Reduction of chemical noise in electrospray ionization mass spectrometry by supplemental IR activation

Supplemental infrared (IR) activation was applied to reduce background chemical noise and increase analyte ion signal in a linear ion trap mass spectrometer. Peptides, proteins, and small molecules were all introduced by electrospray ionization, and when regions of chemical noise were isolated and subjected to IR irradiation, protonated analyte molecules were observed in the product ion mass spectra. By isolating the entire mass range (e.g., m/z 400–2000) and then irradiating all ions in the trap, supplemental IR activation increased the signal of singly protonated peptides by almost 70% and by 40%–55% for the lower charge states of cytochrome c. This increase in analyte ion signal was less dramatic for the higher charge states of peptides and proteins. The chemical noise present in the mass spectra is attributed to incomplete desolvation of the electrospray, as the abundance of the protonated peptides observed upon supplemental IR activation of the chemical noise decreased with higher inlet capillary temperatures. Collision activation was not as effective for desolvating the ions present in the chemical noise.