Figure 4.

Evaluation of sample-relevant spectral libraries for data analysis of unfractionated EPS-urine DIA-MS data. (A) Schematic of spectral library generation from the aforementioned EPS-urine samples, and the two populations of urinary extracellular vesicles (uEV) isolated by ultracentrifugation at 20,000g (lib-EVP20) and 150,000g (lib-EVP150).²² (B) Library size and (C) intersection of proteins of the generated spectral libraries. (D) Schematic of DIA-MS data analysis using each of the generated libraries. (E) Number of detected proteins and (F) intersection of proteins detected in EPS-urine data using each spectral library. (G) Percent observations of the uniquely detected proteins using lib-EVP20 in the DDA-MS data.²² (H) Pathway analysis of genes uniquely detected by each spectral library. (I) Number of uniquely detected proteins mapped against prostate cancer tissue data sets.^43,44