Peptide Extraction for Protein Profiling

Protein profiling is a novel and potentially powerful approach for improved diagnosis of various diseases. To this end, peptides and proteins are captured from serum (for example) and analyzed by mass spectrometry. Pattern analysis of the generated spectra for the presence or absence of specific peaks (biomarkers) allows classification of individuals even without identification of the relevant biomarkers themselves.

For peptide and protein isolation several techniques are available. A simple and fast technique is solid phase extraction using magnetic beads with a certain functionality (Bruker ClinProt Magnetic Beads). This functionality can be global like C8, or more selective like metal-chelating for the isolation of phosphopeptides, for example. The system offers a flexible, automated, high throughput method for the isolation of peptides and proteins using magnetic beads, and subsequent spotting on a MALDI target plate.

Running this magnetic bead application and MALDI measurements on different days with the same samples gave highly reproducible results, indicating that the extraction procedure and sub-sequent MALDI spotting performed as expected. The total number of samples that can be processed in one run is 192. This number has to be divided by the number of types of beads used and the number of spots per sample on the MALDI target plate to get the actual maximum number of samples. For a higher throughput, a robotic arm is needed to reload the deck and to load the Ultraflex. A further increase in throughput can be achieved by using the 96-channel head on the STAR, while the number of samples will still be limited by the available MALDI-MS capacity. Here, a higher laser frequency (200 Hz) will allow more rapid evaluation.

The method provides clean peptide isolates which can be used for protein profiling with an intermediate throughput. The method combines two processes (peptide isolation and MALDI target spotting) with a high degree of flexibility.

Features and

  • Clean peptide isolates for protein profiling
  • Highly flexible protocol
  • Scalable system that allows increase of throughput when needed


  • MICROLAB STAR, 8 channels, autoload
  • Magnetic beads separator including controller from Dynal
  • Electronically regulated, closed container for MALDI matrix ClinProt Magnetic Beads MB-HIC8, MB-HIC18, MB-IMAC Fe and MB-IMAC Cu from Bruker Daltonik
  • ClinProt Magnetic Beads MB-HIC8, MB-HIC18, MB-IMAC Fe and MB-IMAC Cu from Bruker Daltonik



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