Desalting of phosphopeptides by tandem polypyrrole-c18 reverse phase micropipette tip (TMTipPPY-C18) based on hybrid electrostatic, Π–Π stacking and hydrophobic interactions for mass spectrometric analysis

Desalting and concentration of peptides using reverse phase (RP) C18 chromatographic material based on hydrophobic interaction is a routine approach used in mass spectrometry (MS)-based proteomics. However, MS detection of small hydrophilic peptides, in particular, phosphopeptides that bear multiple negative charges, is challenging due to the insufficient binding to C18 stationary phase. We described here the development of a new desalting method that takes the unique properties of polypyrrole (PPY). The presence of positively charged nitrogen atoms under acidic conditions and polyunsaturated bonds in polypyrrole provide a prospect for enhanced adsorption of phosphopeptides or hydrophilic peptides through extra electrostatic and Π–Π stacking interactions in addition to hydrophobic interactions. In tandem with reversed phase C18 chromatographic material, the new type of desalting method termed as TMTipPPY-C18 can significantly improve the MS detection of phosphopeptides with multiple phosphate groups and other small hydrophilic peptides. It has been applied to not only tryptic digest of model proteins but also the analysis of complex lysates of zebrafish eggs. The number of detected phosphate groups on a peptide ranged from 1 to 6. Particularly, polypyrrole based method can also be used in basic condition. Thus it provides a useful means to handle peptides that may not be detectable in acidic condition. It can be envisioned that the TMTipPPY-C18 should be able to facilitate the exploration of large scale phosphoproteome.

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► A new micropipette tip TMTipPPY-C18 was developed for desalting of phosphopeptides.
► TMTipPPY-C18 is based on polypyrrole in tandem with C18 chromatographic material.
► TMTipPPY-C18 combines electrostatic, Π–Π stacking and hydrophobic interactions.
► TMTipPPY-C18 can be used in both acidic and basic experimental conditions.