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Optimized sample preparation is crucial for successful and sensitive detection of peptides by MALDI-TOF MS. In particular, the protein identification of low femtomole amounts of analyte requires further clean-up and concentrating steps to acquire significant spectra. This aspect is even more pronounced if the analysis of post-translational modifications is the goal. A prominent example is the mapping of protein phosphorylation sites, which is often hampered by the lack of phosphopeptides in spectra of crude digests. For that reason, very often micro-columns filled with reversed-phase material for clean-up, or IMAC or TiO2 resins for phosphopeptide enrichment, are employed prior to MALDI-MS analysis.
The performance of these off-line technologies will be compared to a new sample preparation on chip (SPOC) technology. The SPOC technology integrates all steps of sample preparation directly on the MALDI same-sample support by means of a patterned surface forming rings of different wetability and chemical functionality.
The superior performance of this SPOC approach for sample desalting and concentrating of in-gel digests will be presented. Moreover, the analysis of protein phosphorylation using chips with IMAC functionality is compared to off-line column or bead–based strategies with respect to the efficiency and specificity of phosphopeptide enrichment.