1 Sample Information

Analysis from the results of a label free mass spectrometry experiment on paraffin embedded samples stratified as follows:

1.1 Etiology criteria

  • LAA Clots (LAA): n = 6
  • Cardioembolic clots (CE): n = 6

1.2 Cellular composition criteria

  • Red Blood Cell rich Clots (RBC): n = 4
  • Mixed clots (mixed): n = 3
  • Platelet/Fibrin clots (Fib): n = 5

1.3 Sample groups

Sample Etiology Cellular Composition
BH-132-P1 LAA RBC
BH-143-P2 LAA RBC
GOTH-039-P3 LAA RBC
BH-189-P2 LAA PLT/FIB
BH-217-P2 LAA MIXED
GOTH-038-P3 LAA MIXED
BH-159-P1 CEE MIXED
BH-158-P3 CEE RBC
GOTH-040-P5 CEE PLT/FIB
NICN-053-P6 CEE PLT/FIB
NICN-108-P3 CEE PLT/FIB
NICN-164-P2 CEE PLT/FIB

2 Protein counts per sample

As can be seen in the graph above, the samples have very different protein counts. Because the analysis is based on proteins that overlap within and between groups, samples that present low protein counts negatively influence the rest of the analyzes; for this reason, the following samples have been removed from the analysis: NICN_53_P6, NICN_108_P3, BH_189_P2.

3 Venn diagrams

The below Venn diagrams demonstrate the influence of samples with low protein count on the result of protein overlap.

3.1 Etiology criteria

3.1.1 Before removing samples

3.1.2 After removing samples

3.2 Cellular composition criteria

3.2.1 Before removing samples

3.2.2 After removing samples

4 Principal Component Analysis

After processing the data with log-2 transformation and normalization, I performed an exploratory data analysis with principal component analysis. The results show that there is no clear separation between groups regardless of comparison; this fact, along with the small group size, prevents the analysis that would follow.

4.1 Etiology criteria

4.2 Cellular composition criteria