Home Optimization and evaluation of surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) with reversed-phase protein arrays for protein profiling
Article
Licensed
Unlicensed Requires Authentication

Optimization and evaluation of surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) with reversed-phase protein arrays for protein profiling

  • Manuel Aivado , Dimitrios Spentzos , Gil Alterovitz , Hasan H. Otu , Franck Grall , Aristoteles A. N. Giagounidis , Meghan Wells , Je-Yoel Cho , Ulrich Germing , Akos Czibere , Wolf C. Prall , Chris Porter , Marco F. Ramoni and Towia A. Libermann
Published/Copyright: June 1, 2005
Become an author with De Gruyter Brill
Submit Manuscript Author Information
Clinical Chemistry and Laboratory Medicine (CCLM)
From the journal Clinical Chemistry and Laboratory Medicine (CCLM) Volume 43 Issue 2

Abstract

Surface-enhanced laser desorption/ionization (SELDI) time-of-flight mass spectrometry with protein arrays has facilitated the discovery of disease-specific protein profiles in serum. Such results raise hopes that protein profiles may become a powerful diagnostic tool. To this end, reliable and reproducible protein profiles need to be generated from many samples, accurate mass peak heights are necessary, and the experimental variation of the profiles must be known. We adapted the entire processing of protein arrays to a robotics system, thus improving the intra-assay coefficients of variation (CVs) from 45.1% to 27.8% (p<0.001). In addition, we assessed up to 16 technical replicates, and demonstrated that analysis of 2–4 replicates significantly increases the reliability of the protein profiles. A recent report on limited long-term reproducibility seemed to concord with our initial inter-assay CVs, which varied widely and reached up to 56.7%. However, we discovered that the inter-assay CV is strongly dependent on the drying time before application of the matrix molecule. Therefore, we devised a standardized drying process and demonstrated that our optimized SELDI procedure generates reliable and long-term reproducible protein profiles with CVs ranging from 25.7% to 32.6%, depending on the signal-to-noise ratio threshold used.

Keywords: high-throughput; plasma protein profiling; proteomics; serum protein profiling; surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI TOF-MS)
Corresponding author: Towia A. Libermann, PhD, Director, BIDMC Genomics Center and Bioinformatics Core, Beth Israel Deaconess Medical Center, Harvard Institutes of Medicine, Room #247, 4 Blackfan Circle, Boston, MA 02115, USA Phone: +1-617-6673393, Fax: +1-617-9755299,

References

1 Hutchens TW, Yip TT. New desorption strategies for the mass spectrometric analysis of macromolecules. Rapid Commun Mass Spectrom 1993; 7: 576–80. 10.1002/rcm.1290070703Search in Google Scholar

2 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. 10.1016/S0140-6736(02)07746-2Search in Google Scholar

3 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. Search in Google Scholar

4 Li J, Zhang Z, Rosenzweig J, Wang YY, Chan DW. Proteomics and bioinformatics approaches for identification of serum biomarkers to detect breast cancer. Clin Chem 2002; 48: 1296–1304. 10.1093/clinchem/48.8.1296Search in Google Scholar

5 Poon TC, Yip TT, Chan AT, Yip C, Yip V, Mok TS, et al. Comprehensive proteomic profiling identifies serum proteomic signatures for detection of hepatocellular carcinoma and its subtypes. Clin Chem 2003; 49: 752–60. 10.1373/49.5.752Search in Google Scholar PubMed

6 Kozak KR, Amneus MW, Pusey SM, Su F, Luong MN, Luong SA, et al. Identification of biomarkers for ovarian cancer using strong anion-exchange ProteinChips: poten-tial use in diagnosis and prognosis. Proc Natl Acad Sci USA 2003; 100: 12343–8. 10.1073/pnas.2033602100Search in Google Scholar PubMed PubMed Central

7 Banez LL, Prasanna P, Sun L, Ali A, Zou Z, Adam BL, et al. Diagnostic potential of serum proteomic patterns in prostate cancer. J Urol 2003; 170: 442–6. 10.1097/01.ju.0000069431.95404.56Search in Google Scholar PubMed

