Chromatography Forum

I was tuning for a Q1 parent MW of 499 in positive mode. So typically using + 1 amu I would shoot for ~500.

I see 500 but to the left is two significantly higher peaks 498 and 499. I was told this was an affect due to Chlorine or Bromine . Would someone be able to tell me why Chlorine or Bromine causes this?

thanks

A few comments:

Firstly, if you're looking at chlorinated or brominated compounds, you will see more than one big parent ion peak. The reason is that they are present as mixtures of isotopes. Chlorine is 75% 35Cl, and 25% 37Cl, which means that if one chlorine is present, you will see a big parent peak, and another peak at +2, which should be about one third of the height of the main parent peak. Bromine is rougly equal quantities of 79Br and 81Br, so if one bromine is present in your target molecule, you get two roughly equal "biggest" parent ion peaks. The situation is more complicated if you have multiple atoms present of elements that have multiple, common isotopes of a variety of masses. Although bromine and chlorine are the usual suspects, they are not alone; most transition metals have copious isotopes, and sulphur as a significant 4% +2 peak.

Secondly, it's not generally a good idea just to add one to what you think is the molecular weight and hope that this is the correct value for your parent ion. If nothing else, you have to understand the difference between molecular weight and what many chemical packages call "exact mass".

Molecular weight is generally the mass of one mole of the compound with all elements present at their natural abundance mixture of isotopes. That's why HCl is about 36.5. Were you to do LC-MS on the mythical species [HCl+H]+ you wouldn't find it at 37.5, you'd find 75% at 37 and 25% at 39. "Exact mass" from drawing packages is usually the mass of the lowest-molecular weight isotopologue.

The reason the difference is relevant is that in biggish molecules (I'm thinking of 800Da upwards) there's a significant difference between the average molecular weight and the mass of the lowest isotopologue, even if your molecule contains nothing but C, O, H and N. It's generally good practice to set your mass spec with its window centred on the correct mass, and not off to one side without good reason...

Thanks lmh for the detailed explanation.

Not being familiar with LC-MS, could you elaborate on why you search for the mass +1amu?

LC-MS uses ionisation mechanisms such as electrospray, which are low-energy and form the sorts of ions you would see in solution. This means the ions you expect to see in positive mode are additions of H+ (especially to bases), additions of Na+, NH4+ and so on. Addition of H+ is obviously going to give an ion of one unit heavier than the neutral mass. It's nice working with H+ adducts in MS-MS as they generally fragment a little more easily than sodium adducts (I don't know why). In negative MS you tend to see ions formed by loss of H+ from acid groups, or sometimes you get adducts between the neutral molecule and another negative ion, such as formate from the LC solvent.
Contrast this with GC using electron ionisation.