Plasma Peptidome Pattern of Breast Cancer Using Magnetic Beads-Based Plasma Fractionation and MALDI-TOF MS: A Case Control Study in Egypt

Abstract

Objective: The present study aimed to determine peptidome patterns in breast cancer (BC). Methods: We analyzed the plasma proteomic profiling of 80 BC patients and 50 healthy controls, using hydrophobic interaction chromatography magnetic beads (MB-HIC8) separation followed by Matrix assisted laser desorption ionization/ time of flight mass spectrometry (MALDI-TOF MS). Results: ClinProTools software identified 92 peaks that differed among the analyzed groups, 33 peaks were significantly different (P < 0.05). Of those, 22 peaks were up-regulated while 11 peaks were down-regulated in BC patients compared with the healthy controls. Three peptide ion signatures (m/z 1,570.31, 1,897.4 and 2,568.17) were provided by the Quick Classifier model to discriminate BC patients from healthy control subjects with 96.4% accuracy. External validation was performed by an independent group and this achieved a sensitivity of 100% and a specificity of 76.9%. Conclusion: MALDI-TOF MS has good analytical performance in distinguishing BC patients from healthy controls.

Keywords: Matrix assisted laser desorption ionization/ time of flight mass spectrometry; magnetic beads; ClinProTools.

Figure 1

Stack View of the Plasma Protein Profile Mass Spectra of the Loaded Classes in a Three Dimensional Space (red represents 45 breast cancer patients and green represents 30 control subjects).

Figure 2

The Simulated Two-Dimensional Gel Electrophoresis Views of Plasma Protein Profile Mass Spectra of All Samples (the upload, benign group; the download, malignant group).

Figure 3

Zoom of the Mass Range of the Three Peaks (MALDI-TOF MS Linear Mode) Used in the QC Model to Differentiate Breast Cancer Patients (Red) from the Control Subjects (Green). The red line demarcates the peak as an integration region. A, peak at m/z 1570.31 (start mass 1566.09 and end mass 1574.99); B, peak at m/z 1897.4 (start mass 1892.07 and end mass 1909.46); C, peak at m/z 2568.17 (start mass 2560.23 and end mass 2577.52). The peak is up regulated in BC patients than in control subjects.

Figure 4

Two-Dimensional (2D) Peak Distribution View of Peptides with A; m/z 1570 (x-axis) and 1897 (y-axis), B; m/z 1570 (x-axis) and 2568 (y-axis), C; m/z 1897 (x-axis) and 2568 (y-axis)

Figure 5

The Receiver Operating Characteristic (ROC) Curves of the Three Peaks Used in the QC Model to Differentiate Breast Cancer Patients from the Control Subjects.

Figure 6

Reproducibility of Mass Spectra of the Plasma Protein Profile in one BC Patient (Red) and Control Subject (Green), Showing Low Variability between Replicates.