a) b) c) d) Fig. S1. Representative LC-MRM chromatograms of serum phospholipids obtained using MRM transitions from head group loss a) Phosphatidylcholine (PC), b) Phosphatidylethanolamine (PE), c) Phosphatidylinositol (PI), d) Phosphatidylserine (PS).

Fig. S2. PCA score plot: 3D PCA score plot for malignant breast patients (n = 28, red), benign breast patients (n = 28, green) and healthy controls ( n = 28, blue).

Fig. S3. Hierarchical clustering analysis (HCA): HCA represents all 28 samples of each group showing clustering of malignant (red), benign (green) and healthy (blue) controls.

LPC 16:4 AUC=0.84 PE (20:4/24:0) AUC=0.81 PI (22:0/ 22:4) AUC=0.74 PC (18:1/22:2) AUC=0.83 PE (18:2/20:5) AUC=0.79 PS 20:5: 22:6 AUC=0.71 PE (20:0/22.4) AUC=0.80 LPE 20:1 AUC=0.75 Fig. S4. Comparative analysis of malignant and healthy controls: Box-and-whisker plots illustrating the phospholipid concentration differences among malignant samples vs. healthy controls and corresponding ROC curve analysis plot of sensitivity vs. specificity for the marker phospholipids predicting malignant samples against healthy controls.

a. b. AUC=0.99 Fig. S5. Analysis of malignant and healthy controls: a) Cumulative predictive ability of top four phospholipid signature PE (14:1/16:0), PC (18:0/18:0), LPE 14:0 and PE (20:0/22:2) to discriminate malignant samples from healthy controls (AUC=0.99). b) Biochemical similarity metabolite network map of differentially altered phospholipids in malignant vs control plotted using MetaMapp and Cytoscape. The plot depicts clustering of phospholipids with same head group.

AUC=0.91 SM (d18:1/24:0) AUC=0.77 PC (18:1/20:0) SM (d18:1/24:1) AUC=0.86 PE (18:0/22.2) AUC=0.73 AUC=0.82 PE (10:0/18:1) PS (20:5/22:6) AUC=0.72 Fig. S6. Comparative analysis of malignant and benign samples: Box-and-whisker plots illustrating concentration differences along with ROC curve analysis plot of sensitivity vs. specificity for the marker phospholipids predicting malignant samples against benign samples.

a. b. AUC=0.99 Fig. S7. Analysis of malignant and benign samples a) Cumulative predictive ability of top four phospholipid signatures SM (d18:1/24:0), SM (d18:1/24:1), PE (10:0/18:1) and PC (18:1/20:0) to discriminate malignant samples from benign (AUC=0.99). b) Biochemical similarity metabolite network map of differentially altered phospholipids in malignant vs benign samples, plotted using MetaMapp and Cytoscape. The plot depicts clustering of phospholipids with same head group.

Table S1. Demographics and histologic features of samples used for phospholipid analyses

