Hi everyone,

I have a problem with my LCMS runs and I need your help and advice. I am running two compounds using MRM under positive mode of detection. My problem is that when I viewed each components' chromatography output in the MS, each of the two compounds produces two peaks. For both components, one of the peaks area count increases with concentration while the extra peak remain the same.

I always thought that one of the impt features of the MS is its specificity and hence I only expect one peak from each component. Why am I getting an extra peak apart from the one that I expected? Where could it possibly have come from? Why does it happen?

I am quite new to this technology, that's why I ask these question. I hope you can answer them.

what do your blanks look like? What happens if you inject water or methanol? What type of LC are you using? If it has a purge solvent, contamination there can cause extra peaks. Is the extra peak at the same retention time for both analytes (assuming LC conditions are the same)? It may be something in your system. Plasma, humic material, etc. The wrong type of vial caps can clog up the autosampler. What was run on it before you started using it? What type of MS are you using?
By the way, MS is very specific, but if a contaminant has the same molecular weight or breaks appart in the spray chamber to something with the same molecular weight, it can show up.

Dear Anonymous,

Water/MeOH/ACN or any combination of the three give clean fingerprint. However, my blank plasma extract (liq-liq extraction with concentration) produce a clean fingerprint but sometimes there are also some very tiny impurity peaks. When I run plasma blank spiked with standards, I have very consistent extra peaks coming out at retention times different from those of the analytes of interest. I am using an HP1100 autosampler and uses new cap septa/liners each time to prevent contamination from septa/liner.

Thank you for responding and I hope to receive more from everyone out there

What is the solvent composition that your sample is dissolved in? Are you running a gradient?

sample is dissolved in ACN/phosphate/formic acid/water mix and yes, I am running a gradient using combinations of the above-mentioned mixture.

In a gradient, you sometimes get an unretained peak of your compounds if the sample solvent is too strong, meaning that it has too much organic solvent in it. The same can happen if the pH is much different, or if your mobile phase is not a buffer. Could either example explain what you see?

Are both of your analytes carboxylic acids? Carboxylic acids form dimers in solution, especially in the presence of organic solvents. Your problem might be caused by mixed dimer formation. If you leave out the formic acid, does this effect whether you see these extra peaks?