LCMS of dinucleotide phosphates

[arnabroy81]

I am working with a Bruker QTOF attached to a Dionex Ultimate 3000 LC system. I am specifically interested to detect AP6A. Using ammonium formate (1 mM) as buffer A and acetoniltrile as buffer B. I am operating the instrument in negative mode.

We have got good UV peak in HPLC at 260 nm. The problem is I am not able to get a good MS peak in LCMS. The expected m/z is 994. When I am injecting about 1 ug i am able to see a tiny peak which the auto MSMS doesn't even select for fragmentation. However I can choose for MRM. But I want to see good peak for 994. Is there something I can do to increase ionization? I am feeling I am not using optimum parameters / method for this compound.

Looking for advise.

[lmh]

Two immediate suspicions:
(1) With a polyphosphate, there are lots of possibilities for other precursor ions. You are in negative mode, I assume, and from the mass, you're looking for singly-charged ions? You may have almost any combination of counter-ions for the uncharged phosphate groups (expect peaks at intervals of 22 for different degrees of substitution with sodium). You are also likely to see multiply charged ions (also with different combinations of counter-ions).
(2) The compound may not be very stable; you may see intense peaks for fragments, and may benefit from optimising temperatures of drying gas etc., and possibly optimising the spray voltage.