Chromatography Forum

Hi ! I have two different lot of same compound when I ran in LCMS using same method and same time ( Agilent Q-TOF) I see one lot shows molecular ion+sodium ( m/z= 397+22=419) as main peak but the other lot does not shows that it only shows M/Z 397 as molecular ion peak which is right molecular weight of compound ( Mol wt= 396). Is two lots have different compound or there is some other reason for one lot to show molecular ion peak+sodium and other does not show that?Please help

May be this cuase of all reagents as well as the mobile phase by releasing sodium ion from the bottle into MP.
Try to see fragment ions from both m/z 397 and 419 and compare product ions.

What kind of mobile phase additives are you using? Often a low concentration (up to a few mmol) of either ammonium acetate, formic acid or acetic acid can help shift the balance away from the sodiated molecule towards the protonated molecule.

In general I would not ever recommend using the sodiated peak for analysis, as the sodium level is from trace residues rather than anything you intentionally put in. Even if the batches you're analyzing are 99.5% pure, traces of common ions like sodium could be part of that 0.5% and it makes a big difference in terms of the ions you ultimately see.

If your mobile phase bottles seem to be contributing to the sodiated peak issue, you may want to try removing those bottles, subjecting them to a nitric acid wash, rinsing back out with DI water, and then try again. My lab also has an ICP-MS - we have a few glass bottles that originally contained concentrated nitric acid and have been washed many times through before turning them into DI water dispensers. I noticed that the water dispensed out of those bottles did not have appreciably higher sodium counts than the water direct from our DI generator.

Thanks for your suggestions..I will change my mobile phase and clean glasswares too but

Do you use a buffer or acid in your mobile phase?