Table S2. Total phospholipid species detected at sufficient levels for quantification including 52 PC, 68 PE, 45 PI, 26 PS, and 9 SM molecular species PC PE PI PS SM PC 30:0 PC 40:5 PE 28:0 PE 38:4 LPE 14:0 PI 28:0 PI 44:5 PS 34:0 SM34.1 PC 32:0 PC 36:6 PE 30:0 PE 40:4 LPE 16:0 PI 30:0 PI 36:6 PS 36:0 SM34.2 PC 34:0 PC 38:6 PE 32:0 PE 42:4 LPE 18:0 PI 32:0 PI 38:6 PS 38:0 SM36.1 PC 36:0 PC 40:6 PE 34:0 PE 44:4 LPE 20:0 PI 34:0 PI 40:6 PS 34:1 SM36.2 PC 38:0 PC 42:6 PE 36:0 PE 36:5 LPE 22:0 PI 36:0 PI 40:7 PS 36:1 SM40.1 PC 28:1 PC 38:7 PE 38:0 PE 38:5 LPE 14:1 PI 30:1 PI 40:8 PS 38:1 SM40.2 PC 30:1 PC 40:7 PE 40:0 PE 40:5 LPE 16:1 PI 32:1 PI 37:4 PS 40:1 SM42.1 PC 32:1 PC 42:7 PE 28:1 PE 42:5 LPE 18:1 PI 34:1 LPI 14:0 PS 36:2 SM42.2 PC 34:1 PC 40:8 PE 30:1 PE 36:6 LPE 20:1 PI 36:1 LPI 16:0 PS 38:2 SM30.1 PC 36:1 PC 42:8 PE 32:1 PE 38:6 LPE 22:1 PI 38:1 LPI 18:0 PS 40:2   PC 38:1 PC 42:11 PE 34:1 PE 40:6 LPE 18:2 PI 32:2 LPI 14:1 PS 38:3 PC 32:2 PC 44:12 PE 36:1 PE 42:6 LPE 20:2 PI 34:2 LPI 18:1 PS 40:3 PC 34:2 LPC 14:0 PE 38:1 PE 38:7 LPE 18:3 PI 36:2 LPI 14:2 PS 38:4 PC 36:2 LPC 16:0 PE 32:2 PE 40:7 LPE 20:3 PI 32:3 LPI 16:2 PS 40:4 PC 38:2 LPC 18:0 PE 34:2 PE 42:7 LPE 20:4 PI 34:3 LPI 18:2 PS 38:5 PC 32:3 LPC 16:1 PE 36:2 PE 40:8 LPE 22:4 PI 36:3 LPI 20:3 PS 40:5 PC 34:3 LPC 18:1 PE 38:2 PE 42:8 PI 38:3 LPI 20:4 PS 38:6 PC 36:3 LPC 20:1 PE 40:2 PE 44:8 PI 40:3 LPI 22:4 PS 40:6 PC 38:3 LPC 18:2 PE 42:2 PE 42:9 PI 42:3 LPI 22:5 PS 42:9 PC 40:3 LPC 20:2 PE 32:3 PE 42:10 PI 34:4 PS 42:10 PC 34:4 LPC 18:3 PE 34:3 PE 44:10 PI 36:4 PS 42:11 PC 36:4 LPC 20:3 PE 38:3 PE 42:11 PI 38:4 LPS 18:0 PC 38:4 LPC 16:4 PE 40:3 PE 44:11 PI 40:4 LPS 20:0 PC 40:4 LPC 20:4 PE 42:3 PE 44:12 PI 44:4 LPS 22:0 PC 36:5 LPC 22:4 PE 34:4 PE 43:6 PI 36:5 LPS 18:1 PC 38:5 LPC 22:5 PE 36:4 PI 38:5 LPS 20:4

Table S3. AUC values obtained after performing ROC analysis of marker phospholipids [Table heading Lipid: Lipid species with total number of carbon atom and total number of double bonds, Confirmed Name: Confirmed lipid species after obtained after product ion spectra indicating sn1 and sn2 fatty acids, AUC: Area under the curve, MB VS HCB: Malignant vs control, BB vs HCB: Benign vs Control, MB vs BB: Malignant vs Benign]. Sr. No. Lipid Confirmed Name AUC MB VS HCB AUC BB VS HCB AUC MB VS BB 1 PE 30:1 PE 14:1/16:0 0.92 0.73 0.75 2 PC 36:0 PC 18:0/18:0 0.90 0.69 3 LPC 16:4 0.84 0.79 0.52 4 LPE 14:0 0.68 0.67 5 PE 42:2 PE 20:0/22.2 6 PC 40:3 PC 18:1/22:2 0.83 0.56 7 PC 38:2 PC 18:2/20:0 0.77 0.63 8 PE 44:4 PE 20:4/24:0 0.81 9 PC 28:1 PC 12:0/16.1 0.57 0.71 10 PS 38:0 NC* 0.74 11 PE 42:4 PE 20:0/22.4 0.80 0.54 0.76 12 SM34.2 SM d18:1/16:1 13 PE 38:7 PE 18:2/20:5 0.58 14 PC 30:0 PC 14:0/16:0 0.78 0.50 15 PE 40:2 PE 18:0/22.2 0.60 16 LPE 20:1 0.53 17 PS 34:1 0.51 0.72 18 PI 44:4 PI 22:0/ 22:4 19 LPC 20:4 0.66 20 SM42.2 SM d18:1/24:1 0.64 0.86 21 SM42.1 SM d18:1/24:0 0.91 22 PS 42:11 PS 20:5/22:6 23 PC 40:4 PC 18:0/22:4 24 PC 38:1 PC 18:1/20:0 25 PE 28:1 PE 10:0/18:1 0.82