Two unexpected singly charged ions at m/z 1103 and 944 have been observed in mass spectra obtained from electrospray ionization mass spectrometric analysis of liquid chromatography effluents with mobile phases containing trifluoroacetic acid (TFA) that severely interfered with sample analysis. Accurate mass measurement and tandem mass spectrometry studies revealed that these two ions are composed of three components; clusters of trifluoroacetic acid, clusters of mass 159 and iron. Formation of these ions is inhibited by removing TFA from the mobile phases and using formic acid in its place, replacing the stainless steel union with a titanium union or by adding a small blank fused-silica capillary column between the chromatography column and the electrospray tip via a stainless steel union without any adverse effects to chromatographic separation, peak broadening or peptide identifications.
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