cottonwool drenged in isoprop trapped in the loop

But be careful not to use to much cotton wool
You don't want to get some stuck in the cappillary

[Pepter]

To clean the cappillary I shut down the MS

You could do the second suggestion of pepter but I would not recommend it
as you just transfer all the gunk into the ms

I usually clean with isoprop
Using a thin wire with a small loop and some cottonwool drenged in isoprop trapped in the loop

But be careful not to use to much cotton wool
You don't want to get some stuck in the cappillary

Duno whats better "gunk" or this :
1) switch off ms means you need to tune it...
2) switch off ms means you waste time becuase you need to wait for detector stabilization after switching it on
3) switch off means you stop the turbo pump...every stop and run shorther life time of this expensive part
4) when you pulling cappilary out and put it back you scratch the platinum ends...
5) wire loop cottonwool ... worst idea ever you think that they write this way of cleaning because they want you to save time, cash, keep parts longer ... nah.

Its like year and few months of cleaning cappilary in different way then guide procedure. I dont have any problems
with quads. No problem with sensitivity...

[Mr.Brown]

1) switch off ms means you need to tune it...
2) switch off ms means you waste time becuase you need to wait for detector stabilization after switching it on
3) switch off means you stop the turbo pump...every stop and run shorther life time of this expensive part
4) when you pulling cappilary out and put it back you scratch the platinum ends...
5) wire loop cottonwool ... worst idea ever you think that they write this way of cleaning because they want you to save time, cash, keep parts longer ... nah.

1) tuning only takes 10 to 15 minutes
2) do it in the evening, and let it stabilize over night.
3) the turbo pump we used did not have a problem with turning of (as long as you cool it below 100°C first)
4) can't argue with that, its true , you have to be carefully
5) never had a problem, and the capillary was squeaky-clean afterwards

however I had to clean it a lot, because lots of people at the university injected awful things

[thohry]

Thank you all for the help.
Now that I can see I have another question. You said that, when ever shutting off the instrument, the tune must be re-run. Normally we do not tune after shutting off. Is that really a problem ?

[Pepter]

Thank you all for the help.
Now that I can see I have another question. You said that, when ever shutting off the instrument, the tune must be re-run. Normally we do not tune after shutting off. Is that really a problem ?

You tune machine to be sure that your detector is calibrated properly and mass indication is good. When you switching of detector you "destabilizate" it additionally during some maintance you can affect ionization area/ions pathway etc.

[thohry]

Thank you all for the help.
Now that I can see I have another question. You said that, when ever shutting off the instrument, the tune must be re-run. Normally we do not tune after shutting off. Is that really a problem ?

You tune machine to be sure that your detector is calibrated properly and mass indication is good. When you switching of detector you "destabilizate" it additionally during some maintance you can affect ionization area/ions pathway etc.

You mean even when the power is off, and on again (because of the lines) and I still have to tune the instrument ?

[Camisotro]

It's mainly about mass accuracy. So if you shut down the system so completely that the QQQ heaters or vacuum goes offline for more than a few minutes, you will want to run a check tune after it's back up. If you have only taken the ion source offline, you don't need to tune for mass accuracy.

Remember this is an atmospheric pressure ion source. You don't need to turn off the whole rest of the system just to clean the ion source.

[Pepter]

Thank you all for the help.
Now that I can see I have another question. You said that, when ever shutting off the instrument, the tune must be re-run. Normally we do not tune after shutting off. Is that really a problem ?

You tune machine to be sure that your detector is calibrated properly and mass indication is good. When you switching of detector you "destabilizate" it additionally during some maintance you can affect ionization area/ions pathway etc.

You mean even when the power is off, and on again (because of the lines) and I still have to tune the instrument ?

Depends what you do. Here is what we do in our lab
1) reseting detector mainboard (power off/on) - dont run checktune/autotune
2) ionsource clearing - i start with background ion reading in manual tune window, than i check the reading of tune mix if iam not
sure of proper mass reading i run checktune
3) switching off detector (turbopump speed 0%, temp below 100 C) - i run autotune

[shemesh199]

Cleaning the ion source and accessing the ion transfer capillary are two seperate things, for the cleaning of the spray chamber, simply lower the source temperature in the method file to 0 ( will take about 10 minutes to cool down to a reasonable range), then put the instrument in standby and open and clean the spray chamber.

For the ion transfer capillary, you have to vent the system.

Agilent has a new cleaning solution apart from using the wire and cotton technique.

Simply follow the instructions for cleaning the ion transfer capillary, its a simple wash procedure, you use the alconox detergent i believe and perform a set of sonications in this detergent as well as di water.

The advice I can give is to be gentle when taking the capillary in or out, you dont want to damage the 1500$ delicate item.

Also, even more important, remember that things are easy to take off, make sure you remember how to put things back the way they were

After the cleaning, pump down, and after an overnight stabilization of the system, your tune abundances should look awesome!

Best of luck.

[thohry]

Cleaning the ion source and accessing the ion transfer capillary are two seperate things, for the cleaning of the spray chamber, simply lower the source temperature in the method file to 0 ( will take about 10 minutes to cool down to a reasonable range), then put the instrument in standby and open and clean the spray chamber.

For the ion transfer capillary, you have to vent the system.

Agilent has a new cleaning solution apart from using the wire and cotton technique.

Simply follow the instructions for cleaning the ion transfer capillary, its a simple wash procedure, you use the alconox detergent i believe and perform a set of sonications in this detergent as well as di water.

The advice I can give is to be gentle when taking the capillary in or out, you dont want to damage the 1500$ delicate item.

Also, even more important, remember that things are easy to take off, make sure you remember how to put things back the way they were

After the cleaning, pump down, and after an overnight stabilization of the system, your tune abundances should look awesome!

Best of luck.

Thanks for your help.
Could you please give me the part number of the solution.
And I am not sure if the capillary can be sonicated.

[shemesh199]

You are welcome, please have a look at this procedure in detail. You can definitely sonicate, you just protect both ends using a cut (1mL pipette tip).

http://www.chem.agilent.com/Library/Sup ... laries.pdf

Best of luck my friend.