8 Hanash S. Disease proteomics. Nature 2003; 422: 226–32. 10.1038/nature01514Search in Google Scholar PubMed

9 Fung ET, Enderwick C. ProteinChip clinical proteomics: computational challenges and solutions. Biotechniques 2002;Suppl: 34–8, 40–1. 10.2144/mar0205Search in Google Scholar

10 Cordingley HC, Roberts SL, Tooke P, Armitage JR, Lane PW, Wu W, et al. Multifactorial screening design and analysis of SELDI-TOF ProteinChip array optimization experiments. Biotechniques 2003; 34: 364–5, 368–3. 10.2144/03342rr07Search in Google Scholar PubMed

11 Sorace JM, Zhan M. A data review and re-assessment of ovarian cancer serum proteomic profiling. BMC Bioinformatics 2003; 4: 24. 10.1186/1471-2105-4-24Search in Google Scholar PubMed PubMed Central

12 Lee ML, Kuo FC, Whitmore GA, Sklar J. Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations. Proc Natl Acad Sci USA 2000; 97: 9834–9. 10.1073/pnas.97.18.9834Search in Google Scholar PubMed PubMed Central

13 Black MA, Doerge RW. Calculation of the minimum number of replicate spots required for detection of significant gene expression fold change in microarray experiments. Bioinformatics 2002; 18: 1609–16. 10.1093/bioinformatics/18.12.1609Search in Google Scholar PubMed

14 Rogers MA, Clarke P, Noble J, Munro NP, Paul A, Selby PJ, et al. Proteomic profiling of urinary proteins in renal cancer by surface enhanced laser desorption ionization and neural-network analysis: identification of key issues affecting potential clinical utility. Cancer Res 2003; 63: 6971–83. Search in Google Scholar

15 Holmes MD, Pollak MN, Hankinson SE. Lifestyle correlates of plasma insulin-like growth factor I and insulin-like growth factor binding protein 3 concentrations. Cancer Epidemiol Biomarkers Prev 2002; 11: 862–7. Search in Google Scholar

16 BIDMC Genomics Center. www.bidmcgenomics.org/Seldi-Tof. Search in Google Scholar

17 Sneath PHA. Numerical Taxonomy: The principles and practice of numerical classification. San Francisco, CA, USA: WH Freeman, 1973. Search in Google Scholar

18 Boguski MS, McIntosh MW. Biomedical informatics for proteomics. Nature 2003; 422: 233–7. 10.1038/nature01515Search in Google Scholar PubMed

Received: 2004-7-28
Accepted: 2004-11-10
Published Online: 2005-6-1
Published in Print: 2005-4-1

©2005 by Walter de Gruyter Berlin New York

Articles in the same Issue

  1. Quality control for SELDI analysis
  2. Immunobead multiplex RT-PCR detection of carcinoembryonic genes expressing cells in the blood of colorectal cancer patients
  3. Optimization and evaluation of surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) with reversed-phase protein arrays for protein profiling
  4. Simultaneous determination of HIV antibodies, hepatitis C antibodies, and hepatitis B antigens in dried blood spots –a feasibility study using a multi-analyte immunoassay
  5. Hematopoietic cytokines in the sera of patients with pancreatic cancer
  6. Modulation of translation factor's gene expression by histone deacetylase inhibitors in breast cancer cells
  7. Whole genome amplification of buccal cell DNA: genotyping concordance before and after multiple displacement amplification
  8. Y-Chromosome short tandem repeat (STR) haplotypes in a Campania population sample
  9. TaqMan assays for genotyping of single nucleotide polymorphisms present at a disease susceptibility locus on chromosome 6
  10. The secretion of ibuprofen metabolites interferes with the capillary chromatography of urinary homovanillic acid and 4-hydroxy-3-methoxymandelic acid in neuroblastoma diagnosis
  11. Selective measurement of HCHO in urine using direct liquid-phase fluorimetric analysis
  12. A spectrophotometric micromethod for determining erythrocyte protoporphyrin-IX in whole blood or erythrocytes
  13. Simultaneous analysis of MDR1 C3435T, G2677T/A, and C1236T genotypes by multiplexed mutagenically separated PCR
  14. Measurement of reticulocyte and red blood cell indices in patients with iron deficiency anemia and β-thalassemia minor
  15. Chitotriosidase activity in colostrum from African and Caucasian women
  16. Integration between point-of-care cardiac markers in an emergency/cardiology department and the central laboratory: methodological and preliminary clinical evaluation
  17. Controlled storage conditions prolong stability of biochemical components in whole blood
  18. Poor knowledge and faulty thinking regarding hemolysis and potassium elevation
  19. Delayed effects of short-term transdermal application of 7-oxo-dehydroepiandrosterone on its metabolites, some hormonal steroids and relevant proteohormones in healthy male volunteers
  20. Evaluation of a novel semi-automated HPLC procedure for whole blood cyclosporin A confirms equivalence to adjusted monoclonal values from Abbott TDx
  21. Evaluation of the Bio-Rad VARIANT™ II HbA 2/HbA 1C Dual Program for measurement of hemoglobin concentrations and detection of variants
  22. Interferences in coagulation tests – evaluation of the 570-nm method on the Dade Behring BCS analyser
  23. No evidence for involvement of the human inducible nitric oxide synthase gene in susceptibility to coronary artery disease
  24. National survey on the use of measurement of cholinesterase activity in serum
https://doi.org/10.1515/CCLM.2005.022
Keywords for this article
high-throughput; plasma protein profiling; proteomics; serum protein profiling; surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI TOF-MS)

