Chromatography Forum

5971/5890 - Tuned instrument, ran DFTPP -pass. Run curve - all 8270 compound pass except hexachlorobenzene which has a primary ion of 284. The HCB is not present when you quantitate for ion 284 but is there for total ion. I zoomed in on the ion and it is showing 283.65. So i re-tuned the instrument, ran DFTPP - pass, run curve and hexachlorobenzene is present. The primary ion is 283.75 but is stable... but now pentachlorophenol is now absent. The primary ion shows 265.65. I check other ion through out the span of compounds and i will see a large majority of the mid to high 200's around .75 to .85 while ions higher and lower are more centered 0.85, 0.95 or 0.5

So here are my questions.
1. What causes ions in this range to be off center?
2. Why does chemstation set the mass range from (if ion is 266) 265.70 to 266.70? Why not 265.50 to 266.5? Is this an industry standard?

Thanks in advance

This is usually a mass-axis problem. If you're sure your vacuum is good, have no leaks, and the carrier flows are good, dip the RF. I believe the procedure is in the hardware manual or I can post it if you if you can't find it. Don't use a metal screw driver to adjust the coils. There is usually a plastic potentiometer adustment tool in the tool kit shipped with the instrument. Here's a link so you can see what it looks like http://www.hydraulicsliteraturestore.com/tweeker.html
I don't know why Agilent uses 0.7-0.7, but they do and other instrument manufacturers use 0.5-0.5. Good luck and keep us informed.

Thanks cleh! I will give it a try and let you know

On the question of why the ions do not seem to be centered on the integer mass values.

Ions do not have exact integer masses. There is a slight difference in the mass of a nucleide and the noninal (integer mass) for that nucleide. This difference is called mass defect. I don't have a handy link to post on the subject -- perhaps later.

The main isotope of carbon has (by definition) a mass of 12 - exactly. Hydrogen, on this scale has a mass of slightly above 1 and the chlorine isotopes (35 and 37) have masses just under the nominal values. Molecules with a large number of chlorine or bromine atoms have very noticible mass defects.

With your 5971, you can set up SIM mode acquisition and adjust the mass for acquisition for each compund you are analyzing. I've done it. You can get some improvement in response - but if you have a number of analytes, this can be tedious.

Don_Hilton's right, but the whole business of the mass defect really gets me a bit irritated as I feel it makes a simple concept complicated.

Since elements don't have exact masses, nor do molecules. When you're setting up a single ion monitoring experiment, you need to tell the MS what mass to look for, and anyone with two brain-cells to rub together will realise you need to tell it the real mass of the molecule, not some vague approximation. If you calculate the mass of the molecule using integer masses remembered from school chemistry, you will get a mass that isn't right. But nowadays absolutely everyone should be able to use the correct, accurate masses, because if the molecule is more than trivial, you will probably be looking it up in a database or drawing it in a drawing package.

Agilent's software dates back to when more people calculated their masses on the back of an envelope, and back then, more people would have used integer masses. As a result, Agilent assumed that in general they'd underestimate the mass (because typical analytes contain a lot of hydrogen, and hydrogen is greater than mass 1; in general small things are heavier than integers, large things lighter than integers). To avoid disaster, Agilent therefore biased their mass window upwards. Really they did it for those who couldn't be bothered to type 507.3 and only typed 507.

The confusion that most people have today is between the exact mass of a particular isotope peak, and the precisely-stated molecular mass averaging all isotope peaks assuming natural abundance. Both can be given to 4 decimal places or more, but in mass spec terms, the only one that generally matters (assuming you're not looking at hideously multiply charged ions) is the exact mass of an isotopologue.

rant over!

For those who might be intimidated, I will note that many of us ignore mass defect as we set up methods - and they work just fine for the purpose to which we intend them.

And, while setting up for mass defect is a bit of a pain, so is setting up for large volume injection or some of the other less commonly used instrumental techniques. You dig out the information you need, find the menus and fill in the information (the best you can) ahd make a couple of runs to see if it seems to be pretty much right.

Manufactures tend to put the development money on what drives the market. And, ease of method development does not seem to be at the top of the list.

And yes, with ChemStation the assumption was apparently that molecules like hydrocarbons would be of interest - and what I have I set up in SIM mode? Like many other people, it has been a trace analyical method for compunds containing chlorine and bromine... You just smile and go on. No point in fighting what you can't change.