Chromatography Forum

Hi, ive just started using a new Shimadzu 2020 HPLC-MS equiped with a quadrupole detector for ESI work with peptides, m/z 1000-4000. I have previously been using an old finnigans ion trap ms which gave me publication quality spectra showing the protonated peptide as the major peak, as well as the doubly and triply charged species in smaller proportions.

On the new machine however, the major ions seem to be the triply or even quadruply protonated peptides, with no hint of the singly charged peptide. Althought this is only slightly inconvenient for identification, i would prefer that the singly protonated species was present in significant proportions at least from a characterization stand point.

Is there anything i can do to change this scenario, or is it the nature of the machine i am using?

Proteins and peptides by their nature tend to exist with multiple charges. The possible charges depends on the amino acids present and the pH of the solution they are in.

why then do we see primarily the protonated peptide on one of the machines while on the other we usually only see a mixture of the doubly or triply charged peptide?

is it the nature of the mass spectrometer being used, seeing as both use the same solvent systems?