An introduction to SELDI proteomics and its application to oxidative and metabolic stress.

The Ciphergen Surface-enhanced laser desorption ionization - time of flight (SELDI-TOF) system is an extremely versatile and convenient proteomic tool that facilitates the screening of tissue or body fluids. It rapidly identifies proteins that alter as a consequence of a particular disease, toxin or treatment. It is very complementary to genomic studies.

Each "chip" (a thin strip of aluminium, which has 8 small places for loading samples) captures a particular type of protein (acidic, basic, antigens etc) depending on the nature of the chip surface. There are also other chips that will allow you to analyse all proteins in a particular sample.

It only takes about a day to process a whole series of samples and a ELISA-plate holding device (the "Bioprosessor") facilitates the analyse 96 samples simultaneously. Very simply, you prepare the chip, add the sample, wash it with buffer a few times then finally add another compound (an energy absorbing material). The chips are then ready to “read” in a mass spectrometer. The Ciphergen mass spectrometer and dedicated software effectively quantifies the mass and relative abundance of each protein in a sample. The number of proteins quantified in each sample will depend on the tissue and the chip surface. For example, we can routinely quantify about 300-800 proteins from 20 micro-litres of plasma, though much smaller volumes have been used.

In a recent experiment, typical of the work that is being carried out by the Mass Spectrometry Centre 32 plasma samples were analysed in an experiment investigating metabolic and oxidative stress (MOS) were analysed. At the end of the day, at least 300 proteins were quantified in each sample. The data showed that that 105 protein peaks altered significantly due to the imposition of MOS. There were some interesting effects with anti-oxidants too and subsequent studies showed that there were over 100 significant correlations between relative protein abundance with serum indices of liver damage.

In another study, 12 human samples were analysed from subjects with high alcohol consumption rates as reflected by serum carbohydrate-deficient transferrin (CDT). SELDI identified 151 protein peaks and 5 of these were affected in CDT-positive subjects (Figure 1).

Of course, SELDI per se does not provide any information on the species of the protein that alters, only its (i) molecular weight, (ii) abundance and some information on its (iii) biophysical characteristics. This sort of information is very useful in Biomarker discovery. However, more sophisticated techniques are needed to identify the protein of interest. Further technical details can be obtained from the Ciphergen Web Page: www.ciphergen.com.

Legends to Figures 1: Typical section of a trace of plasma using an anionic chip.
Note the different ways the SELDI data can be displayed. The relative abundance of the proteins corresponds with the peak heights (map and trace views) or shading (gel view). From the work MC Fabregas, M Bailey, R Sherwood, TJ Peters, VR Preedy, P Emery, H Wiseman (2004) Surface enhanced laser desorption ionisation-time of flight mass spectrometry (SELDI) for the identification of putative biomarkers of alcohol-toxicity. Alcoholism: Clin Exp Res (Abstract in Press).

PLEASE NOTE that CHARGES for the SELDI-MS have been decided by the Mass Spectrometry Steering Committee as:

• £100 for local user per session (excluding operator and cost of chips)
• £200 for local user per session (including operator but excludes cost of chips)
• £285 for commercial user per session (includes operator but excludes cost of chips)

A session is approximately half-a-day.

Chips should be ordered by individual users (approximately £40 per chip of 8 targets)and will carry a surcharge of £15 per chip for ALL users. Grant holders will pay only the £15 per chip surcharge.