Peptides Generated Ex Vivo from Serum Proteins by Tumor-Specific Exopeptidases Are Not Useful Biomarkers in Ovarian Cancer

Abstract

Background: The serum peptidome may be a valuable source of diagnostic cancer biomarkers. Previous mass spectrometry (MS) studies have suggested that groups of related peptides discriminatory for different cancer types are generated ex vivo from abundant serum proteins by tumor-specific exopeptidases. We tested 2 complementary serum profiling strategies to see if similar peptides could be found that discriminate ovarian cancer from benign cases and healthy controls. Methods: We subjected identically collected and processed serum samples from healthy volunteers and patients to automated polypeptide extraction on octadecylsilane-coated magnetic beads and separately on ZipTips before MALDI-TOF MS profiling at 2 centers. The 2 platforms were compared and case control profiling data analyzed to find altered MS peak intensities. We tested models built from training datasets for both methods for their ability to classify a blinded test set. Results: Both profiling platforms had CVs of approximately 15% and could be applied for high-throughput analysis of clinical samples. The 2 methods generated overlapping peptide profiles, with some differences in peak intensity in different mass regions. In cross-validation, models from training data gave diagnostic accuracies up to 87% for discriminating malignant ovarian cancer from healthy controls and up to 81% for discriminating malignant from benign samples. Diagnostic accuracies up to 71% (malignant vs healthy) and up to 65% (malignant vs benign) were obtained when the models were validated on the blinded test set. Conclusions: For ovarian cancer, altered MALDI-TOF MS peptide profiles alone cannot be used for accurate diagnoses.

Deciphering the peptidome of urine from ovarian cancer patients and healthy controls

“…On the contrary, Timms et al . recently reported that MALDI MS peptide profiling was unable to accurately diagnose OvCa from healthy controls, though the endogenous peptides could provide some diagnostic insight [13]. Needless to say, greater characterization of the endogenous peptidome of various biospecimens related to OvCa is needed to truly assess whether or not peptide-based biomarkers are clinically useful.…”

Relative Quantitation of Neuropeptides at Multiple Developmental Stages of the American Lobster Using N,N-Dimethyl Leucine Isobaric Tandem Mass Tags

“…In a recent paper, Ziptips and magnetic beads were also compared for human serum peptide profiling, and it was determined that Ziptips were a better desalting method in spectral quality, reproducibility, and time consumption. 43 …”

Prediction with Confidence Based on a Random Forest Classifier

“…Proteomic data sets comprise: ovarian cancer data from the UKOPS trial [6]; ovarian cancer (OC ), breast cancer (BC ) and heart disease (HD ) samples collected in the UKCTOCS trial 1 ; Competition data provided by the Leiden Clinical Mass Spectrometry Proteomic Diagnosis Competition and preprocessed as described in [7]; Ciphergen's 7 biomarkers of UKOPS data [8]. The other medical data sets are shortened Abdominal pain data [9], which comprises 33 symptoms of acute abdominal pain, and Microarray data of lung cancer, colon cancer and breast cancer patients provided in the ICMLA 2009 Challenge [10].…”