1 Sample Information

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

1.1 Sample groups

Sample Etiology Cellular Composition
BH-321-P1 LAA RBC
GOTH-168-P5 LAA PLT/FIB(Mixed)
GOTH-172-P5 LAA PLT/FIB(Mixed)
ATH-012-P2 LAA PLT/FIB(Mixed)
ATH-011-P1 LAA RBC
BH-316-P1 LAA RBC
NICN-213-P2 LAA PLT/FIB
BH-323-P3 LAA RBC
NICN-167-P2 LAA PLT/FIB(Mixed)
NICN-196-P1 LAA PLT/FIB
BH-215-P2* LAA PLT/FIB
BH-308-P2 CEE PLT/FIB(Mixed)
GOTH-158-P2 CEE PLT/FIB(Mixed)
BH-287-P1 CEE RBC
BH-278-P3 CEE PLT/FIB
BH-326-P2 CEE PLT/FIB(Mixed)
BH-364-P2 CEE PLT/FIB(Mixed)
NICN-193-P4 CEE PLT/FIB
ATH-018-P1 CEE PLT/FIB
NICN-198-P1 CEE PLT/FIB

2 Protein counts per sample

The plot below shows the relationship between the amount of protein per sample. These results indicate that most samples from the RBC group have a lower proteic content, while samples from the MIX group have, in general, more protein.

3 Venn diagrams

The Venn Diagram generated using the forth data set shows that 71 proteins are overlapping between the RBC, MIX, and FIB Groups - and this intersection is used for comparison between groups, 19 proteins are unique to the RBC samples, and 58 proteins are unique to the FIB samples, and 33 a unique to MIX samples.

4 Data Processing

5 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.

6 Pearson correlation

The correlation matrices with the co-abundant proteins were used to create the adjacency matrices necessary for the network analysis. The correlation analysis was done using the following data sets:

  1. Fibrin samples with proteins exclusive to the FIB group (58 proteins);
  2. MIX samples with proteins exclusive to the MIX group (33 proteins);
  3. Red Blood cells samples with proteins exclusive to the RBC group (19 proteins);

6.1 FIB Samples

6.2 MIX Samples

6.3 RBC Samples

7 Network Analysis

Using the correlation matrices above to extract information on the abundancy profile of the highly correlated proteins with a threshold of +/- 0.80, the network analysis was carried out and resulted in the graphs below. The node size is proportional with the degree (how connected the protein is), the red edges represent positive correlation and blue edges represent negative correlation. The optimal community structure was calculated for the graph, in using the maximal modularity score.

7.1 FIB Samples





7.2 MIX Samples







7.3 RBC Samples







8 Differential Analysis

Here I used a linear model approach to assess differential abundance/expression between the two groups - this analysis resulted in 7 differentially abundant proteins when comparing FIB and RBC and 3 when comparing RBC and MIX, no differentially abundant proteins were found in the FIB vs MIX comparison. The table below shows the metrics of the top-ranked proteins from the linear model fit.

8.1 FIB vs MIX

8.2 FIB vs RBC

8.3 RBC vs MIX