SELDI-TOF Academic Units

Surface Enhanced Laser Desorption Ionisation Time of Flight Mass Spectrometry(SELDI-TOF MS) for biological sample characterisation and biomarker identification.

The recent acquisition of SELDI-TOF MS technology to the University of Southampton Human Genetics Division is a revolutionary advancement in the evolving field of proteomics profiling and biomarker discovery. The system supported through funding from Wessex Cancer Trust, Wessex Medical Research and Hope for Guernsey to Dr Paul Townsend is an ProteinChip SELDI System, Enterprise Edition, 230 V (Figure 1) from BioRad (formerly Ciphergen)


Among the many promising strategies in clinical proteomics, protein expression profiling using SELDI-TOF MS has emerged as a successful tool for the detection and differentiation of many disease types. This technology originally described by Hutchens and Yip (1) is a promising, rapid, approach for presymptomatic screening and preclinical early detection of pathologies. Current projects are aiming to characterise patient and volunteer blood sera for biomarker profiles in cancer (initially focussing on breast cancer).

Studies have provided evidence that this methodology can be used to uncover proteomic expression patterns linked to a disease state. This includes biomarkers or biomarker fingerprints and panels in different cancers affecting different organs including the bladder, prostate, pancreas, breast, ovary, liver, oesophagus, thyroid and the oral cavity. Highly promising results in detection of early-stage cancers were also recently published by different groups (2-9).

SELDI-TOF MS has been developed to meet the demand for a higher throughput in clinical settings and rapid identification of secreted body proteins in readily accessible body fluids or/and tissue. Samples can be collected from:

  • serum
  • tissue/tissue extracts
  • saliva
  • urine
  • amniotic fluid
  • breast milk or breast fluid aspirates

This may provide an alternative none or a minimally invasive approach for potential screening, diagnosis and prognostication of diseases, especially cancers. Most current cancer screening and diagnostic tools have limitations even when used in combination. Once defining marker signatures, this novel technology may become a realistic complement or even alternative to current medical screening/imaging modalities improving their sensitivity and specificity.


SELDI-TOF MS combines the principles of retention chromatography and mass spectrometry, providing a rapid, high-throughput, sensitive screening method capable of detecting and analysing complex protein samples. This new technology makes multi-analyse discovery possible. It can rapidly perform the separation, detection and analysis of proteins at the femtomole level directly from biologic samples.

SELDI-TOF MS employs a variety of selective chips (ProteinChips), on which complex biomaterials can be spotted. The protein chip array is defined by multiple, addressable locations of chemically or biologically defined protein "docking" sites on a chip. Different chip surfaces retain a subset of protein s that are subsequently analysed by a linear TOF MS providing a biomarker profile.



  • ProteinChip IMAC30 array - immobilized metal affinity capture (IMAC) array with a nitriloacetic acid (NTA) surface. Requires activation with transition metals prior to use. Applications include polyhistidine-tagged and phosphorylated protein capture, protein profiling, and protein purification
  • ProteinChip CM10 array - incorporates a negatively charged carboxylate chemistry and acts as a weak cation exchanger. Applications include protein profiling and protein purification
  • ProteinChip Q10 array - incorporates a positively charged quaternary amine chemistry and acts as a strong anion exchanger. Applications include protein profiling and protein purification
  • ProteinChip H50 array - binds proteins through reverse-phase or hydrophobic interaction chromatography; has binding characteristics similar to that of a C6 to C12 alkyl chromatographic support. Typical applications include protein profiling and protein purification
  • ProteinChip H4 array - mimics reverse-phase chromatography with C16 functionality. Typical applications include peptide analysis and on-chip desalting
  • ProteinChip NP20 array - mimics normal-phase chromatography with silicate functionality. Typical applications include protein molecular weight validation and quality control assays

Thus, the protein chip array miniaturises and amplifies the ability of defining protein complexes by investigating variety of purification conditions on different surfaces. Only few microliters of samples can yield sufficient protein/peptide peaks to be analysed by the protein chip reader software.

A typical experiment

A typical experiment requires up to 2-4 hours of bench work followed by automated sample analysis by the SELDI-TOF MS. Each study should have discovery, teaching, blinded and validation sets to consolidate the true identification of biomarkers. This would be followed by purification and finally identification of the biomarker.

Reference List

  1. Yip TT, Hutchens TW. Immobilized metal ion affinity chromatography. Mol.Biotechnol. 1994;1:151-64. PubMed
  2. Petricoin EF, III, Ornstein DK, Paweletz CP, Ardekani A, Hackett PS, Hitt BA et al. Serum proteomic patterns for detection of prostate cancer. J.Natl.Cancer Inst. 2002;94:1576-8. PubMed
  3. Petricoin EF, Ardekani AM, Hitt BA, Levine PJ, Fusaro VA, Steinberg SM et al. Use of proteomic patterns in serum to identify ovarian cancer. Lancet 2002;359:572-7. PubMed
  4. Li J, Orlandi R, White CN, Rosenzweig J, Zhao J, Seregni E et al. Independent validation of candidate breast cancer serum biomarkers identified by mass spectrometry. Clin.Chem. 2005;51:2229-35. PubMed
  5. Adam BL, Qu Y, Davis JW, Ward MD, Clements MA, Cazares LH et al. Serum protein fingerprinting coupled with a pattern-matching algorithm distinguishes prostate cancer from benign prostate hyperplasia and healthy men. Cancer Res. 2002;62:3609-14. PubMed
  6. Srinivas PR, Srivastava S, Hanash S, Wright GL, Jr. Proteomics in early detection of cancer. Clin.Chem. 2001;47:1901-11. PubMed
  7. Vlahou A, Schellhammer PF, Mendrinos S, Patel K, Kondylis FI, Gong L et al. Development of a novel proteomic approach for the detection of transitional cell carcinoma of the bladder in urine. Am.J.Pathol. 2001;158:1491-502. PubMed
  8. Wadsworth JT, Somers KD, Stack BC, Jr., Cazares L, Malik G, Adam BL et al. Identification of patients with head and neck cancer using serum protein profiles. Arch.Otolaryngol.Head Neck Surg. 2004;130:98-104. PubMed
  9. Wright GL, Jr. SELDI proteinchip MS: a platform for biomarker discovery and cancer diagnosis. Expert.Rev.Mol.Diagn. 2002;2:549-63. PubMed