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Choosing the Right UHPLC Column for Peptide Mapping

Analysts are increasingly relying upon LC-MS to perform their peptide and protein digest analyses, and TFA is not often used in conjunction with LC-MS due to its strong signal-suppression properties. Thus, when performing peptide analysis by LC-MS using typical mobile phases such as water/acetonitrile/formic acid, secondary interactions between basic amino acids on the peptide and the underlying silica can lead to broad peaks, peak tailing, and can interfere with optimal resolution between close-eluting peaks. To obtain optimal performance for peptide analysis using either LC-UV or LC-MS, the ideal media should be highly efficient (narrow peaks) and highly inert (minimal peak tailing when using MS-compatible modifiers like formic acid). In addition, a more retentive media is often favorable, particularly for peptide mapping, to maximize retention of small, polar peptide fragments that may not have a high affinity for a typical C18 phase, particularly in the absence of TFA (trifluoroacetic acid). Using this information, Luna Omega PS C18 and C18 were tested alongside a Waters ACQUITY UHPLC column.