Chromatography Forum

Hi,

I hope I posted this topic on the right board if not please move it appropriatelly.

I have just recently started to work with Waters' LC and MS equipment. Prior to that I was basically using Thermo and Agilent systems, so I am not very familliar with the Waters' software and hardware and would like to ask for some help.

I am supposed to work on a Quattro Premier MS system and I have been trying to develop MS and MS/MS tune methods but I am having a very hard time understanding the meaning and effects of most of the tune parameters in the MassLynx MS tune window. I went through all the MassLynx and Quattro Premier manuals which I could find but none of them explains in detail what each and every parameter stands for, they just state the parameter value limits, which I find very frustrating and not useful at all.

Can someone please help me understand (explain) what I am doing when changing these parameters? Or maybe direct me to some literature so I can find the answers for myself.

The parameters in which I am interested in primarily are:

1) in the ES+ source tab:
- Voltages
i) Capillary (ok, this one I actually know it regulates the ionization and formation of the Taylor cone)
ii) Cone (?)
iii) Extractor (?)
iv) RF Lens (?)
- temperatures
i) Source temp (cone temp?)
ii) Desolvation Temp (temp of the ESI probe?)
- Gas Flow
i) Desolvation (nebulization?)
ii) Cone (?)

2) in the Analyser tab:
i) LM Resolution 1
ii) HM Resolution 1
iii) Ion Energy 1
iv) Entrance
v) Collision
vi) Exit
vii) LM Resolution 2
viii) HM Resolution 2
vix) Ion Energy 2
x) Multiplier (I am guessing the voltage in the detector multiplier?)

I would really appreciate it if someone could help me out since I feel like I am flying blind here.

Thanks!
A

I am working from my experience with a Quattro Micro, but my understanding is that the systems are pretty similar. We're running food pesticides, so that gives you an idea of the type of compounds


Capillary

The voltage applied to the ESI capillary. Typical values are between 3.0 and 3.5 kV, rarely go over 3.5

Cone (?)
Voltage applied to the skimmer (entrance or outer) cone. We run between 10 and 30 V typically. VERY compound dependent

iii) Extractor (?)

This is the voltage applied to the inner cone. I typically leave this around 3-4 V

iv) RF Lens (?)

Hexapole. Typically we run 0 or 0.2 V, compound dependent.

- temperatures
i) Source temp (cone temp?)

MS source temp. I set to to 120 and leave it.

ii) Desolvation Temp (temp of the ESI probe?)

Yes. Don't run it above 380 - overtemp can shut your system down. We normally run around 350

- Gas Flow
i) Desolvation (nebulization?)

Yes - typically I run 550 - 600 L/h

ii) Cone (?)

Sweep gas flow, runs 20-50 L/h

2) in the Analyser tab:
i) LM Resolution 1
ii) HM Resolution 1
iii) Ion Energy 1

Peak width and resolution settings for front quad (M1). You tune it and you can pretty much leave this alone. Very stable.

iv) Entrance

Entrance to M2 (collision cell)

I use 20 and normally don't change it

v) Collision

Drift voltage for collision cell. Compound dependent, typically runs 10-20 V

vi) Exit

Exit from collision cell, entrance to Quad 3 (M2). I set it to 20 and normally don't change it.

vii) LM Resolution 2
viii) HM Resolution 2
vix) Ion Energy 2

Peak width and resolution settings for rear quad (M2). You tune it and you can pretty much leave this alone. Very stable.

x) Multiplier (I am guessing the voltage in the detector multiplier?)

Photomultiplier voltage. I run my system at 600 V. Haven't seen much gain in signal by running it higher, so I keep it low to conserve the PM life.

Cone (?)
Voltage applied to the skimmer (entrance or outer) cone. We run between 10 and 30 V typically. VERY compound dependent

iii) Extractor (?)

This is the voltage applied to the inner cone. I typically leave this around 3-4 V

i) Source temp (cone temp?)

MS source temp. I set to to 120 and leave it.

2) in the Analyser tab:
i) LM Resolution 1
ii) HM Resolution 1
iii) Ion Energy 1

Peak width and resolution settings for front quad (M1). You tune it and you can pretty much leave this alone. Very stable.

iv) Entrance

Entrance to M2 (collision cell)

I use 20 and normally don't change it

vi) Exit

Exit from collision cell, entrance to Quad 3 (M2). I set it to 20 and normally don't change it.

Thank you for your explanations, things are more clear now. However, there are still some things that are bugging me which are more of a theoretical nature:

1) do the cone and extractor voltages serve basically as ion optics to guide (and accelerate) ions? You say that these parameters are very compound dependent, so what happens for instance if you choose a too high of a value? I know that your signal will drop but due to what? In-source fragmentation?

2) Source temp: so this is the temperature of the whole source (cone, extractor, ion block, etc.) which basically ends where hexapole starts? Is the meaning of this temperature to make sure that there is no condensation happening inside the source?

3) Do you leave the Source temp at 120 also when the system is in standby?

4) LM and HM resolution are then the parameters to make a compromise between the resolution and sensitivity? And what exactly is ion beam? I don't understand this term.

5) Are Entrance and Exit voltages again just plain ion optics?

6) Do you switch the collision gas off when you are not doing MS/MS or do you leave it on and bring it down to a minimum value?

Thanks!
Alen

Hi Alen,

I see you haven't had answers to your second set of questions for a while so I thought I would try to help out.

1) Setting the cone voltage above 50V will start to induce in-source fragmentation dependant on the nature of the molecule. I use a method for Lipid detection that uses 90V which fragments the lipids very efficiently. As regards the extractor cone I don't see a significant difference between compounds and usually just leave this set to 3-4.

2) Yes

3) I have an end of run method which drops the source temp to 80 deg, but always upload a standard run tunepage 10-15 min before the start to bring everyhting back up to temp.

4) Re L/HM.....Yes. The Ion Beam is just the term given to the flow of focussed ions through the MS

5) Yes. I would change these according to whether you are performing SIM (50 for both) or MRM (2 ent, 3 exit).

6) Swtich it off

Hope this helps

@Mhanley
Thank you very much for the detailed explanation. Again, things are much more clear. I always get confused since every MS manufacturer uses a different term for practically one and the same thing.

However, I still don't get the ion beam setting. My logic tells me the bigger the ion beam the higher sensitivity you get, so why not always max out ion beam 1 & 2?

Cheers
Alen

I leave my collision gas on; the valve is really poor and I find that if I leave it on I get more reproducible areas (thus more stable collision gas flow). Note that it automatically turns itself off for single quad mode.

I leave the source set to 120, even in standby. It seems to go longer between cleanings.

Entrance and exit voltages are ion optics, but you are dealing at the exit with a different ion (post-collision). You can see some enhancement by playing with it, but I've never gotten enough enhancement to worry about it.

Your primary tuning voltages are the skimmer cone and the collision cell voltage, with of course the capillary voltage. For thermally labile compounds you might need to drop the ESI temperature down (desolvation) and/or drop the capillary voltage down for readily ionized compounds.

I have one primary set of parameters that I use for most compounds. I use 325 C desolvation, 550 L/h gas flow, 3.5 KV capillary, 120 source, entrance/exit 20 V and 3V extractor. I then optimize each compound using the collision voltage and the cone voltage; this makes optimization more efficient. I use an actual injection into eluant (no column) in order to optimize as I find this much more consistent with actual injections than the syringe feed.