Selective Isolation at the Femtomole Level of Phosphopeptides From Proteolytic Digests Using 2D-NanoLC-ESI-MS/MS and Titanium Oxide Precolumns

Anal Chem. 2004 Jul 15;76(14):3935-43. doi: 10.1021/ac0498617.

Abstract

Selective detection of phosphopeptides from proteolytic digests is a challenging and highly relevant task in many proteomics applications. Often phosphopeptides are present in small amounts and need selective isolation or enrichment before identification. Here we report a novel automated method for the enrichment of phosphopeptides from complex mixtures. The method employs a two-dimensional column setup, with titanium oxide-based solid-phase material (Titansphere) as the first dimension and reversed-phase material as the second dimension. Phosphopeptides are separated from nonphosphorylated peptides by trapping them under acidic conditions on a TiO(2) precolumn. Nonphosphorylated peptides break through and are trapped on a reversed-phase precolumn after which they are analyzed by nanoflow LC-ESI-MS/MS. Subsequently, phosphopeptides are desorbed from the TiO(2) column under alkaline conditions, reconcentrated onto the reversed-phase precolumn, and analyzed by nanoflow LC-ESI-MS/MS. The selectivity and practicality of using TiO(2) precolumns for trapping phosphopeptides are demonstrated via the analysis of a model peptide RKISASEF, in a 1:1 mixture of a non- and a monophosphorylated form. A sample of 125 fmol of the phosphorylated peptide could easily be isolated from the nonphosphorylated peptide with a recovery above 90%. In addition, proteolytic digests of three different autophosphorylation forms of the 153-kDa homodimeric cGMP-dependent protein kinase are analyzed. From proteolytic digests of the fully autophosphorylated protein at least eight phosphorylation sites are identified, including two previously uncharacterized sites, namely, Ser-26 and Ser-44. Ser-26 is characterized as a minor phosphorylation site in purified PKG samples, while Ser-44 is identified as a novel in vitro autophosphorylation target. These results clearly show that TiO(2) has strong affinity for phosphorylated peptides, and thus, we conclude that this material has a high potential in the field of phosphoproteomics.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Automation
  • Chromatography, Liquid / methods*
  • Nanotechnology
  • Peptide Fragments / chemistry
  • Phosphopeptides / analysis*
  • Phosphopeptides / isolation & purification
  • Proteins / metabolism
  • Spectrometry, Mass, Electrospray Ionization / methods*
  • Titanium / chemistry*

Substances

  • Peptide Fragments
  • Phosphopeptides
  • Proteins
  • titanium dioxide
  • Titanium