A data review and re-assessment of ovarian cancer serum proteomic profiling
Open Access
- 9 June 2003
- journal article
- research article
- Published by Springer Nature in BMC Bioinformatics
- Vol. 4 (1) , 24
- https://doi.org/10.1186/1471-2105-4-24
Abstract
The early detection of ovarian cancer has the potential to dramatically reduce mortality. Recently, the use of mass spectrometry to develop profiles of patient serum proteins, combined with advanced data mining algorithms has been reported as a promising method to achieve this goal. In this report, we analyze the Ovarian Dataset 8-7-02 downloaded from the Clinical Proteomics Program Databank website, using nonparametric statistics and stepwise discriminant analysis to develop rules to diagnose patients, as well as to understand general patterns in the data that may guide future research. The mass spectrometry serum profiles derived from cancer and controls exhibited numerous statistical differences. For example, use of the Wilcoxon test in comparing the intensity at each of the 15,154 mass to charge (M/Z) values between the cancer and controls, resulted in the detection of 3,591 M/Z values whose intensities differed by a p-value of 10-6 or less. The region containing the M/Z values of greatest statistical difference between cancer and controls occurred at M/Z values less than 500. For example the M/Z values of 2.7921478 and 245.53704 could be used to significantly separate the cancer from control groups. Three other sets of M/Z values were developed using a training set that could distinguish between cancer and control subjects in a test set with 100% sensitivity and specificity. The ability to discriminate between cancer and control subjects based on the M/Z values of 2.7921478 and 245.53704 reveals the existence of a significant non-biologic experimental bias between these two groups. This bias may invalidate attempts to use this dataset to find patterns of reproducible diagnostic value. To minimize false discovery, results using mass spectrometry and data mining algorithms should be carefully reviewed and benchmarked with routine statistical methods.Keywords
This publication has 20 references indexed in Scilit:
- A comprehensive approach to the analysis of matrix‐assisted laser desorption/ionization‐time of flight proteomics spectra from serum samplesProteomics, 2003
- Proteomic approaches to tumor marker discovery.Archives of Pathology & Laboratory Medicine, 2002
- Serum Proteomic Patterns for Detection of Prostate CancerJNCI Journal of the National Cancer Institute, 2002
- Genomics and proteomics: application of novel technology to early detection and prevention of cancerCancer Detection Prevention, 2002
- Boosted Decision Tree Analysis of Surface-enhanced Laser Desorption/Ionization Mass Spectral Serum Profiles Discriminates Prostate Cancer from Noncancer PatientsClinical Chemistry, 2002
- Clinical proteomics: translating benchside promise into bedside realityNature Reviews Drug Discovery, 2002
- Development of a Novel Proteomic Approach for the Detection of Transitional Cell Carcinoma of the Bladder in UrineThe American Journal of Pathology, 2001
- Electrospray Ionization Mass Spectrometry Analysis of Lysophospholipids in Human Ascitic Fluids: Comparison of the Lysophospholipid Contents in Malignant vs Nonmalignant Ascitic FluidsAnalytical Biochemistry, 2001
- The role and clinical applications of bioactive lysolipids in ovarian cancerJournal of the Society for Gynecologic Investigation, 2001
- Cancer Proteomics: The State of the ArtDisease Markers, 2001