Fig. 2.

Comparative analysis of the performance of SWATH MS versus DDA MS.

Venn diagrams depicting number and overlap of matrisomal proteins detected by DDA and SWATH MS in A) liver and B) lung tissue across 2 biological replicates and 3 technical replicates. Proteins uniquely identified by each method are highlighted. Venn diagrams depicting the number and overlap of unique matrisome peptides identified in C) liver and D) lung tissue across 3 technical replicates (R1-R3) in DDA and SWATH MS. Only peptides with 99% confidence of identification or higher were compared.