Articles in the same Issue

  1. Quality control for SELDI analysis
  2. Immunobead multiplex RT-PCR detection of carcinoembryonic genes expressing cells in the blood of colorectal cancer patients
  3. Optimization and evaluation of surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) with reversed-phase protein arrays for protein profiling
  4. Simultaneous determination of HIV antibodies, hepatitis C antibodies, and hepatitis B antigens in dried blood spots –a feasibility study using a multi-analyte immunoassay
  5. Hematopoietic cytokines in the sera of patients with pancreatic cancer
  6. Modulation of translation factor's gene expression by histone deacetylase inhibitors in breast cancer cells
  7. Whole genome amplification of buccal cell DNA: genotyping concordance before and after multiple displacement amplification
  8. Y-Chromosome short tandem repeat (STR) haplotypes in a Campania population sample
  9. TaqMan assays for genotyping of single nucleotide polymorphisms present at a disease susceptibility locus on chromosome 6
  10. The secretion of ibuprofen metabolites interferes with the capillary chromatography of urinary homovanillic acid and 4-hydroxy-3-methoxymandelic acid in neuroblastoma diagnosis
  11. Selective measurement of HCHO in urine using direct liquid-phase fluorimetric analysis
  12. A spectrophotometric micromethod for determining erythrocyte protoporphyrin-IX in whole blood or erythrocytes
  13. Simultaneous analysis of MDR1 C3435T, G2677T/A, and C1236T genotypes by multiplexed mutagenically separated PCR
  14. Measurement of reticulocyte and red blood cell indices in patients with iron deficiency anemia and β-thalassemia minor
  15. Chitotriosidase activity in colostrum from African and Caucasian women
  16. Integration between point-of-care cardiac markers in an emergency/cardiology department and the central laboratory: methodological and preliminary clinical evaluation
  17. Controlled storage conditions prolong stability of biochemical components in whole blood
  18. Poor knowledge and faulty thinking regarding hemolysis and potassium elevation
  19. Delayed effects of short-term transdermal application of 7-oxo-dehydroepiandrosterone on its metabolites, some hormonal steroids and relevant proteohormones in healthy male volunteers
  20. Evaluation of a novel semi-automated HPLC procedure for whole blood cyclosporin A confirms equivalence to adjusted monoclonal values from Abbott TDx
  21. Evaluation of the Bio-Rad VARIANT™ II HbA 2/HbA 1C Dual Program for measurement of hemoglobin concentrations and detection of variants
  22. Interferences in coagulation tests – evaluation of the 570-nm method on the Dade Behring BCS analyser
  23. No evidence for involvement of the human inducible nitric oxide synthase gene in susceptibility to coronary artery disease
  24. National survey on the use of measurement of cholinesterase activity in serum
Sign up now to receive a 20% welcome discount
Institutional Access
How does access work?
Have an idea on how to improve our website?
Please write us.
© 2025 De Gruyter Brill
Downloaded on 28.10.2025 from https://www.degruyterbrill.com/document/doi/10.1515/CCLM.2005.022/html
Scroll to top button