In some cases, experiments with peptides can be challenging due to the chemical properties of the individual peptides. Major aspects that can negatively affect your experiments and suggested solutions for troubleshooting are listed below:
Peptide solubility:
A frequent problem in such experiments is the low solubility in water of some peptides. This can be improved by addition of a compatible organic solvent to both the running and the sample buffer used in your switchSENSE experiment. A commonly used solvent is dimethyl sulfoxide (DMSO) which may be supplemented to the experimental buffer up to 5 % v/v.
Peptide charge:
If a peptide contains charged amino acids, it is likely to exhibit a large mass to charge ratio which can prove to be problematic, especially when working with charged surfaces. The consequences range from extensive unspecific surface adsorption to the absence of specific binding due to electrostatic repulsion. If you observe such a behavior, try to increase to salt concentration of your running and sample buffer. This will increase the shielding of the charges of the peptide molecule.